Starting qr.refine on Mon May 20 18:00:48 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/1u87.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/1u87.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/1u87.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 None 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: 3506 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3471 Classifications: {'peptide': 209} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 197} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'GSH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.48, per 1000 atoms: 0.14 Number of scatterers: 3506 At special positions: 0 Unit cell: (123.05, 123.05, 72.51, 90, 90, 120) Space group: P 63 2 2 (No. 182) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 316 8.00 N 282 7.00 C 1138 6.00 H 1756 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: 0.68 Adding C-beta torsion restraints... Number of C-beta restraints generated: 396 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 1751 1.15 - 1.31: 294 1.31 - 1.48: 702 1.48 - 1.64: 780 1.64 - 1.81: 23 Bond restraints: 3550 Sorted by residual: bond pdb=" CA1 GSH A 500 " pdb=" N1 GSH A 500 " ideal model delta sigma weight residual 1.472 1.446 0.026 2.00e-02 2.50e+03 1.65e+00 bond pdb=" C LYS A 78 " pdb=" N HIS A 79 " ideal model delta sigma weight residual 1.329 1.344 -0.015 1.40e-02 5.10e+03 1.08e+00 bond pdb=" CB1 GSH A 500 " pdb=" CA1 GSH A 500 " ideal model delta sigma weight residual 1.526 1.515 0.011 1.20e-02 6.94e+03 9.04e-01 bond pdb=" C1 GSH A 500 " pdb=" CA1 GSH A 500 " ideal model delta sigma weight residual 1.535 1.519 0.016 1.80e-02 3.09e+03 7.61e-01 bond pdb=" C MET A 1 " pdb=" N SER A 2 " ideal model delta sigma weight residual 1.329 1.341 -0.012 1.40e-02 5.10e+03 7.05e-01 ... (remaining 3545 not shown) Histogram of bond angle deviations from ideal: 93.86 - 101.88: 12 101.88 - 109.90: 2860 109.90 - 117.92: 1906 117.92 - 125.94: 1623 125.94 - 133.96: 43 Bond angle restraints: 6444 Sorted by residual: angle pdb=" C1 GSH A 500 " pdb=" CA1 GSH A 500 " pdb=" HA1 GSH A 500 " ideal model delta sigma weight residual 124.92 93.86 31.06 3.00e+00 1.11e-01 1.07e+02 angle pdb=" CB1 GSH A 500 " pdb=" CA1 GSH A 500 " pdb=" HA1 GSH A 500 " ideal model delta sigma weight residual 124.92 94.32 30.60 3.00e+00 1.11e-01 1.04e+02 angle pdb=" CB1 GSH A 500 " pdb=" CA1 GSH A 500 " pdb=" C1 GSH A 500 " ideal model delta sigma weight residual 109.47 133.94 -24.47 3.00e+00 1.11e-01 6.65e+01 angle pdb=" N1 GSH A 500 " pdb=" CA1 GSH A 500 " pdb=" HA1 GSH A 500 " ideal model delta sigma weight residual 124.92 101.61 23.31 3.00e+00 1.11e-01 6.04e+01 angle pdb=" N2 GSH A 500 " pdb=" CA2 GSH A 500 " pdb=" HA2 GSH A 500 " ideal model delta sigma weight residual 124.87 110.34 14.53 3.00e+00 1.11e-01 2.35e+01 ... (remaining 6439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.68: 1411 11.68 - 23.37: 152 23.37 - 35.05: 60 35.05 - 46.73: 30 46.73 - 58.42: 19 Dihedral angle restraints: 1672 sinusoidal: 918 harmonic: 754 Sorted by residual: dihedral pdb=" CA LEU A 65 " pdb=" C LEU A 65 " pdb=" N THR A 66 " pdb=" CA THR A 66 " ideal model delta harmonic sigma weight residual 180.00 163.28 16.72 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA ASP A 60 " pdb=" C ASP A 60 " pdb=" N GLY A 61 " pdb=" CA GLY A 61 " ideal model delta harmonic sigma weight residual -180.00 -164.52 -15.48 0 5.00e+00 4.00e-02 9.59e+00 dihedral pdb=" N LYS A 113 " pdb=" CA LYS A 113 " pdb=" CB LYS A 113 " pdb=" CG LYS A 113 " ideal model delta sinusoidal sigma weight residual -60.00 -117.56 57.56 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 1669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.712: 254 0.712 - 1.424: 0 1.424 - 2.135: 0 2.135 - 2.847: 0 2.847 - 3.559: 1 Chirality restraints: 255 Sorted by residual: chirality pdb=" CA1 GSH A 500 " pdb=" CB1 GSH A 500 " pdb=" C1 GSH A 500 " pdb=" N1 GSH A 500 " both_signs ideal model delta sigma weight residual False -2.66 0.90 -3.56 2.00e-01 2.50e+01 3.17e+02 chirality pdb=" CA2 GSH A 500 " pdb=" CB2 GSH A 500 " pdb=" C2 GSH A 500 " pdb=" N2 GSH A 500 " both_signs ideal model delta sigma weight residual False -2.47 -2.73 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA ILE A 4 " pdb=" N ILE A 4 " pdb=" C ILE A 4 " pdb=" CB ILE A 4 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 252 not shown) Planarity restraints: 502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 166 " -0.029 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO A 167 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 167 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 167 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 126 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO A 127 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 127 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 127 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 52 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.28e+00 pdb=" N PRO A 53 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 53 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 53 " 0.016 5.00e-02 4.00e+02 ... (remaining 499 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 283 2.14 - 2.75: 6109 2.75 - 3.37: 10261 3.37 - 3.98: 13757 3.98 - 4.60: 20440 Nonbonded interactions: 50850 Sorted by model distance: nonbonded pdb=" O ILE A 10 " pdb="HH12 ARG A 18 " model vdw 1.522 1.800 nonbonded pdb=" HE1 TRP A 8 " pdb=" O2 GSH A 500 " model vdw 1.584 1.800 nonbonded pdb=" O ASP A 114 " pdb=" H LEU A 118 " model vdw 1.612 1.800 nonbonded pdb=" HZ3 LYS A 180 " pdb=" OE2 GLU A 184 " model vdw 1.627 1.800 nonbonded pdb=" HZ2 LYS A 131 " pdb=" OD1 ASP A 135 " model vdw 1.636 1.800 ... (remaining 50845 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 14 15.96 2 O 316 7.97 2 N 282 6.97 2 C 1138 5.97 2 H 1756 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: 1.11 clash: 2.3 rota: 4.79 rama: f: 91.30 o: 0.97 Z: -2.68 cb: 0.00 shift start/prev: 0.000 0.000 LBFGS: function start/end, n_calls: -555.705390 -604.058654 102 cycle 0: bond: 0.009 angle: 1.53 clash: 0.6 rota: 3.19 rama: f: 97.10 o: 0.48 Z: -1.38 cb: 0.00 shift start/prev: 0.234 0.234 LBFGS: function start/end, n_calls: -604.058654 -608.067685 102 cycle 1: bond: 0.009 angle: 1.51 clash: 0.3 rota: 1.60 rama: f: 98.55 o: 0.48 Z: -1.43 cb: 0.00 shift start/prev: 0.316 0.135 LBFGS: function start/end, n_calls: -608.067685 -609.477579 102 cycle 2: bond: 0.009 angle: 1.50 clash: 0.0 rota: 1.06 rama: f: 98.07 o: 0.48 Z: -1.59 cb: 0.00 shift start/prev: 0.364 0.085 calculator(opt), total_time (target_and_gradients) 47.763646841049194 calculator(opt), number_of_target_and_gradients_calls (target_and_gradients) 306 See 1u87_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 108.31 seconds wall clock time: 113.04 seconds /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)