Starting qr.refine on Mon May 20 18:42:21 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/1fp9.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/1fp9.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/1fp9.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 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 425": "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: 7982 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 7982 Classifications: {'peptide': 500} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 38, 'TRANS': 461} Time building chain proxies: 0.92, per 1000 atoms: 0.12 Number of scatterers: 7982 At special positions: 0 Unit cell: (104.913, 52.445, 104.908, 90, 96.42, 90) Space group: C 1 2 1 (No. 5) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 O 707 8.00 N 703 7.00 C 2641 6.00 H 3920 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: 1.54 Adding C-beta torsion restraints... Number of C-beta restraints generated: 910 Time building geometry restraints manager: 1.79 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: 3919 1.14 - 1.31: 661 1.31 - 1.48: 1830 1.48 - 1.64: 1692 1.64 - 1.81: 21 Bond restraints: 8123 Sorted by residual: bond pdb=" C GLY A 153 " pdb=" N LEU A 154 " ideal model delta sigma weight residual 1.329 1.345 -0.016 1.40e-02 5.10e+03 1.25e+00 bond pdb=" C ALA A 119 " pdb=" N SER A 120 " ideal model delta sigma weight residual 1.329 1.341 -0.012 1.40e-02 5.10e+03 7.06e-01 bond pdb=" C LEU A 477 " pdb=" N LEU A 478 " ideal model delta sigma weight residual 1.329 1.317 0.012 1.40e-02 5.10e+03 6.97e-01 bond pdb=" N GLY A 333 " pdb=" CA GLY A 333 " ideal model delta sigma weight residual 1.451 1.463 -0.012 1.60e-02 3.91e+03 6.06e-01 bond pdb=" C PHE A 90 " pdb=" N PRO A 91 " ideal model delta sigma weight residual 1.341 1.329 0.012 1.60e-02 3.91e+03 5.98e-01 ... (remaining 8118 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.56: 204 106.56 - 113.44: 8997 113.44 - 120.33: 2950 120.33 - 127.22: 2411 127.22 - 134.10: 93 Bond angle restraints: 14655 Sorted by residual: angle pdb=" CA LEU A 161 " pdb=" C LEU A 161 " pdb=" N PRO A 162 " ideal model delta sigma weight residual 116.90 121.33 -4.43 1.50e+00 4.44e-01 8.73e+00 angle pdb=" CA ARG A 75 " pdb=" C ARG A 75 " pdb=" N PRO A 76 " ideal model delta sigma weight residual 116.90 121.29 -4.39 1.50e+00 4.44e-01 8.56e+00 angle pdb=" CA TRP A 105 " pdb=" C TRP A 105 " pdb=" N PRO A 106 " ideal model delta sigma weight residual 116.90 121.17 -4.27 1.50e+00 4.44e-01 8.12e+00 angle pdb=" CA VAL A 431 " pdb=" C VAL A 431 " pdb=" N PRO A 432 " ideal model delta sigma weight residual 116.90 121.04 -4.14 1.50e+00 4.44e-01 7.61e+00 angle pdb=" CA SER A 57 " pdb=" C SER A 57 " pdb=" N PRO A 58 " ideal model delta sigma weight residual 116.90 119.94 -3.04 1.50e+00 4.44e-01 4.10e+00 ... (remaining 14650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 3490 17.72 - 35.44: 224 35.44 - 53.15: 93 53.15 - 70.87: 24 70.87 - 88.59: 8 Dihedral angle restraints: 3839 sinusoidal: 2018 harmonic: 1821 Sorted by residual: dihedral pdb=" CA TYR A 20 " pdb=" C TYR A 20 " pdb=" N GLY A 21 " pdb=" CA GLY A 21 " ideal model delta harmonic sigma weight residual 180.00 159.11 20.89 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CB GLU A 132 " pdb=" CG GLU A 132 " pdb=" CD GLU A 132 " pdb=" OE1 GLU A 132 " ideal model delta sinusoidal sigma weight residual 0.00 85.38 -85.38 1 3.00e+01 1.11e-03 9.81e+00 dihedral pdb=" CA ARG A 296 " pdb=" CB ARG A 296 " pdb=" CG ARG A 296 " pdb=" CD ARG A 296 " ideal model delta sinusoidal sigma weight residual 60.00 118.43 -58.43 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 3836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 341 0.026 - 0.053: 143 0.053 - 0.079: 39 0.079 - 0.106: 26 0.106 - 0.132: 15 Chirality restraints: 564 Sorted by residual: chirality pdb=" CA VAL A 317 " pdb=" N VAL A 317 " pdb=" C VAL A 317 " pdb=" CB VAL A 317 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE A 304 " pdb=" N ILE A 304 " pdb=" C ILE A 304 " pdb=" CB ILE A 304 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA VAL A 387 " pdb=" N VAL A 387 " pdb=" C VAL A 387 " pdb=" CB VAL A 387 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 ... (remaining 561 not shown) Planarity restraints: 1211 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 87 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO A 88 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 88 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 88 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 346 " 0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO A 347 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 347 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 347 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 105 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 106 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 106 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 106 " -0.018 5.00e-02 4.00e+02 ... (remaining 1208 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 565 2.10 - 2.72: 12943 2.72 - 3.35: 25353 3.35 - 3.97: 34206 3.97 - 4.60: 50553 Nonbonded interactions: 123620 Sorted by model distance: nonbonded pdb=" O TRP A 44 " pdb=" H ILE A 211 " model vdw 1.472 1.800 nonbonded pdb=" H VAL A 95 " pdb=" O ALA A 474 " model vdw 1.539 1.800 nonbonded pdb=" O TRP A 231 " pdb=" H ARG A 264 " model vdw 1.556 1.800 nonbonded pdb=" O PRO A 215 " pdb="HH22 ARG A 279 " model vdw 1.583 1.800 nonbonded pdb=" HG1 THR A 393 " pdb=" OD1 ASN A 396 " model vdw 1.583 1.800 ... (remaining 123615 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 707 7.97 2 N 703 6.97 2 C 2641 5.97 2 H 3920 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: 0.95 clash: 4.0 rota: 2.49 rama: f: 93.17 o: 0.00 Z: -2.56 cb: 0.00 shift start/prev: 0.000 0.000 LBFGS: function start/end, n_calls: -1231.973456 -1343.547437 101 cycle 0: bond: 0.009 angle: 1.46 clash: 0.6 rota: 0.75 rama: f: 97.39 o: 0.00 Z: -1.29 cb: 0.22 shift start/prev: 0.221 0.221 LBFGS: function start/end, n_calls: -1343.547437 -1349.531302 102 cycle 1: bond: 0.009 angle: 1.44 clash: 0.3 rota: 0.75 rama: f: 97.59 o: 0.00 Z: -1.28 cb: 0.22 shift start/prev: 0.286 0.108 LBFGS: function start/end, n_calls: -1349.531302 -1352.079816 102 cycle 2: bond: 0.009 angle: 1.44 clash: 0.3 rota: 0.75 rama: f: 97.59 o: 0.00 Z: -1.26 cb: 0.22 shift start/prev: 0.315 0.053 calculator(opt), total_time (target_and_gradients) 83.06110429763794 calculator(opt), number_of_target_and_gradients_calls (target_and_gradients) 305 See 1fp9_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 278.80 seconds wall clock time: 4 minutes 45.57 seconds (285.57 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)