Starting qr.refine on Mon May 20 19:15:33 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/2pej.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/2pej.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/2pej.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 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 85": "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: 10709 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1791 Classifications: {'peptide': 109} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "B" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1774 Classifications: {'peptide': 108} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "C" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1789 Classifications: {'peptide': 109} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "D" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1760 Classifications: {'peptide': 107} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "E" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1808 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "F" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1787 Classifications: {'peptide': 109} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Time building chain proxies: 1.24, per 1000 atoms: 0.12 Number of scatterers: 10709 At special positions: 0 Unit cell: (93.446, 93.446, 411.544, 90, 90, 90) Space group: P 41 21 2 (No. 92) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 O 986 8.00 N 925 7.00 C 3305 6.00 H 5475 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: 2.10 Adding C-beta torsion restraints... Number of C-beta restraints generated: 1256 Time building geometry restraints manager: 2.45 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: 5475 1.14 - 1.31: 897 1.31 - 1.47: 1900 1.47 - 1.64: 2460 1.64 - 1.81: 36 Bond restraints: 10768 Sorted by residual: bond pdb=" C GLU D 63 " pdb=" N ASN D 64 " ideal model delta sigma weight residual 1.329 1.346 -0.017 1.40e-02 5.10e+03 1.41e+00 bond pdb=" CB PHE F 85 " pdb=" CG PHE F 85 " ideal model delta sigma weight residual 1.502 1.525 -0.023 2.30e-02 1.89e+03 1.04e+00 bond pdb=" C HIS A 48 " pdb=" O HIS A 48 " ideal model delta sigma weight residual 1.231 1.251 -0.020 2.00e-02 2.50e+03 9.98e-01 bond pdb=" CB ARG E 103 " pdb=" CG ARG E 103 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 7.89e-01 bond pdb=" N PRO D 35 " pdb=" CA PRO D 35 " ideal model delta sigma weight residual 1.466 1.478 -0.012 1.50e-02 4.44e+03 6.62e-01 ... (remaining 10763 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.59: 173 106.59 - 113.48: 13302 113.48 - 120.36: 3349 120.36 - 127.25: 2721 127.25 - 134.14: 43 Bond angle restraints: 19588 Sorted by residual: angle pdb=" CA LEU D 86 " pdb=" C LEU D 86 " pdb=" N PRO D 87 " ideal model delta sigma weight residual 116.90 121.13 -4.23 1.50e+00 4.44e-01 7.96e+00 angle pdb=" CA LEU E 86 " pdb=" C LEU E 86 " pdb=" N PRO E 87 " ideal model delta sigma weight residual 116.90 120.68 -3.78 1.50e+00 4.44e-01 6.36e+00 angle pdb=" CA LEU F 86 " pdb=" C LEU F 86 " pdb=" N PRO F 87 " ideal model delta sigma weight residual 116.90 120.17 -3.27 1.50e+00 4.44e-01 4.76e+00 angle pdb=" CA LEU C 86 " pdb=" C LEU C 86 " pdb=" N PRO C 87 " ideal model delta sigma weight residual 116.90 120.17 -3.27 1.50e+00 4.44e-01 4.76e+00 angle pdb=" CA ARG A 75 " pdb=" CB ARG A 75 " pdb=" CG ARG A 75 " ideal model delta sigma weight residual 114.10 118.31 -4.21 2.00e+00 2.50e-01 4.42e+00 ... (remaining 19583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4412 17.93 - 35.87: 339 35.87 - 53.80: 125 53.80 - 71.73: 50 71.73 - 89.66: 4 Dihedral angle restraints: 4930 sinusoidal: 2840 harmonic: 2090 Sorted by residual: dihedral pdb=" CA VAL F 82 " pdb=" C VAL F 82 " pdb=" N LEU F 83 " pdb=" CA LEU F 83 " ideal model delta harmonic sigma weight residual -180.00 -158.90 -21.10 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA GLU C 2 " pdb=" C GLU C 2 " pdb=" N PHE C 3 " pdb=" CA PHE C 3 " ideal model delta harmonic sigma weight residual -180.00 -161.22 -18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA LYS F 4 " pdb=" C LYS F 4 " pdb=" N LYS F 5 " pdb=" CA LYS F 5 " ideal model delta harmonic sigma weight residual 180.00 161.25 18.75 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 4927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 643 0.033 - 0.066: 156 0.066 - 0.100: 45 0.100 - 0.133: 6 0.133 - 0.166: 1 Chirality restraints: 851 Sorted by residual: chirality pdb=" CG LEU D 83 " pdb=" CB LEU D 83 " pdb=" CD1 LEU D 83 " pdb=" CD2 LEU D 83 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.88e-01 chirality pdb=" CA ILE E 71 " pdb=" N ILE E 71 " pdb=" C ILE E 71 " pdb=" CB ILE E 71 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA PRO B 35 " pdb=" N PRO B 35 " pdb=" C PRO B 35 " pdb=" CB PRO B 35 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.03e-01 ... (remaining 848 not shown) Planarity restraints: 1541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 86 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO C 87 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 87 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 87 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 14 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.04e+00 pdb=" C LEU D 14 " 0.025 2.00e-02 2.50e+03 pdb=" O LEU D 14 " -0.009 2.00e-02 2.50e+03 pdb=" N GLN D 15 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 71 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.50e+00 pdb=" C ILE E 71 " 0.021 2.00e-02 2.50e+03 pdb=" O ILE E 71 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU E 72 " -0.007 2.00e-02 2.50e+03 ... (remaining 1538 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 727 2.05 - 2.69: 15918 2.69 - 3.33: 34244 3.33 - 3.96: 42798 3.96 - 4.60: 64267 Nonbonded interactions: 157954 Sorted by model distance: nonbonded pdb=" O MET D 60 " pdb=" H ASN D 64 " model vdw 1.417 1.800 nonbonded pdb=" O SER E 97 " pdb=" HD1 HIS E 101 " model vdw 1.467 1.800 nonbonded pdb=" O ILE E 39 " pdb=" H GLU E 43 " model vdw 1.534 1.800 nonbonded pdb=" OG1 THR A 33 " pdb=" H ASN A 34 " model vdw 1.537 1.800 nonbonded pdb=" O LEU D 30 " pdb=" H ASN D 34 " model vdw 1.555 1.800 ... (remaining 157949 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 18 15.96 2 O 986 7.97 2 N 925 6.97 2 C 3305 5.97 2 H 5475 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: 0.005 angle: 0.97 clash: 7.0 rota: 9.04 rama: f: 88.91 o: 1.09 Z: -1.99 cb: 0.00 shift start/prev: 0.000 0.000 LBFGS: function start/end, n_calls: -1927.865321 -2078.549614 102 cycle 0: bond: 0.008 angle: 1.44 clash: 1.0 rota: 3.75 rama: f: 97.66 o: 0.16 Z: -1.76 cb: 0.00 shift start/prev: 0.236 0.236 LBFGS: function start/end, n_calls: -2078.549614 -2089.777302 102 cycle 1: bond: 0.008 angle: 1.39 clash: 0.6 rota: 3.07 rama: f: 97.50 o: 0.00 Z: -1.57 cb: 0.00 shift start/prev: 0.310 0.123 LBFGS: function start/end, n_calls: -2089.777302 -2094.921285 102 cycle 2: bond: 0.008 angle: 1.41 clash: 0.5 rota: 2.73 rama: f: 97.66 o: 0.00 Z: -1.45 cb: 0.00 shift start/prev: 0.359 0.084 calculator(opt), total_time (target_and_gradients) 99.9940037727356 calculator(opt), number_of_target_and_gradients_calls (target_and_gradients) 306 See 2pej_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 420.90 seconds wall clock time: 7 minutes 8.48 seconds (428.48 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)