Starting qr.refine on Mon May 20 18:24:14 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/3fm7.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/3fm7.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/3fm7.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 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 77": "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: 6838 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1598 Classifications: {'peptide': 103} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "B" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1609 Classifications: {'peptide': 104} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 102} Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 435 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 23} Chain: "D" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 435 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 24} Chain: "E" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1381 Classifications: {'peptide': 85} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 82} Chain: "F" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1380 Classifications: {'peptide': 85} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 82} Time building chain proxies: 0.82, per 1000 atoms: 0.12 Number of scatterers: 6838 At special positions: 0 Unit cell: (115.79, 115.79, 90.5, 90, 90, 120) Space group: P 62 (No. 171) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 O 666 8.00 N 569 7.00 C 2187 6.00 H 3394 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: 1.33 Adding C-beta torsion restraints... Number of C-beta restraints generated: 818 Time building geometry restraints manager: 1.56 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: 3382 1.14 - 1.31: 591 1.31 - 1.48: 1396 1.48 - 1.65: 1505 1.65 - 1.82: 32 Bond restraints: 6906 Sorted by residual: bond pdb=" N ALA C 117 " pdb=" CA ALA C 117 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.90e-02 2.77e+03 1.82e+00 bond pdb=" C GLN C 116 " pdb=" N ALA C 117 " ideal model delta sigma weight residual 1.329 1.346 -0.017 1.40e-02 5.10e+03 1.48e+00 bond pdb=" CA ASP B 35 " pdb=" C ASP B 35 " ideal model delta sigma weight residual 1.525 1.550 -0.025 2.10e-02 2.27e+03 1.44e+00 bond pdb=" CA GLN C 116 " pdb=" CB GLN C 116 " ideal model delta sigma weight residual 1.530 1.554 -0.024 2.00e-02 2.50e+03 1.42e+00 bond pdb=" CB LYS F 36 " pdb=" CG LYS F 36 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.24e+00 ... (remaining 6901 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.46: 94 106.46 - 113.34: 8143 113.34 - 120.23: 2051 120.23 - 127.12: 2120 127.12 - 134.01: 37 Bond angle restraints: 12445 Sorted by residual: angle pdb=" C GLN C 116 " pdb=" N ALA C 117 " pdb=" CA ALA C 117 " ideal model delta sigma weight residual 121.70 128.43 -6.73 1.80e+00 3.09e-01 1.40e+01 angle pdb=" CA ILE A 19 " pdb=" CB ILE A 19 " pdb=" CG1 ILE A 19 " ideal model delta sigma weight residual 110.40 115.10 -4.70 1.70e+00 3.46e-01 7.65e+00 angle pdb=" C MET E 13 " pdb=" CA MET E 13 " pdb=" CB MET E 13 " ideal model delta sigma weight residual 110.10 115.14 -5.04 1.90e+00 2.77e-01 7.04e+00 angle pdb=" CA ASP B 35 " pdb=" C ASP B 35 " pdb=" N LYS B 36 " ideal model delta sigma weight residual 116.20 121.48 -5.28 2.00e+00 2.50e-01 6.97e+00 angle pdb=" CA ILE F 38 " pdb=" CB ILE F 38 " pdb=" CG1 ILE F 38 " ideal model delta sigma weight residual 110.40 114.87 -4.47 1.70e+00 3.46e-01 6.91e+00 ... (remaining 12440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 2819 17.52 - 35.04: 284 35.04 - 52.56: 102 52.56 - 70.08: 38 70.08 - 87.60: 10 Dihedral angle restraints: 3253 sinusoidal: 1731 harmonic: 1522 Sorted by residual: dihedral pdb=" CA ASN C 114 " pdb=" C ASN C 114 " pdb=" N VAL C 115 " pdb=" CA VAL C 115 " ideal model delta harmonic sigma weight residual 180.00 126.50 53.50 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA MET E 13 " pdb=" C MET E 13 " pdb=" N SER E 14 " pdb=" CA SER E 14 " ideal model delta harmonic sigma weight residual -180.00 -144.38 -35.62 0 5.00e+00 4.00e-02 5.08e+01 dihedral pdb=" CA MET F 13 " pdb=" C MET F 13 " pdb=" N SER F 14 " pdb=" CA SER F 14 " ideal model delta harmonic sigma weight residual 180.00 149.98 30.02 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 3250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 353 0.038 - 0.077: 128 0.077 - 0.115: 38 0.115 - 0.154: 17 0.154 - 0.192: 3 Chirality restraints: 539 Sorted by residual: chirality pdb=" CA ILE A 67 " pdb=" N ILE A 67 " pdb=" C ILE A 67 " pdb=" CB ILE A 67 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" CA ILE A 103 " pdb=" N ILE A 103 " pdb=" C ILE A 103 " pdb=" CB ILE A 103 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.23e-01 chirality pdb=" CA ILE E 83 " pdb=" N ILE E 83 " pdb=" C ILE E 83 " pdb=" CB ILE E 83 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.14e-01 ... (remaining 536 not shown) Planarity restraints: 1018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 43 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.02e+00 pdb=" C GLN B 43 " -0.025 2.00e-02 2.50e+03 pdb=" O GLN B 43 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL B 44 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 27 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C ILE A 27 " -0.024 2.00e-02 2.50e+03 pdb=" O ILE A 27 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY A 28 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 14 " 0.006 2.00e-02 2.50e+03 1.12e-02 1.26e+00 pdb=" N VAL B 15 " -0.019 2.00e-02 2.50e+03 pdb=" CA VAL B 15 " 0.005 2.00e-02 2.50e+03 pdb=" H VAL B 15 " 0.008 2.00e-02 2.50e+03 ... (remaining 1015 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 611 2.13 - 2.75: 11831 2.75 - 3.36: 19618 3.36 - 3.98: 27620 3.98 - 4.60: 39827 Nonbonded interactions: 99507 Sorted by model distance: nonbonded pdb=" OD1 ASN A 97 " pdb=" H THR A 99 " model vdw 1.512 1.800 nonbonded pdb=" O VAL E 58 " pdb=" H GLY F 63 " model vdw 1.564 1.800 nonbonded pdb=" O GLU B 46 " pdb=" HG1 THR B 50 " model vdw 1.567 1.800 nonbonded pdb=" O THR A 26 " pdb=" H GLY A 28 " model vdw 1.570 1.800 nonbonded pdb=" HZ1 LYS B 70 " pdb=" O ASN B 97 " model vdw 1.573 1.800 ... (remaining 99502 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 22 15.96 2 O 666 7.97 2 N 569 6.97 2 C 2187 5.97 2 H 3394 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: 8.9 rota: 16.36 rama: f: 84.01 o: 3.10 Z: -4.63 cb: 0.00 shift start/prev: 0.000 0.000 LBFGS: function start/end, n_calls: -980.492591 -1105.156966 101 cycle 0: bond: 0.009 angle: 1.72 clash: 0.9 rota: 7.12 rama: f: 93.08 o: 1.19 Z: -2.72 cb: 0.98 shift start/prev: 0.286 0.286 LBFGS: function start/end, n_calls: -1105.156966 -1116.057446 102 cycle 1: bond: 0.009 angle: 1.66 clash: 1.0 rota: 6.60 rama: f: 93.32 o: 0.72 Z: -2.66 cb: 0.24 shift start/prev: 0.385 0.161 LBFGS: function start/end, n_calls: -1116.057446 -1121.305076 102 cycle 2: bond: 0.009 angle: 1.66 clash: 0.9 rota: 5.54 rama: f: 93.08 o: 0.48 Z: -2.52 cb: 0.49 shift start/prev: 0.451 0.115 calculator(opt), total_time (target_and_gradients) 71.88498330116272 calculator(opt), number_of_target_and_gradients_calls (target_and_gradients) 305 See 3fm7_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 224.13 seconds wall clock time: 3 minutes 51.81 seconds (231.81 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)