diff --git a/CHANGES.md b/CHANGES.md index 19e7508899..57075a16b5 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -4,6 +4,11 @@ - For a list of open issues and known problems, see https://github.com/radical-cybertools/radical.pilot/issues?q=is%3Aissue+is%3Aopen+ +0.32 Release 2015-05-18 +-------------------------------------------------------------------------------- + + - Hotfix release for MPIRUN_RSH on Stampede (#572). + 0.31 Release 2015-04-30 -------------------------------------------------------------------------------- diff --git a/VERSION b/VERSION index 48b9990e0b..00d0c14da8 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -0.31 +0.32 diff --git a/src/radical/pilot/agent/radical-pilot-agent-multicore.py b/src/radical/pilot/agent/radical-pilot-agent-multicore.py index c128825a14..adc1e9ddb8 100755 --- a/src/radical/pilot/agent/radical-pilot-agent-multicore.py +++ b/src/radical/pilot/agent/radical-pilot-agent-multicore.py @@ -1756,7 +1756,6 @@ def construct_command(self, task_exec, task_args, task_numcores, return dplace_command, None - # ============================================================================== # class LaunchMethodMPIRUNRSH(LaunchMethod): @@ -1767,13 +1766,18 @@ def __init__(self, name, config, logger, scheduler): LaunchMethod.__init__(self, name, config, logger, scheduler) - # -------------------------------------------------------------------------- # def _configure(self): - # mpirun_rsh (e.g. on Gordon@ SDSC) - self.launch_command = self._which('mpirun_rsh') + # mpirun_rsh (e.g. on Gordon@SDSC, Stampede@TACC) + if not self._which('mpirun_rsh'): + raise Exception("mpirun_rsh could not be found") + + # We don't use the full pathname as the user might load a different + # compiler / MPI library suite from his CU pre_exec that requires + # the launcher from that version, as experienced on stampede in #572. + self.launch_command = 'mpirun_rsh' # -------------------------------------------------------------------------- # diff --git a/tests/issue_572.py b/tests/issue_572.py new file mode 100755 index 0000000000..75becf7811 --- /dev/null +++ b/tests/issue_572.py @@ -0,0 +1,164 @@ +#!/usr/bin/env python + +__copyright__ = "Copyright 2015, http://radical.rutgers.edu" +__license__ = "MIT" + +import sys +import radical.pilot as rp +import radical.utils as ru + +dh = ru.DebugHelper () + +CNT = 0 +RUNTIME = 10 +SLEEP = 1 +CORES = 16 +UNITS = 1 +SCHED = rp.SCHED_DIRECT_SUBMISSION + +RESOURCE = 'xsede.stampede' +PROJECT = 'TG-MCB090174' +QUEUE = 'development' +SCHEMA = 'ssh' + + +#------------------------------------------------------------------------------ +# +def pilot_state_cb (pilot, state): + + if not pilot: + return + + print "[Callback]: ComputePilot '%s' state: %s." % (pilot.uid, state) + + if state == rp.FAILED: + sys.exit (1) + + +#------------------------------------------------------------------------------ +# +def unit_state_cb (unit, state): + + if not unit: + return + + global CNT + + print "[Callback]: unit %s on %s: %s." % (unit.uid, unit.pilot_id, state) + + if state in [rp.FAILED, rp.DONE, rp.CANCELED]: + CNT += 1 + print "[Callback]: # %6d" % CNT + + + if state == rp.FAILED: + print "stderr: %s" % unit.stderr + sys.exit(2) + + +#------------------------------------------------------------------------------ +# +def wait_queue_size_cb(umgr, wait_queue_size): + + print "[Callback]: wait_queue_size: %s." % wait_queue_size + + +#------------------------------------------------------------------------------ +# +if __name__ == "__main__": + + # we can optionally pass session name to RP + if len(sys.argv) > 1: + session_name = sys.argv[1] + else: + session_name = None + + # Create a new session. No need to try/except this: if session creation + # fails, there is not much we can do anyways... + session = rp.Session(name=session_name) + print "session id: %s" % session.uid + + # all other pilot code is now tried/excepted. If an exception is caught, we + # can rely on the session object to exist and be valid, and we can thus tear + # the whole RP stack down via a 'session.close()' call in the 'finally' + # clause... + try: + + pmgr = rp.PilotManager(session=session) + pmgr.register_callback(pilot_state_cb) + + pdesc = rp.ComputePilotDescription() + pdesc.resource = RESOURCE + pdesc.cores = CORES + pdesc.project = PROJECT + pdesc.queue = QUEUE + pdesc.runtime = RUNTIME + pdesc.cleanup = False + pdesc.access_schema = SCHEMA + + pilot = pmgr.submit_pilots(pdesc) + + umgr = rp.UnitManager(session=session, scheduler=SCHED) + umgr.register_callback(unit_state_cb, rp.UNIT_STATE) + umgr.register_callback(wait_queue_size_cb, rp.WAIT_QUEUE_SIZE) + umgr.add_pilots(pilot) + + cuds = list() + for unit_count in range(0, UNITS): + cud = rp.ComputeUnitDescription() + cud.pre_exec = [ + 'module load gromacs', + 'echo 2 | trjconv -f tmp.gro -s tmp.gro -o tmpha.gro', + 'module load -intel +intel/14.0.1.106', + 'export PYTHONPATH=/home1/03036/jp43/.local/lib/python2.7/site-packages', + 'module load python/2.7.6', + 'export PATH=/home1/03036/jp43/.local/bin:$PATH', + 'echo "Using mpirun_rsh: `which mpirun_rsh`"' + ] + cud.executable = "/opt/apps/intel14/mvapich2_2_0/python/2.7.6/lib/python2.7/site-packages/mpi4py/bin/python-mpi" + cud.arguments = ["lsdm.py", "-f", "config.ini", "-c", + "tmpha.gro", "-n" "neighbors.nn", "-w", "weight.w"] + cud.cores = 4 + cud.mpi = True + cud.input_staging = [ + 'issue_572_files/config.ini', + 'issue_572_files/lsdm.py', + 'issue_572_files/tmp.gro' + ] + cuds.append(cud) + + units = umgr.submit_units(cuds) + + umgr.wait_units() + + for cu in units: + print "* Task %s state %s, exit code: %s, started: %s, finished: %s" \ + % (cu.uid, cu.state, cu.exit_code, cu.start_time, cu.stop_time) + + except Exception as e: + # Something unexpected happened in the pilot code above + print "caught Exception: %s" % e + raise + + except (KeyboardInterrupt, SystemExit) as e: + # the callback called sys.exit(), and we can here catch the + # corresponding KeyboardInterrupt exception for shutdown. We also catch + # SystemExit (which gets raised if the main threads exits for some other + # reason). + print "need to exit now: %s" % e + + finally: + # always clean up the session, no matter if we caught an exception or + # not. + print "closing session" + session.close () + + # the above is equivalent to + # + # session.close (cleanup=True, terminate=True) + # + # it will thus both clean out the session's database record, and kill + # all remaining pilots (none in our example). + + +#------------------------------------------------------------------------------- diff --git a/tests/issue_572_files/config.ini b/tests/issue_572_files/config.ini new file mode 100644 index 0000000000..7366f365e2 --- /dev/null +++ b/tests/issue_572_files/config.ini @@ -0,0 +1,14 @@ +[LSDMAP] +;metric used to compute the distance matrix (rmsd, cmd, dihedral) +metric=rmsd + +[LOCALSCALE] +;status (constant, kneighbor, user) +status=constant + +;constant epsilon used in case status is constant +epsilon=0.15 + +;value of k in case status is kneighbor +k=10 + diff --git a/tests/issue_572_files/lsdm.py b/tests/issue_572_files/lsdm.py new file mode 100644 index 0000000000..37975e4e57 --- /dev/null +++ b/tests/issue_572_files/lsdm.py @@ -0,0 +1,378 @@ +import os +import sys +import numpy as np +import argparse +import ConfigParser +import pickle +import random +import logging + +from lsdmap.rw import reader +from lsdmap.mpi import p_arpack +from lsdmap.mpi import p_index +from lsdmap.util import metric as mt + +from mpi4py import MPI + +class LSDMap(object): + + def initialize(self, comm, config, args): + + rank = comm.Get_rank() + + self.config = config + self.args = args + + struct_file = reader.open(args.struct_file) + self.struct_filename = struct_file.filename + self.npoints = struct_file.nlines + + self.idxs_thread = p_index.get_idxs_thread(comm, self.npoints) + + if hasattr(struct_file, '_skip'): # multi-thread reading + coords_thread = struct_file.readlines(self.idxs_thread) + self.coords = np.vstack(comm.allgather(coords_thread)) + else: # serial reading + if rank == 0: + self.coords = struct_file.readlines() + else: + self.coords = None + self.coords = comm.bcast(self.coords, root=0) + + logging.info('input coordinates loaded') + + self.initialize_local_scale() + self.initialize_weights() + self.initialize_metric() + + self.neigs = 10 + + def initialize_local_scale(self): + + config = self.config + args = self.args + + known_status = ['constant', 'kneighbor', 'user', 'kneighbor_mean'] + _mapped = {'const': 'constant', 'cst': 'constant', 'mean-kneighbor': 'mean_kneighbor'} + + if args.epsfile is None: + status = config.get('LOCALSCALE','status') + if status in _mapped: + status = _mapped[status] + if not status in known_status: + raise ValueError("local scale status should be one of "+ ', '.join(known_status)) + if status in ['kneighbor', 'kneighbor_mean']: + value = None + self.k = config.getint('LOCALSCALE', 'k') + if status == 'constant': + value = config.getfloat('LOCALSCALE', 'epsilon') + value = value*np.ones(self.npoints) + if status == 'user': + raise NameError("status 'user' specified in configuration file but epsfile not provided. Please consider option flag -e") + else: + espfile = reader.open(epsfile) + status ='user' + value = epsfile.readlines() + + self.status_epsilon = status + self.epsilon = value + + + def initialize_weights(self): + + config = self.config + args = self.args + + if args.wfile is None: + self.weights = np.ones(self.npoints, dtype='float') + else: + if os.path.isfile(args.wfile): + wfile = reader.open(args.wfile) + weights = wfile.readlines() + self.weights = self.npoints*weights/np.sum(weights) + else: + logging.warning('.w file does not exist, set weights to 1.0.') + self.weights = np.ones(self.npoints, dtype='float') + + def initialize_metric(self): + + _known_prms = ['r0'] + + config = self.config + self.metric = config.get('LSDMAP','metric') + + self.metric_prms = {} + for prm in _known_prms: + try: + self.metric_prms[prm] = config.getfloat('LSDMAP', prm) + except: + pass + + def create_arg_parser(self): + + parser = argparse.ArgumentParser(description="Run LSDMap..") # message displayed when typing lsdmap -h + + # required options + parser.add_argument("-f", + type=str, + dest="config_file", + required=True, + help='Configuration file (input): ini') + + parser.add_argument("-c", + type=str, + dest="struct_file", + required=True, + nargs='*', + help = 'Structure file (input): gro, xvg') + + # other options + parser.add_argument("-o", + type=str, + dest="output_file", + help='Pickle file containing LSDMap object (output, opt.): p') + + parser.add_argument("-d", + type=str, + dest="dmfile", + help="File containing the distance matrix (output, opt.): .dm") + + parser.add_argument("-n", + type=str, + dest="nnfile", + help='File containing the indices of the nearest neighbors of all configurations\ + within the structure file (output, opt.): nn.\n When --ns or --nc flags are not\ + specified: store only the neighbors within the range of the local scale.') + + parser.add_argument("-w", + type=str, + dest="wfile", + help='File containing the weights of every point in a row (input, opt.): .w') + + parser.add_argument("-e", + type=str, + dest="epsfile", + help='File containing the local scales of every point in a row (input, opt.): .eps') + + parser.add_argument("--ns", + type=int, + dest="nneighbors", + help="Number of nearest neighbors stored in .nn file; should be used with option -n") + + parser.add_argument("--nc", + type=float, + dest="nneighbors_cutoff", + help="Only the indices of neighbors closer than a distance of nneighbors_cutoff are stored in .nn file; should be used with option -n") + + return parser + + + def compute_kernel(self, comm, npoints_thread, distance_matrix_thread, weights_thread, epsilon_thread): + # for a detailed description of the following operations, see the paper: + # Determination of reaction coordinates via locally scaled diffusion map + # Mary A. Rohrdanz, Wenwei Zheng, Mauro Maggioni, and Cecilia Clementi + # The Journal of Chemical Physics 134, 124116 (2011) + + p_vector_thread = np.zeros(npoints_thread, dtype='float') + d_vector_thread = np.zeros(npoints_thread, dtype='float') + + # compute LSDMap kernel, Eq. (5) of the above paper + kernel = np.sqrt((weights_thread[:, np.newaxis]).dot(self.weights[np.newaxis])) * \ + np.exp(-distance_matrix_thread**2/(2*epsilon_thread[:, np.newaxis].dot(self.epsilon[np.newaxis]))) + + p_vector_thread = np.sum(kernel, axis=1) + p_vector = np.hstack(comm.allgather(p_vector_thread)) # Eq. (6) + self.p_vector = p_vector + + kernel /= np.sqrt(p_vector_thread[:,np.newaxis].dot(p_vector[np.newaxis])) # Eq. (7) + d_vector_thread = np.sum(kernel, axis=1) + d_vector = np.hstack(comm.allgather(d_vector_thread)) # Compute D given between Eqs. (7) and (8) + self.d_vector = d_vector + + kernel /= np.sqrt(d_vector_thread[:,np.newaxis].dot(d_vector[np.newaxis])) # Eq (8) (slightly modified) + + return kernel + + + def save(self, config, args): + """ + save LSDMap object in .lsdmap file and eigenvalues/eigenvectors in .eg/.ev files + """ + + if isinstance(self.struct_filename, list): + struct_filename = self.struct_filename[0] + else: + struct_filename = self.struct_filename + + path, ext = os.path.splitext(struct_filename) + np.savetxt(path + '.eg', np.fliplr(self.eigs[np.newaxis]), fmt='%9.6f') + np.savetxt(path + '.ev', np.fliplr(self.evs), fmt='%15.7e') + + if args.output_file is None: + try: + lsdmap_filename = config.get('LSDMAP', 'lsdmfile') + except: + return + else: + lsdmap_filename = args.output_file + with open(lsdmap_filename, "w") as file: + pickle.dump(self, file) + + + def save_nneighbors(self, comm, args, DistanceMatrix_thread, epsilon_thread): + + size = comm.Get_size() # number of threads + rank = comm.Get_rank() # number of the current thread + if rank == 0: + try: + os.remove(args.nnfile) + except OSError: + pass + nnfile = open(args.nnfile, 'a') + for idx in xrange(size): + if idx == 0: + idx_neighbor_matrix = DistanceMatrix_thread.idx_neighbor_matrix() + neighbor_matrix = DistanceMatrix_thread.neighbor_matrix() + epsilon = epsilon_thread + else: + idx_neighbor_matrix = comm.recv(source=idx, tag=idx) + neighbor_matrix = comm.recv(source=idx, tag=1000+idx) + epsilon = comm.recv(source=idx, tag=2000+idx) + if args.nneighbors is not None: # save first "args.nneighbors" nearest neighbors + for idxs in idx_neighbor_matrix: + np.savetxt(nnfile, idxs[:min(args.nneighbors,self.npoints)][np.newaxis], fmt='%d') + elif args.nneighbors_cutoff is not None: # save all nearest neighbors within "args.nneighbors_cutoff" + for idxrow, row in enumerate(neighbor_matrix): + for idxcol, col in enumerate(row): + if col > args.nneighbors_cutoff: + break + np.savetxt(nnfile, idx_neighbor_matrix[idxrow,:idxcol][np.newaxis], fmt='%d') + else: # save all nearest neighbors within the range of the local scale + for idxrow, row in enumerate(neighbor_matrix): + for idxcol, col in enumerate(row): + if col > epsilon[idxrow]: + break + np.savetxt(nnfile, idx_neighbor_matrix[idxrow,:idxcol][np.newaxis], fmt='%d') + nnfile.close() + else: + idx_neighbor_matrix = DistanceMatrix_thread.idx_neighbor_matrix() + neighbor_matrix = DistanceMatrix_thread.neighbor_matrix() + comm.send(idx_neighbor_matrix, dest=0, tag=rank) + comm.send(neighbor_matrix, dest=0, tag=1000+rank) + comm.send(epsilon_thread, dest=0, tag=2000+rank) + + def save_distance_matrix(self, comm, args, distance_matrix_thread): + + size = comm.Get_size() # number of threads + rank = comm.Get_rank() # number of the current thread + if rank == 0: + try: + os.remove(args.dmfile) + except OSError: + pass + dmfile = open(args.dmfile, 'a') + for idx in xrange(size): + if idx == 0: + distance_matrix = distance_matrix_thread + else: + distance_matrix = comm.recv(source=idx, tag=idx) + np.savetxt(dmfile, distance_matrix) + dmfile.close() + else: + comm.send(distance_matrix_thread, dest=0, tag=rank) + + def run(self): + + #initialize mpi variables + comm = MPI.COMM_WORLD # MPI environment + size = comm.Get_size() # number of threads + rank = comm.Get_rank() # number of the current thread + + parser = self.create_arg_parser() + args = parser.parse_args() # set argument parser + + config = ConfigParser.SafeConfigParser() + config.read(args.config_file) # set config file parser + + logging.basicConfig(filename='lsdmap.log', + filemode='w', + format="%(levelname)s:%(name)s:%(asctime)s: %(message)s", + datefmt="%H:%M:%S", + level=logging.DEBUG) + + + logging.info('intializing LSDMap...') + self.initialize(comm, config, args) + logging.info('LSDMap initialized') + + if size > self.npoints: + logging.error("number of threads should be less than the number of frames") + raise ValueError + + npoints_thread = len(self.idxs_thread) + coords_thread = np.array([self.coords[idx] for idx in self.idxs_thread]) + weights_thread = np.array([self.weights[idx] for idx in self.idxs_thread]) + + # compute the distance matrix + DistanceMatrix = mt.DistanceMatrix(coords_thread, self.coords, metric=self.metric, metric_prms=self.metric_prms) + distance_matrix_thread = DistanceMatrix.distance_matrix + logging.info("distance matrix computed") + + # compute kth neighbor local scales if needed + if self.status_epsilon in ['kneighbor', 'kneighbor_mean']: + epsilon_thread = [] + idx_neighbor_matrix_thread = DistanceMatrix.idx_neighbor_matrix() + for idx, line in enumerate(idx_neighbor_matrix_thread): + cum_weight = 0 + for jdx in line[1:]: + cum_weight += self.weights[jdx] + if cum_weight >= self.k: + break + epsilon_thread.append(distance_matrix_thread[idx,jdx]) + + self.epsilon = np.hstack(comm.allgather(epsilon_thread)) # gather epsilon values + if self.status_epsilon == 'kneighbor_mean': + mean_value_epsilon = np.mean(self.epsilon) # compute the mean value of the local scales + self.epsilon = mean_value_epsilon * np.ones(self.npoints) # and set it as the new constant local scale + + logging.info("kneighbor local scales computed") + + epsilon_thread = np.array([self.epsilon[idx] for idx in self.idxs_thread]) + + # compute kernel + kernel = self.compute_kernel(comm, npoints_thread, distance_matrix_thread, weights_thread, epsilon_thread) + + # diagonalize kernel + params= p_arpack._ParallelSymmetricArpackParams(comm, kernel, self.neigs) + while not params.converged: + params.iterate() + eigs, evs = params.extract(return_eigenvectors=True) + + # normalize eigenvectors + self.evsu = np.copy(evs) # store unormalized eigenvectors + evs /= np.sqrt(self.d_vector[:,np.newaxis]) + norm = np.sqrt(np.sum(evs**2, axis=0)) + evs /= norm[np.newaxis,:] + + + # store eigenvalues/eigenvectors + self.eigs = eigs + self.evs = evs + + logging.info("kernel diagonalized") + + if rank ==0: + self.save(config, args) + logging.info("Eigenvalues/eigenvectors saved (.eg/.ev files)") + + # store nearest neighbors in .nn file if specified via -n option + if args.nnfile is not None: + self.save_nneighbors(comm, args, DistanceMatrix, epsilon_thread) + + if args.dmfile is not None: + self.save_distance_matrix(comm, args, distance_matrix_thread) + + logging.info("LSDMap computation done") + +if __name__ == '__main__': + LSDMap().run() diff --git a/tests/issue_572_files/tmp.gro b/tests/issue_572_files/tmp.gro new file mode 100644 index 0000000000..5e313f8a69 --- /dev/null +++ b/tests/issue_572_files/tmp.gro @@ -0,0 +1,25000 @@ +Protein t= 0.00000 + 22 + 1ACE HH31 1 24.812 25.183 24.788 -1.1597 0.6294 0.2956 + 1ACE CH3 2 24.765 25.086 24.802 0.1507 -0.1335 -0.4063 + 1ACE HH32 3 24.734 25.040 24.708 -1.5030 -1.1063 0.5817 + 1ACE HH33 4 24.676 25.093 24.864 -0.3052 -1.2970 -0.9136 + 1ACE C 5 24.857 24.995 24.876 -0.0114 -0.5512 -0.4215 + 1ACE O 6 24.829 24.975 25.000 0.1240 0.2060 -0.3490 + 2ALA N 7 24.964 24.947 24.814 -0.8030 0.3719 -0.3338 + 2ALA H 8 24.982 24.969 24.717 -0.4177 0.4482 -0.2460 + 2ALA CA 9 25.049 24.844 24.870 0.5455 -0.6542 -0.9632 + 2ALA HA 10 24.979 24.779 24.923 -1.4496 2.2030 -0.0267 + 2ALA CB 11 25.098 24.757 24.753 0.2174 0.2823 0.6084 + 2ALA HB1 12 25.168 24.810 24.689 1.7052 -2.0294 0.2518 + 2ALA HB2 13 25.014 24.707 24.704 -0.8259 3.2578 -0.7915 + 2ALA HB3 14 25.156 24.676 24.796 -1.2360 -0.5703 1.0128 + 2ALA C 15 25.157 24.891 24.971 0.2995 0.4196 -0.0629 + 2ALA O 16 25.273 24.883 24.945 -0.1202 0.0038 0.1259 + 3NME N 17 25.112 24.935 25.084 0.2327 -0.0973 0.5646 + 3NME H 18 25.011 24.940 25.090 -0.0381 0.7744 -3.2673 + 3NME CH3 19 25.193 24.992 25.187 -0.3510 -0.2003 0.6123 + 3NME HH31 20 25.214 25.096 25.160 -0.4807 -0.0401 1.0853 + 3NME HH32 21 25.144 24.988 25.284 -0.7954 1.7414 0.5016 + 3NME HH33 22 25.286 24.934 25.195 0.7286 1.2608 -0.9727 + 50.00000 50.00000 50.00000 +Protein t= 0.00000 + 22 + 1ACE HH31 1 24.761 24.804 24.851 0.8774 -0.5951 0.2689 + 1ACE CH3 2 24.722 24.836 24.947 0.4883 -0.2689 0.0095 + 1ACE HH32 3 24.735 24.760 25.024 -1.1673 -0.8011 -0.2060 + 1ACE HH33 4 24.617 24.863 24.933 0.4978 -0.9842 -1.4687 + 1ACE C 5 24.793 24.965 24.992 0.3853 0.1583 -0.0916 + 1ACE O 6 24.725 25.072 24.989 -0.0038 -0.0248 0.1450 + 2ALA N 7 24.914 24.956 25.053 -0.0286 0.1831 0.5341 + 2ALA H 8 24.946 24.867 25.088 -0.7381 0.1640 1.1520 + 2ALA CA 9 24.991 25.070 25.101 -0.2022 1.0033 -1.2074 + 2ALA HA 10 24.935 25.142 25.161 0.7229 1.5621 -1.0033 + 2ALA CB 11 25.089 25.001 25.195 -0.5341 0.5550 -0.0935 + 2ALA HB1 12 25.142 24.923 25.140 -0.0191 0.9327 -0.1373 + 2ALA HB2 13 25.032 24.960 25.278 -2.4529 -0.4044 -1.8463 + 2ALA HB3 14 25.153 25.080 25.233 -1.1139 0.4559 1.1044 + 2ALA C 15 25.066 25.148 24.993 -0.0038 -0.1869 0.0687 + 2ALA O 16 25.083 25.097 24.884 -0.1640 -0.4539 0.1049 + 3NME N 17 25.110 25.271 25.023 -0.2003 0.3014 -0.5989 + 3NME H 18 25.088 25.298 25.118 -1.0872 -0.4578 -0.5684 + 3NME CH3 19 25.157 25.372 24.930 -0.0458 -0.5398 -0.4692 + 3NME HH31 20 25.213 25.326 24.849 1.6022 -0.2537 0.4692 + 3NME HH32 21 25.072 25.434 24.901 -1.0223 -1.9379 -0.6485 + 3NME HH33 22 25.221 25.442 24.983 -1.9436 0.0572 1.0891 + 50.00000 50.00000 50.00000 +Protein t= 0.00000 + 22 + 1ACE HH31 1 24.667 25.270 25.405 0.7019 1.1482 1.3905 + 1ACE CH3 2 24.745 25.196 25.428 0.2861 0.3319 0.2441 + 1ACE HH32 3 24.749 25.173 25.535 1.7414 -1.4706 -0.1793 + 1ACE HH33 4 24.835 25.250 25.400 -0.3471 -0.3815 -3.3665 + 1ACE C 5 24.748 25.071 25.343 0.3910 -0.2880 0.5341 + 1ACE O 6 24.747 24.959 25.394 -0.1774 -0.5417 0.1926 + 2ALA N 7 24.761 25.094 25.212 -1.2913 -0.0286 0.4768 + 2ALA H 8 24.789 25.188 25.191 3.8586 -1.4343 0.3185 + 2ALA CA 9 24.771 24.993 25.105 -0.0782 -0.7362 0.8221 + 2ALA HA 10 24.707 24.912 25.140 0.1221 -0.5760 1.5945 + 2ALA CB 11 24.708 25.047 24.978 0.2193 0.5455 0.6046 + 2ALA HB1 12 24.738 25.150 24.962 2.4414 -0.3834 -1.6804 + 2ALA HB2 13 24.599 25.048 24.985 0.1011 -0.8812 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24.845 25.101 -0.9251 -0.7439 0.8736 + 2ALA O 16 24.916 24.796 25.005 -0.7153 0.1545 0.2213 + 3NME N 17 24.914 24.843 25.223 -0.2880 -0.1678 0.1717 + 3NME H 18 24.866 24.886 25.300 -0.4559 -1.6994 0.9518 + 3NME CH3 19 25.048 24.791 25.253 0.1431 -0.8068 -0.0324 + 3NME HH31 20 25.119 24.830 25.180 -0.3147 0.0210 -0.0458 + 3NME HH32 21 25.080 24.827 25.350 1.1330 -0.1202 -0.6104 + 3NME HH33 22 25.044 24.682 25.250 0.2155 -0.8469 1.0052 + 50.00000 50.00000 50.00000 +Protein t= 0.00000 + 22 + 1ACE HH31 1 24.947 25.146 25.371 0.8354 1.8959 0.3376 + 1ACE CH3 2 25.055 25.135 25.361 0.6790 0.2213 0.2174 + 1ACE HH32 3 25.100 25.126 25.460 2.5635 -2.7180 -0.8526 + 1ACE HH33 4 25.093 25.220 25.304 0.5226 0.6599 0.7553 + 1ACE C 5 25.082 25.007 25.278 0.4978 -0.3643 -0.0591 + 1ACE O 6 25.192 24.954 25.290 -0.0210 0.2384 -0.2480 + 2ALA N 7 24.980 24.953 25.210 -0.0477 -0.6485 -0.4425 + 2ALA H 8 24.900 25.014 25.217 -0.5379 -1.5774 2.6817 + 2ALA CA 9 24.973 24.823 25.152 0.2937 -0.2480 0.0057 + 2ALA 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24.987 24.946 24.982 -1.1864 -0.4711 -0.2594 + 2ALA O 16 25.062 24.994 25.066 -0.0076 0.3109 -0.0515 + 3NME N 17 24.881 24.883 25.020 0.3452 -1.0586 -0.5245 + 3NME H 18 24.830 24.845 24.941 3.1185 -0.4406 -2.7180 + 3NME CH3 19 24.839 24.836 25.152 0.3567 0.2460 0.2747 + 3NME HH31 20 24.828 24.923 25.217 0.6580 -0.3147 1.0777 + 3NME HH32 21 24.748 24.777 25.158 -0.6542 1.9665 2.1038 + 3NME HH33 22 24.921 24.780 25.195 -0.0401 -0.1373 0.5455 + 50.00000 50.00000 50.00000 +Protein t= 0.00000 + 22 + 1ACE HH31 1 24.947 25.262 25.326 1.1711 1.7052 1.1539 + 1ACE CH3 2 25.044 25.212 25.336 0.2651 -0.4616 -0.3548 + 1ACE HH32 3 25.072 25.184 25.437 3.5324 0.5074 -0.9403 + 1ACE HH33 4 25.120 25.283 25.302 1.0986 -1.1406 0.0668 + 1ACE C 5 25.045 25.093 25.240 0.0763 0.2289 0.3738 + 1ACE O 6 25.077 24.983 25.282 0.3529 -0.1125 -0.4673 + 2ALA N 7 25.014 25.120 25.113 0.1812 0.0324 0.1202 + 2ALA H 8 24.997 25.219 25.098 -0.0839 0.2651 1.7815 + 2ALA CA 9 25.008 25.031 25.000 -0.0896 0.3490 -0.0877 + 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15 25.167 24.895 25.050 0.0114 0.0172 -0.4902 + 2ALA O 16 25.262 24.815 25.038 0.5779 -0.2708 0.3395 + 3NME N 17 25.190 25.026 25.066 -1.0624 0.4311 -0.0057 + 3NME H 18 25.109 25.078 25.096 -0.2060 0.4349 2.3861 + 3NME CH3 19 25.326 25.082 25.064 0.5779 0.1621 -0.0248 + 3NME HH31 20 25.371 25.028 24.981 -0.9518 -1.0281 -0.0973 + 3NME HH32 21 25.313 25.188 25.042 -0.0343 0.5455 1.9894 + 3NME HH33 22 25.381 25.064 25.157 1.3943 -2.9507 -1.0681 + 50.00000 50.00000 50.00000 +Protein t= 0.00000 + 22 + 1ACE HH31 1 24.993 25.252 25.211 0.5512 0.2098 0.8011 + 1ACE CH3 2 24.980 25.164 25.275 0.3777 -0.2232 0.1945 + 1ACE HH32 3 24.879 25.154 25.314 -0.2117 -0.8678 -1.4267 + 1ACE HH33 4 25.050 25.170 25.359 3.7937 -3.4695 -2.2507 + 1ACE C 5 25.014 25.043 25.196 -0.2575 0.2480 0.0248 + 1ACE O 6 25.091 24.955 25.238 -0.2613 -0.2575 -0.2899 + 2ALA N 7 24.952 25.036 25.077 0.5188 -0.0954 0.2651 + 2ALA H 8 24.891 25.111 25.045 0.5283 0.3567 1.2646 + 2ALA CA 9 24.972 24.936 24.972 -0.1717 0.0477 0.0000 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25.191 25.028 25.097 0.1736 -0.1621 -0.1354 + 3NME H 18 25.108 25.074 25.062 -0.6123 -0.8774 0.7477 + 3NME CH3 19 25.277 25.112 25.180 0.4406 -0.0973 -0.2918 + 3NME HH31 20 25.303 25.061 25.273 -1.1673 -0.9480 -0.2899 + 3NME HH32 21 25.362 25.143 25.119 -0.2594 0.4787 -0.9785 + 3NME HH33 22 25.230 25.207 25.203 1.6212 0.7343 -1.2760 + 50.00000 50.00000 50.00000 +Protein t= 0.00000 + 22 + 1ACE HH31 1 24.627 25.072 24.990 0.3948 -0.4063 0.4807 + 1ACE CH3 2 24.606 25.066 25.097 -0.7019 -0.5913 0.2575 + 1ACE HH32 3 24.556 24.972 25.122 -0.6790 -0.1183 2.1381 + 1ACE HH33 4 24.548 25.157 25.115 -0.8316 -0.4120 -0.9937 + 1ACE C 5 24.740 25.069 25.174 -0.2861 -0.0553 0.1030 + 1ACE O 6 24.791 25.176 25.198 -0.2861 -0.2079 -0.2308 + 2ALA N 7 24.797 24.955 25.211 0.2594 0.0343 0.1431 + 2ALA H 8 24.746 24.870 25.192 -1.0624 1.0223 -0.8087 + 2ALA CA 9 24.937 24.943 25.258 0.0629 0.1316 0.2174 + 2ALA HA 10 24.958 25.037 25.311 1.3733 -0.3471 0.5779 + 2ALA CB 11 24.957 24.826 25.359 -0.3777 -0.1259 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25.097 24.656 24.826 -0.2403 -0.1488 0.0668 + 3NME N 17 25.178 24.842 24.918 0.3605 0.2823 -0.3338 + 3NME H 18 25.175 24.916 24.987 1.6098 1.0204 -1.0376 + 3NME CH3 19 25.300 24.841 24.833 -0.4768 -0.2556 -0.0134 + 3NME HH31 20 25.323 24.737 24.807 -2.9526 -0.8411 0.0057 + 3NME HH32 21 25.281 24.887 24.736 -1.7033 -2.7256 -0.9995 + 3NME HH33 22 25.390 24.885 24.875 0.9155 -1.2665 -1.8272 + 50.00000 50.00000 50.00000 +Protein t= 0.00000 + 22 + 1ACE HH31 1 24.532 25.265 25.036 -0.2232 0.2003 0.3109 + 1ACE CH3 2 24.613 25.299 25.100 0.3662 -0.2937 -0.1717 + 1ACE HH32 3 24.600 25.267 25.203 0.6084 -1.4343 -0.4997 + 1ACE HH33 4 24.620 25.408 25.088 0.3910 -0.3719 -0.9060 + 1ACE C 5 24.744 25.247 25.040 -0.7801 0.2251 0.4539 + 1ACE O 6 24.851 25.311 25.033 -0.3262 0.8297 -0.1068 + 2ALA N 7 24.746 25.114 25.026 0.6771 -0.0820 -0.4749 + 2ALA H 8 24.660 25.067 25.051 0.1564 1.7242 1.3027 + 2ALA CA 9 24.871 25.039 24.991 0.5589 -0.2937 0.0286 + 2ALA HA 10 24.956 25.088 25.038 1.4381 -1.1578 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24.992 24.933 25.063 -0.2842 0.0095 0.5150 + 2ALA HA 10 25.061 24.873 25.004 0.4730 1.4877 -0.1354 + 2ALA CB 11 24.854 24.881 25.021 0.3719 -0.0248 0.2995 + 2ALA HB1 12 24.775 24.928 25.080 -3.1261 -2.3384 -2.3384 + 2ALA HB2 13 24.853 24.772 25.027 1.1940 -0.1411 -1.3466 + 2ALA HB3 14 24.831 24.927 24.925 1.1196 1.9779 1.0471 + 2ALA C 15 25.017 25.085 25.022 -0.2193 0.1545 0.2232 + 2ALA O 16 24.985 25.128 24.912 -0.9327 -0.0229 0.8793 + 3NME N 17 25.058 25.173 25.114 0.2995 0.1926 0.2270 + 3NME H 18 25.076 25.128 25.203 -1.6193 -1.3657 -0.1431 + 3NME CH3 19 25.077 25.320 25.101 -0.4501 0.3414 -0.1907 + 3NME HH31 20 25.144 25.374 25.169 -0.9785 0.9727 -0.1488 + 3NME HH32 21 25.101 25.347 24.997 0.3471 -1.1368 -0.4025 + 3NME HH33 22 24.982 25.367 25.124 -0.3967 -0.5932 2.0199 + 50.00000 50.00000 50.00000 +Protein t= 0.00000 + 22 + 1ACE HH31 1 24.616 24.997 25.086 1.7910 -0.7381 1.4286 + 1ACE CH3 2 24.673 25.044 25.006 0.0992 0.3338 0.8183 + 1ACE HH32 3 24.662 25.150 25.029 -1.5545 0.2689 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24.786 25.337 25.030 -0.6886 0.4044 1.4763 + 1ACE CH3 2 24.705 25.284 24.981 0.4101 -0.2861 0.3719 + 1ACE HH32 3 24.709 25.300 24.873 1.6422 -0.0782 0.4444 + 1ACE HH33 4 24.624 25.341 25.026 1.4515 2.0733 -0.6256 + 1ACE C 5 24.701 25.134 25.014 -0.6332 0.2174 0.1583 + 1ACE O 6 24.632 25.097 25.108 -0.9975 0.4196 -0.1812 + 2ALA N 7 24.782 25.057 24.943 -0.1316 0.0610 0.6142 + 2ALA H 8 24.855 25.094 24.883 -0.3662 0.5722 0.6485 + 2ALA CA 9 24.790 24.911 24.971 -0.2956 0.1392 0.1583 + 2ALA HA 10 24.691 24.876 24.999 -0.4482 1.1101 0.8392 + 2ALA CB 11 24.836 24.838 24.844 0.1659 -0.5913 -0.8469 + 2ALA HB1 12 24.926 24.891 24.813 -0.1564 0.6580 0.2365 + 2ALA HB2 13 24.760 24.858 24.768 -0.5741 0.5913 0.1678 + 2ALA HB3 14 24.859 24.733 24.862 1.0128 -0.4025 -0.8068 + 2ALA C 15 24.880 24.872 25.098 -0.3548 -0.3338 0.2937 + 2ALA O 16 24.976 24.940 25.137 -0.7229 0.0744 0.0782 + 3NME N 17 24.851 24.762 25.161 0.4368 0.2098 -0.2346 + 3NME H 18 24.774 24.711 25.120 -0.5245 0.5074 1.1826 + 3NME 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25.115 24.758 25.247 0.2995 -0.2899 -0.0725 + 3NME H 18 25.018 24.737 25.268 0.0648 0.0782 -0.7439 + 3NME CH3 19 25.226 24.703 25.329 -0.5264 -0.6790 0.7076 + 3NME HH31 20 25.217 24.704 25.437 -2.4509 1.4305 0.5703 + 3NME HH32 21 25.250 24.602 25.296 -1.9321 -0.8621 0.1907 + 3NME HH33 22 25.314 24.760 25.301 -0.5493 -1.7281 -1.6422 + 50.00000 50.00000 50.00000 +Protein t= 0.00000 + 22 + 1ACE HH31 1 24.796 25.222 25.292 0.7114 -0.9441 -0.4196 + 1ACE CH3 2 24.748 25.204 25.196 -0.5322 0.8144 -0.1278 + 1ACE HH32 3 24.776 25.288 25.133 0.1335 1.1292 0.5970 + 1ACE HH33 4 24.641 25.193 25.215 -0.3395 0.4787 0.7877 + 1ACE C 5 24.809 25.078 25.142 -0.1869 -0.1640 0.2651 + 1ACE O 6 24.744 24.985 25.102 0.6752 0.3490 -0.8507 + 2ALA N 7 24.940 25.071 25.136 -0.6504 0.3376 0.0572 + 2ALA H 8 24.993 25.151 25.166 -1.3695 0.4311 1.1044 + 2ALA CA 9 25.022 24.961 25.081 0.1335 -0.5665 0.4311 + 2ALA HA 10 24.985 24.931 24.983 0.0992 0.7763 0.0191 + 2ALA CB 11 25.156 25.018 25.036 -0.0916 0.3262 -0.0820 + 2ALA HB1 12 25.214 25.029 25.128 0.6638 -3.0785 -0.0629 + 2ALA HB2 13 25.141 25.113 24.986 -0.6638 0.7095 0.7782 + 2ALA HB3 14 25.200 24.943 24.970 0.4616 -1.2512 1.9836 + 2ALA C 15 25.044 24.836 25.176 -0.2079 -0.0153 0.1202 + 2ALA O 16 25.154 24.780 25.183 0.0877 -0.2098 -0.2441 + 3NME N 17 24.943 24.808 25.257 -0.2079 -0.2842 0.5665 + 3NME H 18 24.855 24.858 25.251 -0.2155 -0.4349 -0.5302 + 3NME CH3 19 24.969 24.729 25.386 0.0458 -0.6485 0.5150 + 3NME HH31 20 24.976 24.804 25.465 1.2112 0.3166 -0.4978 + 3NME HH32 21 24.884 24.663 25.403 -0.8507 0.9537 2.5826 + 3NME HH33 22 25.062 24.674 25.377 0.6866 0.3872 0.7305 + 50.00000 50.00000 50.00000 +Protein t= 0.00000 + 22 + 1ACE HH31 1 24.763 25.240 25.165 -3.6430 2.1133 1.1520 + 1ACE CH3 2 24.716 25.142 25.173 0.2918 -0.0153 -0.3834 + 1ACE HH32 3 24.655 25.137 25.083 0.0019 0.9670 -0.2575 + 1ACE HH33 4 24.656 25.138 25.264 0.8564 -1.6422 -0.0553 + 1ACE C 5 24.826 25.033 25.171 -1.0071 0.9289 0.5722 + 1ACE O 6 24.916 25.038 25.251 0.2651 0.0076 -0.4807 + 2ALA N 7 24.817 24.936 25.077 0.0496 -0.2480 0.1087 + 2ALA H 8 24.728 24.925 25.031 -1.3618 1.1120 2.3880 + 2ALA CA 9 24.923 24.831 25.049 0.1011 0.7133 -0.2365 + 2ALA HA 10 24.949 24.783 25.144 0.0381 -0.3777 -0.7668 + 2ALA CB 11 24.862 24.725 24.958 -0.5646 -0.6809 -0.7172 + 2ALA HB1 12 24.849 24.771 24.859 -1.3542 2.2564 0.6866 + 2ALA HB2 13 24.768 24.690 25.000 -0.8545 0.4711 -0.3815 + 2ALA HB3 14 24.936 24.648 24.939 3.3913 3.2177 -1.9646 + 2ALA C 15 25.057 24.892 25.000 0.3281 -0.7191 0.0515 + 2ALA O 16 25.139 24.822 24.949 0.1926 0.3662 0.3815 + 3NME N 17 25.074 25.026 25.002 -0.2575 0.1907 0.2899 + 3NME H 18 25.006 25.081 25.052 0.7381 0.5302 1.2627 + 3NME CH3 19 25.176 25.088 24.920 -0.1068 -0.2403 -0.9537 + 3NME HH31 20 25.276 25.055 24.949 -0.6447 -1.6899 -0.7172 + 3NME HH32 21 25.158 25.072 24.814 -2.8534 1.7757 -0.8564 + 3NME HH33 22 25.168 25.196 24.935 0.4215 0.2251 -3.7537 + 50.00000 50.00000 50.00000 +Protein t= 0.00000 + 22 + 1ACE HH31 1 24.980 25.389 25.029 0.1659 -0.0343 -0.5016 + 1ACE CH3 2 24.884 25.356 24.989 0.5398 -0.5112 -1.0071 + 1ACE HH32 3 24.892 25.346 24.881 2.7084 0.6657 -0.9842 + 1ACE HH33 4 24.816 25.437 25.013 0.2346 -0.8526 -0.7362 + 1ACE C 5 24.844 25.232 25.060 -0.3605 0.1335 -0.1011 + 1ACE O 6 24.775 25.239 25.160 0.0782 0.1087 0.1869 + 2ALA N 7 24.892 25.118 25.016 0.4864 -0.4482 0.5455 + 2ALA H 8 24.959 25.124 24.940 -1.5984 1.5125 -1.1711 + 2ALA CA 9 24.880 24.986 25.078 -0.3052 -0.6695 0.2460 + 2ALA HA 10 24.871 25.003 25.185 1.8673 0.2441 0.3204 + 2ALA CB 11 24.740 24.927 25.048 0.4387 0.5016 -0.0229 + 2ALA HB1 12 24.741 24.901 24.942 -2.4204 -1.7872 0.4463 + 2ALA HB2 13 24.668 25.000 25.085 -2.2011 -1.9207 -0.1717 + 2ALA HB3 14 24.734 24.836 25.107 0.3166 0.0362 -0.7458 + 2ALA C 15 25.010 24.904 25.060 0.2174 -0.7019 0.8297 + 2ALA O 16 25.122 24.955 25.057 -0.2575 -0.0610 -0.0248 + 3NME N 17 24.988 24.772 25.049 -0.8640 -0.2346 -0.4425 + 3NME H 18 24.890 24.752 25.032 -0.8602 0.4826 -1.4229 + 3NME CH3 19 25.090 24.671 25.043 -0.7057 0.0114 0.1087 + 3NME HH31 20 25.061 24.579 25.095 -0.7648 -0.3853 -0.6142 + 3NME HH32 21 25.112 24.647 24.939 1.2188 -1.0433 0.7229 + 3NME HH33 22 25.183 24.705 25.089 -1.0242 0.0591 0.7324 + 50.00000 50.00000 50.00000 +Protein t= 0.00000 + 22 + 1ACE HH31 1 24.811 25.301 24.780 0.6180 -0.2651 0.0000 + 1ACE CH3 2 24.750 25.248 24.853 -0.2804 0.6886 -0.0191 + 1ACE HH32 3 24.673 25.187 24.807 1.4954 -1.2569 -0.5035 + 1ACE HH33 4 24.702 25.325 24.912 1.3180 2.3346 -0.8202 + 1ACE C 5 24.841 25.155 24.931 -0.6142 -0.5836 -0.7973 + 1ACE O 6 24.849 25.174 25.050 0.0229 0.0095 -0.3433 + 2ALA N 7 24.900 25.052 24.876 0.4730 -0.1507 0.1297 + 2ALA H 8 24.888 25.037 24.777 -0.8907 0.5951 0.1755 + 2ALA CA 9 24.995 24.965 24.942 -1.0700 0.2937 0.5817 + 2ALA HA 10 24.991 24.970 25.051 1.4915 2.0008 0.6294 + 2ALA CB 11 24.978 24.819 24.904 0.0877 0.1335 0.1049 + 2ALA HB1 12 24.984 24.797 24.798 -1.5526 -0.9480 0.2079 + 2ALA HB2 13 24.878 24.787 24.934 0.2174 0.3338 0.7706 + 2ALA HB3 14 25.041 24.750 24.961 1.1196 -1.1768 -2.5330 + 2ALA C 15 25.138 25.024 24.910 0.5608 -0.2918 -0.4559 + 2ALA O 16 25.177 25.033 24.796 0.5703 0.0610 -0.4959 + 3NME N 17 25.217 25.052 25.015 0.1011 0.0210 -0.4654 + 3NME H 18 25.185 25.011 25.101 -2.7809 -0.2480 -1.5984 + 3NME CH3 19 25.353 25.108 25.012 0.6905 -0.1602 -0.1183 + 3NME HH31 20 25.414 25.037 24.957 -0.5569 -0.4501 -1.1749 + 3NME HH32 21 25.351 25.208 24.967 -0.1850 0.6828 1.7471 + 3NME HH33 22 25.389 25.116 25.114 -1.3332 0.5627 0.5684 + 50.00000 50.00000 50.00000 +Protein t= 0.00000 + 22 + 1ACE HH31 1 24.911 25.145 25.418 -0.5741 0.1831 0.8049 + 1ACE CH3 2 24.821 25.130 25.359 -0.0038 -0.6008 0.1144 + 1ACE HH32 3 24.803 25.213 25.290 2.5654 0.0324 0.1736 + 1ACE HH33 4 24.739 25.123 25.431 0.4253 -1.2569 0.5379 + 1ACE C 5 24.848 25.012 25.271 0.1698 0.3834 0.3548 + 1ACE O 6 24.855 24.905 25.323 0.1030 0.3223 0.1984 + 2ALA N 7 24.869 25.021 25.140 -0.7305 0.2937 -0.0877 + 2ALA H 8 24.894 25.114 25.111 2.2049 -0.2537 0.5245 + 2ALA CA 9 24.860 24.908 25.043 0.2270 -0.0820 0.2384 + 2ALA HA 10 24.794 24.831 25.083 1.0490 -0.7915 0.2232 + 2ALA CB 11 24.803 24.956 24.907 -0.0172 -0.0629 -0.5608 + 2ALA HB1 12 24.866 25.037 24.870 -2.5883 2.2430 -0.0305 + 2ALA HB2 13 24.702 24.992 24.928 0.3204 0.2956 0.4787 + 2ALA HB3 14 24.798 24.869 24.841 -0.7076 1.3485 -2.4052 + 2ALA C 15 25.004 24.843 25.033 -0.3204 0.0839 -0.1698 + 2ALA O 16 25.057 24.822 24.922 -0.1011 -0.2785 0.3033 + 3NME N 17 25.061 24.816 25.147 -0.1602 -0.4921 0.5322 + 3NME H 18 24.994 24.820 25.223 -0.5436 1.1139 0.1335 + 3NME CH3 19 25.187 24.736 25.170 0.4616 -0.0229 -0.1278 + 3NME HH31 20 25.199 24.707 25.275 0.3338 0.6943 0.0954 + 3NME HH32 21 25.195 24.654 25.100 -1.0185 -1.4019 1.2722 + 3NME HH33 22 25.261 24.814 25.148 0.6466 -0.5035 -1.1635 + 50.00000 50.00000 50.00000