Starting qr.refine on Mon May 20 18:09:35 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/4iy2.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/4iy2.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/4iy2.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 518": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 518": "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: 4856 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2428 Classifications: {'peptide': 152} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 144} Chain: "C" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2428 Classifications: {'peptide': 152} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 144} Time building chain proxies: 0.61, per 1000 atoms: 0.13 Number of scatterers: 4856 At special positions: 0 Unit cell: (102.513, 104.593, 105.694, 90, 90, 90) Space group: I 21 21 21 (No. 24) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Se 12 33.99 S 4 16.00 O 482 8.00 N 382 7.00 C 1558 6.00 H 2418 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: 0.93 Adding C-beta torsion restraints... Number of C-beta restraints generated: 576 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.17: 2414 1.17 - 1.37: 816 1.37 - 1.56: 1640 1.56 - 1.76: 0 1.76 - 1.95: 28 Bond restraints: 4898 Sorted by residual: bond pdb=" CA THR C 451 " pdb=" CB THR C 451 " ideal model delta sigma weight residual 1.540 1.521 0.019 2.70e-02 1.37e+03 5.07e-01 bond pdb=" CA THR C 509 " pdb=" CB THR C 509 " ideal model delta sigma weight residual 1.540 1.522 0.018 2.70e-02 1.37e+03 4.65e-01 bond pdb=" N GLU A 556 " pdb=" CA GLU A 556 " ideal model delta sigma weight residual 1.458 1.471 -0.013 1.90e-02 2.77e+03 4.39e-01 bond pdb=" C THR A 451 " pdb=" N PRO A 452 " ideal model delta sigma weight residual 1.341 1.331 0.010 1.60e-02 3.91e+03 4.22e-01 bond pdb=" C MSE A 470 " pdb=" N SER A 471 " ideal model delta sigma weight residual 1.329 1.338 -0.009 1.40e-02 5.10e+03 3.89e-01 ... (remaining 4893 not shown) Histogram of bond angle deviations from ideal: 97.76 - 104.48: 36 104.48 - 111.20: 5549 111.20 - 117.91: 1159 117.91 - 124.63: 1973 124.63 - 131.35: 181 Bond angle restraints: 8898 Sorted by residual: angle pdb=" C GLY A 555 " pdb=" N GLU A 556 " pdb=" CA GLU A 556 " ideal model delta sigma weight residual 121.70 128.44 -6.74 1.80e+00 3.09e-01 1.40e+01 angle pdb=" C GLY C 555 " pdb=" N GLU C 556 " pdb=" CA GLU C 556 " ideal model delta sigma weight residual 121.70 127.36 -5.66 1.80e+00 3.09e-01 9.89e+00 angle pdb=" CA GLY C 555 " pdb=" C GLY C 555 " pdb=" N GLU C 556 " ideal model delta sigma weight residual 116.20 120.88 -4.68 2.00e+00 2.50e-01 5.49e+00 angle pdb=" CA ASP A 504 " pdb=" C ASP A 504 " pdb=" N PRO A 505 " ideal model delta sigma weight residual 116.90 119.84 -2.94 1.50e+00 4.44e-01 3.85e+00 angle pdb=" CA THR C 451 " pdb=" C THR C 451 " pdb=" N PRO C 452 " ideal model delta sigma weight residual 116.90 119.66 -2.76 1.50e+00 4.44e-01 3.38e+00 ... (remaining 8893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.86: 2058 14.86 - 29.73: 141 29.73 - 44.59: 55 44.59 - 59.45: 31 59.45 - 74.32: 3 Dihedral angle restraints: 2288 sinusoidal: 1262 harmonic: 1026 Sorted by residual: dihedral pdb=" N LEU C 569 " pdb=" CA LEU C 569 " pdb=" CB LEU C 569 " pdb=" CG LEU C 569 " ideal model delta sinusoidal sigma weight residual 180.00 -121.47 -58.53 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N LEU A 569 " pdb=" CA LEU A 569 " pdb=" CB LEU A 569 " pdb=" CG LEU A 569 " ideal model delta sinusoidal sigma weight residual -180.00 -124.42 -55.58 3 1.50e+01 4.44e-03 9.36e+00 dihedral pdb=" CB ARG C 442 " pdb=" CG ARG C 442 " pdb=" CD ARG C 442 " pdb=" NE ARG C 442 " ideal model delta sinusoidal sigma weight residual 60.00 112.28 -52.28 3 1.50e+01 4.44e-03 9.10e+00 ... (remaining 2285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 269 0.030 - 0.061: 73 0.061 - 0.091: 25 0.091 - 0.121: 17 0.121 - 0.152: 6 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA VAL A 525 " pdb=" N VAL A 525 " pdb=" C VAL A 525 " pdb=" CB VAL A 525 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA ILE C 547 " pdb=" N ILE C 547 " pdb=" C ILE C 547 " pdb=" CB ILE C 547 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE A 547 " pdb=" N ILE A 547 " pdb=" C ILE A 547 " pdb=" CB ILE A 547 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 ... (remaining 387 not shown) Planarity restraints: 726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 509 " 0.019 5.00e-02 4.00e+02 2.83e-02 1.28e+00 pdb=" N PRO A 510 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 510 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 510 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 481 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO C 482 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO C 482 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 482 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 509 " -0.017 5.00e-02 4.00e+02 2.57e-02 1.06e+00 pdb=" N PRO C 510 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 510 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 510 " -0.014 5.00e-02 4.00e+02 ... (remaining 723 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.16: 410 2.16 - 2.82: 10280 2.82 - 3.48: 15454 3.48 - 4.14: 21454 4.14 - 4.80: 33430 Nonbonded interactions: 81028 Sorted by model distance: nonbonded pdb=" H GLY A 461 " pdb=" O PHE A 484 " model vdw 1.500 1.800 nonbonded pdb=" O GLU C 485 " pdb="HD22 ASN C 490 " model vdw 1.535 1.800 nonbonded pdb=" H GLY C 461 " pdb=" O PHE C 484 " model vdw 1.537 1.800 nonbonded pdb=" O PHE A 467 " pdb=" H SER A 471 " model vdw 1.566 1.800 nonbonded pdb=" O GLU A 485 " pdb="HD22 ASN A 490 " model vdw 1.568 1.800 ... (remaining 81023 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: 6 Type Number sf(0) Gaussians Se 12 33.92 2 S 4 15.96 2 O 482 7.97 2 N 382 6.97 2 C 1558 5.97 2 H 2418 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: 0.003 angle: 0.91 clash: 2.1 rota: 4.32 rama: f: 94.00 o: 0.00 Z: -2.68 cb: 0.00 shift start/prev: 0.000 0.000 LBFGS: function start/end, n_calls: -845.409364 -916.342659 101 cycle 0: bond: 0.009 angle: 1.58 clash: 0.4 rota: 3.96 rama: f: 98.67 o: 0.00 Z: -0.87 cb: 0.00 shift start/prev: 0.238 0.238 LBFGS: function start/end, n_calls: -916.342659 -921.629295 102 cycle 1: bond: 0.009 angle: 1.55 clash: 0.2 rota: 3.60 rama: f: 99.33 o: 0.00 Z: -1.42 cb: 0.69 shift start/prev: 0.323 0.132 LBFGS: function start/end, n_calls: -921.629295 -923.945509 102 cycle 2: bond: 0.009 angle: 1.55 clash: 0.2 rota: 2.52 rama: f: 99.33 o: 0.00 Z: -1.06 cb: 0.00 shift start/prev: 0.379 0.094 calculator(opt), total_time (target_and_gradients) 53.99349808692932 calculator(opt), number_of_target_and_gradients_calls (target_and_gradients) 305 See 4iy2_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 144.95 seconds wall clock time: 2 minutes 30.27 seconds (150.27 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)