Starting qr.refine on Mon May 20 18:04:56 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/2h1g.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/2h1g.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/2h1g.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 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 66": "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: 4293 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2139 Classifications: {'peptide': 136} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 127} Chain: "B" Number of atoms: 2154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2154 Classifications: {'peptide': 137} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 128} Time building chain proxies: 0.55, per 1000 atoms: 0.13 Number of scatterers: 4293 At special positions: 0 Unit cell: (47.031, 59.522, 109.562, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 O 405 8.00 N 349 7.00 C 1391 6.00 H 2138 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: 0.79 Adding C-beta torsion restraints... Number of C-beta restraints generated: 506 Time building geometry restraints manager: 0.93 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: 2138 1.14 - 1.31: 365 1.31 - 1.48: 864 1.48 - 1.64: 960 1.64 - 1.81: 20 Bond restraints: 4347 Sorted by residual: bond pdb=" CB PRO B 82 " pdb=" CG PRO B 82 " ideal model delta sigma weight residual 1.492 1.433 0.059 5.00e-02 4.00e+02 1.38e+00 bond pdb=" C ASP A 41 " pdb=" N ALA A 42 " ideal model delta sigma weight residual 1.329 1.344 -0.015 1.40e-02 5.10e+03 1.10e+00 bond pdb=" C VAL A 137 " pdb=" N SER A 138 " ideal model delta sigma weight residual 1.329 1.344 -0.015 1.40e-02 5.10e+03 1.09e+00 bond pdb=" CB PRO B 139 " pdb=" CG PRO B 139 " ideal model delta sigma weight residual 1.492 1.538 -0.046 5.00e-02 4.00e+02 8.42e-01 bond pdb=" C ASP B 41 " pdb=" N ALA B 42 " ideal model delta sigma weight residual 1.329 1.342 -0.013 1.40e-02 5.10e+03 8.17e-01 ... (remaining 4342 not shown) Histogram of bond angle deviations from ideal: 100.29 - 107.02: 110 107.02 - 113.76: 5250 113.76 - 120.49: 1359 120.49 - 127.23: 1139 127.23 - 133.97: 31 Bond angle restraints: 7889 Sorted by residual: angle pdb=" C ILE A 172 " pdb=" N LYS A 173 " pdb=" CA LYS A 173 " ideal model delta sigma weight residual 121.70 114.50 7.20 1.80e+00 3.09e-01 1.60e+01 angle pdb=" C VAL A 137 " pdb=" N SER A 138 " pdb=" CA SER A 138 " ideal model delta sigma weight residual 121.70 128.46 -6.76 1.80e+00 3.09e-01 1.41e+01 angle pdb=" CA GLU B 75 " pdb=" C GLU B 75 " pdb=" N PRO B 76 " ideal model delta sigma weight residual 116.90 121.49 -4.59 1.50e+00 4.44e-01 9.38e+00 angle pdb=" CA PHE B 81 " pdb=" C PHE B 81 " pdb=" N PRO B 82 " ideal model delta sigma weight residual 116.90 121.44 -4.54 1.50e+00 4.44e-01 9.17e+00 angle pdb=" CA GLU A 75 " pdb=" C GLU A 75 " pdb=" N PRO A 76 " ideal model delta sigma weight residual 116.90 121.18 -4.28 1.50e+00 4.44e-01 8.12e+00 ... (remaining 7884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.46: 1869 16.46 - 32.91: 118 32.91 - 49.37: 50 49.37 - 65.83: 13 65.83 - 82.28: 5 Dihedral angle restraints: 2055 sinusoidal: 1106 harmonic: 949 Sorted by residual: dihedral pdb=" CA LYS A 79 " pdb=" C LYS A 79 " pdb=" N GLU A 80 " pdb=" CA GLU A 80 " ideal model delta harmonic sigma weight residual 180.00 -163.17 -16.83 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" N LYS B 61 " pdb=" CA LYS B 61 " pdb=" CB LYS B 61 " pdb=" CG LYS B 61 " ideal model delta sinusoidal sigma weight residual -60.00 -111.00 51.00 3 1.50e+01 4.44e-03 8.96e+00 dihedral pdb=" N ASN B 170 " pdb=" CA ASN B 170 " pdb=" CB ASN B 170 " pdb=" CG ASN B 170 " ideal model delta sinusoidal sigma weight residual -60.00 -110.80 50.80 3 1.50e+01 4.44e-03 8.94e+00 ... (remaining 2052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 189 0.028 - 0.056: 81 0.056 - 0.083: 28 0.083 - 0.111: 17 0.111 - 0.139: 16 Chirality restraints: 331 Sorted by residual: chirality pdb=" CA ILE B 55 " pdb=" N ILE B 55 " pdb=" C ILE B 55 " pdb=" CB ILE B 55 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE A 55 " pdb=" N ILE A 55 " pdb=" C ILE A 55 " pdb=" CB ILE A 55 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA VAL A 123 " pdb=" N VAL A 123 " pdb=" C VAL A 123 " pdb=" CB VAL A 123 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 328 not shown) Planarity restraints: 641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 81 " -0.019 5.00e-02 4.00e+02 2.95e-02 1.39e+00 pdb=" N PRO A 82 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 81 " 0.018 5.00e-02 4.00e+02 2.72e-02 1.18e+00 pdb=" N PRO B 82 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 75 " -0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO B 76 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 76 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 76 " -0.015 5.00e-02 4.00e+02 ... (remaining 638 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 348 2.16 - 2.77: 7935 2.77 - 3.38: 12752 3.38 - 3.99: 17471 3.99 - 4.60: 25801 Nonbonded interactions: 64307 Sorted by model distance: nonbonded pdb=" HH TYR A 88 " pdb=" OE1 GLU A 97 " model vdw 1.548 1.800 nonbonded pdb=" OD1 ASP A 41 " pdb=" HZ3 LYS A 151 " model vdw 1.560 1.800 nonbonded pdb=" OD1 ASN A 102 " pdb=" H GLU A 105 " model vdw 1.564 1.800 nonbonded pdb=" O MET B 84 " pdb=" H TYR B 88 " model vdw 1.565 1.800 nonbonded pdb=" OE1 GLU B 149 " pdb=" H GLU B 149 " model vdw 1.622 1.800 ... (remaining 64302 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 10 15.96 2 O 405 7.97 2 N 349 6.97 2 C 1391 5.97 2 H 2138 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: 1.04 clash: 2.3 rota: 3.35 rama: f: 94.42 o: 0.74 Z: -0.93 cb: 0.00 shift start/prev: 0.000 0.000 LBFGS: function start/end, n_calls: -679.765142 -736.148787 101 cycle 0: bond: 0.009 angle: 1.55 clash: 0.2 rota: 0.84 rama: f: 98.14 o: 0.37 Z: 0.10 cb: 0.00 shift start/prev: 0.200 0.200 LBFGS: function start/end, n_calls: -736.148787 -739.683771 102 cycle 1: bond: 0.009 angle: 1.52 clash: 0.5 rota: 0.42 rama: f: 99.26 o: 0.74 Z: -0.29 cb: 0.00 shift start/prev: 0.277 0.117 LBFGS: function start/end, n_calls: -739.683771 -741.297563 102 cycle 2: bond: 0.009 angle: 1.52 clash: 0.7 rota: 0.84 rama: f: 99.26 o: 0.74 Z: -0.34 cb: 0.00 shift start/prev: 0.323 0.081 calculator(opt), total_time (target_and_gradients) 49.062169313430786 calculator(opt), number_of_target_and_gradients_calls (target_and_gradients) 305 See 2h1g_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 125.72 seconds wall clock time: 2 minutes 10.91 seconds (130.91 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)