Starting qr.refine on Mon May 20 18:14:47 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/1fb5.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- mode=opt restraints=qm engine=aimnet2 clustering=false minimizer=lbfgs gradient_only=true use_reduce=False select_within_radius=7 number_of_micro_cycles=3 max_iterations_refine=100 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/1fb5.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/1fb5.pdb" } use_reduce = False cluster { clustering = false select_within_radius = 7 } quantum { engine_name = mopac *aimnet2 torchani terachem turbomole pyscf orca \ gaussian xtb server } refine { mode = *opt refine gtest number_of_micro_cycles = 3 max_iterations_refine = 100 gradient_only = true } Starting job =============================================================================== Validate inputs: ------------------------------------------------------------------------------- Refinement start **************** max_atoms = 50000 debug_rss = False debug = False scattering_table = wk1995 it1992 *n_gaussian electron neutron use_reduce = False cluster { charge_cutoff = 8 clustering = False charge_embedding = False two_buffers = False maxnum_residues_in_cluster = 15 bcc_threshold = 9 select_within_radius = 7 clustering_method = gnc *bcc altloc_method = average *subtract save_clusters = True bond_with_altloc = True re_calculate_rmsd_tolerance = 0.5 } restraints = cctbx *qm expansion = False quantum { engine_name = mopac *aimnet2 torchani terachem turbomole pyscf orca \ gaussian xtb server basis = Auto charge = None method = Auto memory = None nproc = 1 server_url = "http://127.0.0.1:8000" qm_addon = gcp dftd3 gcp-d3 qm_addon_method = None } refine { dry_run = False sf_algorithm = *direct fft refinement_target_name = *ml ls_wunit_k1 mode = *opt refine gtest number_of_macro_cycles = 1 number_of_weight_search_cycles = 50 number_of_refine_cycles = 5 number_of_micro_cycles = 3 data_weight = None skip_weight_search = False adjust_restraints_weight_scale_value = 2 max_iterations_weight = 50 max_iterations_refine = 100 use_ase_lbfgs = False line_search = True stpmax = 0.2 gradient_only = True refine_sites = True refine_adp = False restraints_weight_scale = 1 shake_sites = False use_convergence_test = True max_bond_rmsd = 0.03 max_angle_rmsd = 1.7 stop_one_found_first_good_weight = True max_r_work_r_free_gap = 5 r_tolerance = 0.001 rmsd_tolerance = 0.01 opt_log = False pre_opt = False pre_opt_stpmax = 0.1 pre_opt_iter = 10 pre_opt_switch = 2 pre_opt_gconv = 3000 minimizer = *lbfgs lbfgsb shift_evaluation = max *mean } parallel { method = *multiprocessing slurm pbs sge lsf threading nproc = 1 qsub_command = None } output_file_name_prefix = None output_folder_name = "pdb" rst_file = None dump_gradients = None output { filename = None file_name = None prefix = None suffix = None serial = 0 serial_format = "%03d" target_output_format = None *pdb mmcif overwrite = False } ------------------------------------------------------------------------------- Extracting model **************** Symmetric amino acids flipped Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-gpu-00/raid1/scratch1/pavel/phenix/modules/chem_data/mon_lib" Total number of atoms: 5100 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 5082 Classifications: {'peptide': 320} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 306} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Classifications: {'peptide': 1} Time building chain proxies: 0.68, per 1000 atoms: 0.13 Number of scatterers: 5100 At special positions: 0 Unit cell: (184.7, 184.7, 184.7, 90, 90, 90) Space group: P 43 3 2 (No. 212) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 O 476 8.00 N 427 7.00 C 1617 6.00 H 2569 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: Warning: Ignoring bond with distance_ideal = None: atom_selection_1 = None atom_selection_2 = None Total number of added/changed bonds: 0 Custom angles: Warning: Ignoring angle with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None Total number of new custom angles: 0 Total number of changed angles: 0 Custom dihedrals: Warning: Ignoring dihedral with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None atom_selection_4 = None Total number of custom dihedrals: 0 Custom planarities: Warning: Ignoring planarity with with sigma <= 0: Total number of custom planarities: 0 Custom parallelities: Warning: Ignoring parallelity with empty atom selection. Total number of custom parallelities: 0 Custom bonds: Warning: Ignoring bond with distance_ideal = None: atom_selection_1 = None atom_selection_2 = None Total number of added/changed bonds: 0 Custom angles: Warning: Ignoring angle with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None Total number of new custom angles: 0 Total number of changed angles: 0 Custom dihedrals: Warning: Ignoring dihedral with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None atom_selection_4 = None Total number of custom dihedrals: 0 Custom planarities: Warning: Ignoring planarity with with sigma <= 0: Total number of custom planarities: 0 Custom parallelities: Warning: Ignoring parallelity with empty atom selection. Total number of custom parallelities: 0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.02 Adding C-beta torsion restraints... Number of C-beta restraints generated: 602 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.14: 2567 1.14 - 1.31: 421 1.31 - 1.48: 1001 1.48 - 1.64: 1142 1.64 - 1.81: 20 Bond restraints: 5151 Sorted by residual: bond pdb=" N NVA A 900 " pdb=" H NVA A 900 " ideal model delta sigma weight residual 0.860 1.031 -0.171 2.00e-02 2.50e+03 7.35e+01 bond pdb=" N NVA A 900 " pdb=" CA NVA A 900 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.90e-02 2.77e+03 5.27e+00 bond pdb=" C TYR A 345 " pdb=" N SER A 346 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.40e-02 5.10e+03 6.19e-01 bond pdb=" C PHE A 86 " pdb=" N GLU A 87 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.40e-02 5.10e+03 5.67e-01 bond pdb=" N PRO A 250 " pdb=" CA PRO A 250 " ideal model delta sigma weight residual 1.466 1.477 -0.011 1.50e-02 4.44e+03 4.91e-01 ... (remaining 5146 not shown) Histogram of bond angle deviations from ideal: 100.54 - 107.22: 203 107.22 - 113.90: 6236 113.90 - 120.58: 1567 120.58 - 127.26: 1309 127.26 - 133.94: 29 Bond angle restraints: 9344 Sorted by residual: angle pdb=" C GLY A 162 " pdb=" N LEU A 163 " pdb=" CA LEU A 163 " ideal model delta sigma weight residual 121.70 126.79 -5.09 1.80e+00 3.09e-01 8.01e+00 angle pdb=" C LEU A 186 " pdb=" N LYS A 187 " pdb=" CA LYS A 187 " ideal model delta sigma weight residual 121.70 125.75 -4.05 1.80e+00 3.09e-01 5.06e+00 angle pdb=" C TYR A 345 " pdb=" N SER A 346 " pdb=" CA SER A 346 " ideal model delta sigma weight residual 121.70 125.70 -4.00 1.80e+00 3.09e-01 4.95e+00 angle pdb=" C SER A 90 " pdb=" N THR A 91 " pdb=" CA THR A 91 " ideal model delta sigma weight residual 121.70 125.60 -3.90 1.80e+00 3.09e-01 4.70e+00 angle pdb=" CA NVA A 900 " pdb=" N NVA A 900 " pdb=" H NVA A 900 " ideal model delta sigma weight residual 114.00 107.76 6.24 3.00e+00 1.11e-01 4.33e+00 ... (remaining 9339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.76: 2171 18.76 - 37.52: 173 37.52 - 56.28: 44 56.28 - 75.04: 19 75.04 - 93.80: 3 Dihedral angle restraints: 2410 sinusoidal: 1325 harmonic: 1085 Sorted by residual: dihedral pdb=" CG NVA A 900 " pdb=" CA NVA A 900 " pdb=" CB NVA A 900 " pdb=" HA NVA A 900 " ideal model delta sinusoidal sigma weight residual -62.82 30.98 -93.80 1 3.00e+01 1.11e-03 1.14e+01 dihedral pdb=" CA GLN A 279 " pdb=" C GLN A 279 " pdb=" N ALA A 280 " pdb=" CA ALA A 280 " ideal model delta harmonic sigma weight residual 180.00 164.26 15.74 0 5.00e+00 4.00e-02 9.91e+00 dihedral pdb=" CA LEU A 278 " pdb=" C LEU A 278 " pdb=" N GLN A 279 " pdb=" CA GLN A 279 " ideal model delta harmonic sigma weight residual 180.00 164.32 15.68 0 5.00e+00 4.00e-02 9.84e+00 ... (remaining 2407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 240 0.027 - 0.053: 95 0.053 - 0.080: 41 0.080 - 0.107: 11 0.107 - 0.133: 10 Chirality restraints: 397 Sorted by residual: chirality pdb=" CA ILE A 85 " pdb=" N ILE A 85 " pdb=" C ILE A 85 " pdb=" CB ILE A 85 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE A 261 " pdb=" N ILE A 261 " pdb=" C ILE A 261 " pdb=" CB ILE A 261 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE A 157 " pdb=" N ILE A 157 " pdb=" C ILE A 157 " pdb=" CB ILE A 157 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 ... (remaining 394 not shown) Planarity restraints: 747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 304 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO A 305 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 305 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 305 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 324 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO A 325 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 325 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 325 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 107 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO A 108 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " 0.018 5.00e-02 4.00e+02 ... (remaining 744 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 366 2.08 - 2.71: 8387 2.71 - 3.34: 16010 3.34 - 3.97: 21835 3.97 - 4.60: 32372 Nonbonded interactions: 78970 Sorted by model distance: nonbonded pdb=" OG1 THR A 178 " pdb="HD22 ASN A 329 " model vdw 1.454 1.800 nonbonded pdb="HH22 ARG A 94 " pdb=" O PHE A 110 " model vdw sym.op. 1.547 1.800 y,z,x nonbonded pdb=" HG1 THR A 299 " pdb=" O ARG A 320 " model vdw 1.581 1.800 nonbonded pdb=" O PHE A 48 " pdb=" HZ3 LYS A 210 " model vdw 1.594 1.800 nonbonded pdb=" O VAL A 339 " pdb=" HG1 THR A 343 " model vdw 1.596 1.800 ... (remaining 78965 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 11 15.96 2 O 476 7.97 2 N 427 6.97 2 C 1617 5.97 2 H 2569 1.00 3 sf(0) = scattering factor at diffraction angle 0. Setting QM defaults Setting QM method to HF Setting QM basis to 6-31g start: bond: 0.004 angle: 1.01 clash: 10.2 rota: 16.00 rama: f: 81.76 o: 4.09 Z: -3.47 cb: 0.00 shift start/prev: 0.000 0.000 LBFGS: function start/end, n_calls: -810.667049 -891.985171 101 cycle 0: bond: 0.009 angle: 1.69 clash: 2.0 rota: 9.82 rama: f: 91.51 o: 2.20 Z: -3.08 cb: 0.33 shift start/prev: 0.248 0.248 LBFGS: function start/end, n_calls: -891.985171 -898.062754 102 cycle 1: bond: 0.009 angle: 1.66 clash: 1.8 rota: 8.00 rama: f: 92.77 o: 1.26 Z: -3.01 cb: 0.66 shift start/prev: 0.341 0.143 LBFGS: function start/end, n_calls: -898.062754 -901.117394 102 cycle 2: bond: 0.009 angle: 1.67 clash: 1.6 rota: 7.64 rama: f: 92.77 o: 1.57 Z: -3.04 cb: 0.66 shift start/prev: 0.402 0.104 calculator(opt), total_time (target_and_gradients) 56.41468596458435 calculator(opt), number_of_target_and_gradients_calls (target_and_gradients) 305 See 1fb5_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 154.87 seconds wall clock time: 2 minutes 40.73 seconds (160.73 seconds total) /net/cci-gpu-00/raid1/scratch1/pavel/phenix/conda_base/lib/python3.8/site-packages/ase/__init__.py:21: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. if LooseVersion(np.__version__) < '1.9': /net/cci-gpu-00/raid1/scratch1/pavel/phenix/conda_base/lib/python3.8/site-packages/setuptools/_distutils/version.py:346: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. other = LooseVersion(other)