Starting qr.refine on Mon May 20 18:47:09 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/2yhj.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/2yhj.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/2yhj.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 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 95": "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: 8784 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4392 Classifications: {'peptide': 285} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain: "B" Number of atoms: 4392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4392 Classifications: {'peptide': 285} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Time building chain proxies: 1.03, per 1000 atoms: 0.12 Number of scatterers: 8784 At special positions: 0 Unit cell: (159.697, 159.697, 159.697, 90, 90, 90) Space group: P 21 3 (No. 198) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 4 16.00 O 904 8.00 N 728 7.00 C 2814 6.00 H 4334 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: 1.70 Adding C-beta torsion restraints... Number of C-beta restraints generated: 1052 Time building geometry restraints manager: 2.00 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: 4332 1.14 - 1.31: 760 1.31 - 1.48: 1852 1.48 - 1.64: 1922 1.64 - 1.81: 6 Bond restraints: 8872 Sorted by residual: bond pdb=" C TYR B 232 " pdb=" N PRO B 233 " ideal model delta sigma weight residual 1.341 1.330 0.011 1.60e-02 3.91e+03 4.64e-01 bond pdb=" C TYR A 232 " pdb=" N PRO A 233 " ideal model delta sigma weight residual 1.341 1.330 0.011 1.60e-02 3.91e+03 4.50e-01 bond pdb=" C ASN A 64 " pdb=" N PRO A 65 " ideal model delta sigma weight residual 1.341 1.330 0.011 1.60e-02 3.91e+03 4.33e-01 bond pdb=" C GLU A 54 " pdb=" O GLU A 54 " ideal model delta sigma weight residual 1.231 1.244 -0.013 2.00e-02 2.50e+03 4.15e-01 bond pdb=" CA TYR B 130 " pdb=" CB TYR B 130 " ideal model delta sigma weight residual 1.530 1.543 -0.013 2.00e-02 2.50e+03 4.15e-01 ... (remaining 8867 not shown) Histogram of bond angle deviations from ideal: 100.98 - 107.57: 328 107.57 - 114.16: 10560 114.16 - 120.76: 2688 120.76 - 127.35: 2346 127.35 - 133.94: 36 Bond angle restraints: 15958 Sorted by residual: angle pdb=" CA GLU A 54 " pdb=" C GLU A 54 " pdb=" N PRO A 55 " ideal model delta sigma weight residual 116.90 121.25 -4.35 1.50e+00 4.44e-01 8.41e+00 angle pdb=" N PHE A 71 " pdb=" CA PHE A 71 " pdb=" C PHE A 71 " ideal model delta sigma weight residual 111.00 106.05 4.95 2.80e+00 1.28e-01 3.13e+00 angle pdb=" C PHE A 268 " pdb=" N ASN A 269 " pdb=" CA ASN A 269 " ideal model delta sigma weight residual 121.70 124.87 -3.17 1.80e+00 3.09e-01 3.11e+00 angle pdb=" N PHE B 71 " pdb=" CA PHE B 71 " pdb=" C PHE B 71 " ideal model delta sigma weight residual 111.00 106.21 4.79 2.80e+00 1.28e-01 2.92e+00 angle pdb=" C ILE A 263 " pdb=" N TYR A 264 " pdb=" CA TYR A 264 " ideal model delta sigma weight residual 121.70 124.72 -3.02 1.80e+00 3.09e-01 2.82e+00 ... (remaining 15953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 3977 17.25 - 34.51: 137 34.51 - 51.76: 57 51.76 - 69.02: 32 69.02 - 86.27: 7 Dihedral angle restraints: 4210 sinusoidal: 2252 harmonic: 1958 Sorted by residual: dihedral pdb=" CB LYS B 273 " pdb=" CG LYS B 273 " pdb=" CD LYS B 273 " pdb=" CE LYS B 273 " ideal model delta sinusoidal sigma weight residual -60.00 -118.42 58.42 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N ASN A 269 " pdb=" CA ASN A 269 " pdb=" CB ASN A 269 " pdb=" CG ASN A 269 " ideal model delta sinusoidal sigma weight residual -60.00 -114.13 54.13 3 1.50e+01 4.44e-03 9.26e+00 dihedral pdb=" N ASN B 269 " pdb=" CA ASN B 269 " pdb=" CB ASN B 269 " pdb=" CG ASN B 269 " ideal model delta sinusoidal sigma weight residual -60.00 -111.59 51.59 3 1.50e+01 4.44e-03 9.03e+00 ... (remaining 4207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 399 0.027 - 0.055: 195 0.055 - 0.082: 34 0.082 - 0.109: 48 0.109 - 0.136: 24 Chirality restraints: 700 Sorted by residual: chirality pdb=" CA ILE B 314 " pdb=" N ILE B 314 " pdb=" C ILE B 314 " pdb=" CB ILE B 314 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ILE A 314 " pdb=" N ILE A 314 " pdb=" C ILE A 314 " pdb=" CB ILE A 314 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA ILE B 62 " pdb=" N ILE B 62 " pdb=" C ILE B 62 " pdb=" CB ILE B 62 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 ... (remaining 697 not shown) Planarity restraints: 1346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 54 " -0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO B 55 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 55 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 55 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 64 " 0.017 5.00e-02 4.00e+02 2.51e-02 1.01e+00 pdb=" N PRO A 65 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 65 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 65 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 64 " -0.016 5.00e-02 4.00e+02 2.43e-02 9.46e-01 pdb=" N PRO B 65 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO B 65 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 65 " -0.014 5.00e-02 4.00e+02 ... (remaining 1343 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 532 2.10 - 2.73: 14393 2.73 - 3.35: 24871 3.35 - 3.98: 35976 3.98 - 4.60: 52196 Nonbonded interactions: 127968 Sorted by model distance: nonbonded pdb="HH11 ARG A 143 " pdb=" OD2 ASP A 151 " model vdw 1.480 1.800 nonbonded pdb="HH11 ARG B 143 " pdb=" OD2 ASP B 151 " model vdw 1.493 1.800 nonbonded pdb=" OD2 ASP B 39 " pdb=" H HIS B 146 " model vdw 1.542 1.800 nonbonded pdb=" H SER A 265 " pdb=" O VAL A 272 " model vdw 1.548 1.800 nonbonded pdb=" OG SER A 38 " pdb=" HZ3 LYS A 273 " model vdw 1.565 1.800 ... (remaining 127963 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 4 15.96 2 O 904 7.97 2 N 728 6.97 2 C 2814 5.97 2 H 4334 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: 0.87 clash: 1.6 rota: 1.81 rama: f: 97.17 o: 0.35 Z: -0.95 cb: 0.00 shift start/prev: 0.000 0.000 LBFGS: function start/end, n_calls: -1369.563444 -1480.138109 101 cycle 0: bond: 0.009 angle: 1.49 clash: 0.1 rota: 0.80 rama: f: 97.88 o: 0.00 Z: -1.04 cb: 0.00 shift start/prev: 0.206 0.206 LBFGS: function start/end, n_calls: -1480.138109 -1486.937360 102 cycle 1: bond: 0.009 angle: 1.47 clash: 0.0 rota: 0.60 rama: f: 97.70 o: 0.00 Z: -0.96 cb: 0.00 shift start/prev: 0.268 0.104 LBFGS: function start/end, n_calls: -1486.937360 -1490.199459 102 cycle 2: bond: 0.009 angle: 1.49 clash: 0.0 rota: 0.40 rama: f: 97.88 o: 0.00 Z: -0.99 cb: 0.00 shift start/prev: 0.318 0.083 calculator(opt), total_time (target_and_gradients) 87.30173707008362 calculator(opt), number_of_target_and_gradients_calls (target_and_gradients) 305 See 2yhj_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 315.82 seconds wall clock time: 5 minutes 23.74 seconds (323.74 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)