Starting qr.refine on Mon May 20 18:17:30 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/1u9o.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/1u9o.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/1u9o.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 PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 148": "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: 5976 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2988 Classifications: {'peptide': 194} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 185} Chain: "B" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2988 Classifications: {'peptide': 194} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 185} Time building chain proxies: 0.72, per 1000 atoms: 0.12 Number of scatterers: 5976 At special positions: 0 Unit cell: (140.5, 140.5, 76.69, 90, 90, 120) Space group: R 3 :H (No. 146) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 O 586 8.00 N 520 7.00 C 1908 6.00 H 2954 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: 1.13 Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Time building geometry restraints manager: 1.32 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: 2954 1.14 - 1.31: 528 1.31 - 1.47: 1236 1.47 - 1.64: 1304 1.64 - 1.80: 16 Bond restraints: 6038 Sorted by residual: bond pdb=" C ALA A 161 " pdb=" N ALA A 162 " ideal model delta sigma weight residual 1.329 1.353 -0.024 1.40e-02 5.10e+03 3.01e+00 bond pdb=" CA THR A 89 " pdb=" C THR A 89 " ideal model delta sigma weight residual 1.525 1.544 -0.019 2.10e-02 2.27e+03 8.31e-01 bond pdb=" C TRP B 138 " pdb=" N SER B 139 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.40e-02 5.10e+03 6.73e-01 bond pdb=" C ARG A 40 " pdb=" N PRO A 41 " ideal model delta sigma weight residual 1.341 1.329 0.012 1.60e-02 3.91e+03 5.54e-01 bond pdb=" C ASP A 154 " pdb=" N ALA A 155 " ideal model delta sigma weight residual 1.329 1.339 -0.010 1.40e-02 5.10e+03 5.48e-01 ... (remaining 6033 not shown) Histogram of bond angle deviations from ideal: 100.25 - 107.01: 120 107.01 - 113.77: 7047 113.77 - 120.53: 2115 120.53 - 127.29: 1569 127.29 - 134.06: 39 Bond angle restraints: 10890 Sorted by residual: angle pdb=" CA ARG B 58 " pdb=" C ARG B 58 " pdb=" N PRO B 59 " ideal model delta sigma weight residual 116.90 121.01 -4.11 1.50e+00 4.44e-01 7.51e+00 angle pdb=" CA ARG A 58 " pdb=" C ARG A 58 " pdb=" N PRO A 59 " ideal model delta sigma weight residual 116.90 120.81 -3.91 1.50e+00 4.44e-01 6.78e+00 angle pdb=" CA TYR B 62 " pdb=" C TYR B 62 " pdb=" N PHE B 63 " ideal model delta sigma weight residual 116.20 121.16 -4.96 2.00e+00 2.50e-01 6.16e+00 angle pdb=" C LEU A 183 " pdb=" N PHE A 184 " pdb=" CA PHE A 184 " ideal model delta sigma weight residual 121.70 118.09 3.61 1.80e+00 3.09e-01 4.03e+00 angle pdb=" CA THR A 89 " pdb=" C THR A 89 " pdb=" N LEU A 90 " ideal model delta sigma weight residual 116.20 120.19 -3.99 2.00e+00 2.50e-01 3.98e+00 ... (remaining 10885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.70: 2583 14.70 - 29.39: 168 29.39 - 44.08: 62 44.08 - 58.78: 26 58.78 - 73.47: 7 Dihedral angle restraints: 2846 sinusoidal: 1524 harmonic: 1322 Sorted by residual: dihedral pdb=" CA ILE A 29 " pdb=" CB ILE A 29 " pdb=" CG1 ILE A 29 " pdb=" CD1 ILE A 29 " ideal model delta sinusoidal sigma weight residual -60.00 -117.03 57.03 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CA ARG A 25 " pdb=" CB ARG A 25 " pdb=" CG ARG A 25 " pdb=" CD ARG A 25 " ideal model delta sinusoidal sigma weight residual 180.00 124.26 55.74 3 1.50e+01 4.44e-03 9.36e+00 dihedral pdb=" N ILE B 146 " pdb=" CA ILE B 146 " pdb=" CB ILE B 146 " pdb=" CG1 ILE B 146 " ideal model delta sinusoidal sigma weight residual -60.00 -113.41 53.41 3 1.50e+01 4.44e-03 9.20e+00 ... (remaining 2843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 306 0.024 - 0.049: 112 0.049 - 0.073: 42 0.073 - 0.098: 19 0.098 - 0.122: 5 Chirality restraints: 484 Sorted by residual: chirality pdb=" CA VAL A 194 " pdb=" N VAL A 194 " pdb=" C VAL A 194 " pdb=" CB VAL A 194 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 chirality pdb=" CA VAL B 194 " pdb=" N VAL B 194 " pdb=" C VAL B 194 " pdb=" CB VAL B 194 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA ILE A 45 " pdb=" N ILE A 45 " pdb=" C ILE A 45 " pdb=" CB ILE A 45 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.28e-01 ... (remaining 481 not shown) Planarity restraints: 922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 93 " -0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO B 94 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 94 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 94 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 120 " -0.005 2.00e-02 2.50e+03 1.05e-02 1.10e+00 pdb=" C VAL A 120 " 0.018 2.00e-02 2.50e+03 pdb=" O VAL A 120 " -0.007 2.00e-02 2.50e+03 pdb=" N THR A 121 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 173 " -0.005 2.00e-02 2.50e+03 9.11e-03 8.31e-01 pdb=" C THR A 173 " 0.016 2.00e-02 2.50e+03 pdb=" O THR A 173 " -0.006 2.00e-02 2.50e+03 pdb=" N ALA A 174 " -0.005 2.00e-02 2.50e+03 ... (remaining 919 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.00: 333 2.00 - 2.65: 7186 2.65 - 3.30: 19354 3.30 - 3.95: 24290 3.95 - 4.60: 36427 Nonbonded interactions: 87590 Sorted by model distance: nonbonded pdb=" O ASP A 23 " pdb=" H LEU A 27 " model vdw 1.353 1.800 nonbonded pdb=" OE2 GLU A 34 " pdb=" HD1 HIS A 117 " model vdw 1.487 1.800 nonbonded pdb=" O ALA A 172 " pdb="HD22 ASN A 176 " model vdw 1.532 1.800 nonbonded pdb=" O GLN A 191 " pdb=" HG SER B 139 " model vdw 1.560 1.800 nonbonded pdb=" HE1 TRP B 138 " pdb=" OE2 GLU B 180 " model vdw 1.562 1.800 ... (remaining 87585 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 8 15.96 2 O 586 7.97 2 N 520 6.97 2 C 1908 5.97 2 H 2954 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: 0.94 clash: 4.0 rota: 5.13 rama: f: 88.02 o: 1.82 Z: -2.97 cb: 0.00 shift start/prev: 0.000 0.000 LBFGS: function start/end, n_calls: -1005.816721 -1088.379604 101 cycle 0: bond: 0.008 angle: 1.37 clash: 0.0 rota: 3.21 rama: f: 96.88 o: 0.26 Z: -1.84 cb: 0.00 shift start/prev: 0.215 0.215 LBFGS: function start/end, n_calls: -1088.379604 -1094.733627 102 cycle 1: bond: 0.008 angle: 1.35 clash: 0.0 rota: 2.24 rama: f: 96.88 o: 0.00 Z: -1.66 cb: 0.27 shift start/prev: 0.292 0.123 LBFGS: function start/end, n_calls: -1094.733627 -1097.739484 102 cycle 2: bond: 0.008 angle: 1.36 clash: 0.0 rota: 2.24 rama: f: 97.66 o: 0.26 Z: -1.97 cb: 0.27 shift start/prev: 0.342 0.084 calculator(opt), total_time (target_and_gradients) 61.369611978530884 calculator(opt), number_of_target_and_gradients_calls (target_and_gradients) 305 See 1u9o_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 186.09 seconds wall clock time: 3 minutes 11.66 seconds (191.66 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)