Starting qr.refine on Sat Apr 6 08:10:15 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs/regularized_V3a/2ogu.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- debug_rss=true expansion=true mode=opt restraints=qm engine=aimnet2 clustering=false minimizer=lbfgs gradient_only=true use_reduce=False select_within_radius=7 number_of_micro_cycles=100 max_iterations_refine=100 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs/regularized_V3a/2ogu.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs/regularized_V3a/2ogu.pdb" } debug_rss = true use_reduce = False cluster { clustering = false select_within_radius = 7 } expansion = true quantum { engine_name = mopac *aimnet2 torchani terachem turbomole pyscf orca \ gaussian xtb server } refine { mode = *opt refine gtest number_of_micro_cycles = 100 max_iterations_refine = 100 gradient_only = true } Starting job =============================================================================== Validate inputs: ------------------------------------------------------------------------------- Refinement start **************** max_atoms = 50000 debug_rss = True 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 = True 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 = 100 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_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 GLU 276": "OE1" <-> "OE2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A TYR 310": "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: 3448 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3448 Classifications: {'peptide': 221} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 213} Time building chain proxies: 0.49, per 1000 atoms: 0.14 Number of scatterers: 3448 At special positions: 0 Unit cell: (165.889, 165.889, 82.223, 90, 90, 120) Space group: R 3 2 :H (No. 155) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 7 16.00 O 338 8.00 N 305 7.00 C 1069 6.00 H 1729 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: 0.66 Adding C-beta torsion restraints... Number of C-beta restraints generated: 406 Time building geometry restraints manager: 0.77 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: 1726 1.14 - 1.31: 315 1.31 - 1.47: 643 1.47 - 1.64: 774 1.64 - 1.81: 11 Bond restraints: 3469 Sorted by residual: bond pdb=" C GLY A 322 " pdb=" N LYS A 323 " ideal model delta sigma weight residual 1.329 1.346 -0.017 1.40e-02 5.10e+03 1.40e+00 bond pdb=" C MET A 239 " pdb=" N SER A 240 " ideal model delta sigma weight residual 1.329 1.339 -0.010 1.40e-02 5.10e+03 5.54e-01 bond pdb=" C MET A 264 " pdb=" N VAL A 265 " ideal model delta sigma weight residual 1.329 1.339 -0.010 1.40e-02 5.10e+03 5.13e-01 bond pdb=" C PRO A 306 " pdb=" N PRO A 307 " ideal model delta sigma weight residual 1.341 1.330 0.011 1.60e-02 3.91e+03 4.84e-01 bond pdb=" C ILE A 229 " pdb=" N SER A 230 " ideal model delta sigma weight residual 1.329 1.338 -0.009 1.40e-02 5.10e+03 4.53e-01 ... (remaining 3464 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.65: 44 106.65 - 113.46: 4212 113.46 - 120.27: 1059 120.27 - 127.09: 958 127.09 - 133.90: 13 Bond angle restraints: 6286 Sorted by residual: angle pdb=" CA LEU A 134 " pdb=" CB LEU A 134 " pdb=" CG LEU A 134 " ideal model delta sigma weight residual 116.30 123.25 -6.95 3.50e+00 8.16e-02 3.94e+00 angle pdb=" CA ASP A 163 " pdb=" C ASP A 163 " pdb=" N PRO A 164 " ideal model delta sigma weight residual 116.90 119.86 -2.96 1.50e+00 4.44e-01 3.90e+00 angle pdb=" CA VAL A 267 " pdb=" C VAL A 267 " pdb=" N PRO A 268 " ideal model delta sigma weight residual 116.90 119.67 -2.77 1.50e+00 4.44e-01 3.41e+00 angle pdb=" C VAL A 265 " pdb=" CA VAL A 265 " pdb=" CB VAL A 265 " ideal model delta sigma weight residual 111.40 107.92 3.48 1.90e+00 2.77e-01 3.35e+00 angle pdb=" CA ILE A 269 " pdb=" C ILE A 269 " pdb=" N PRO A 270 " ideal model delta sigma weight residual 116.90 119.50 -2.60 1.50e+00 4.44e-01 3.00e+00 ... (remaining 6281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.78: 1393 15.78 - 31.57: 131 31.57 - 47.35: 50 47.35 - 63.13: 23 63.13 - 78.91: 1 Dihedral angle restraints: 1598 sinusoidal: 909 harmonic: 689 Sorted by residual: dihedral pdb=" CA THR A 261 " pdb=" C THR A 261 " pdb=" N ARG A 262 " pdb=" CA ARG A 262 " ideal model delta harmonic sigma weight residual 180.00 163.24 16.76 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA ARG A 199 " pdb=" C ARG A 199 " pdb=" N LYS A 200 " pdb=" CA LYS A 200 " ideal model delta harmonic sigma weight residual 180.00 164.08 15.92 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ASP A 287 " pdb=" CB ASP A 287 " pdb=" CG ASP A 287 " pdb=" OD1 ASP A 287 " ideal model delta sinusoidal sigma weight residual -30.00 -84.01 54.01 1 2.00e+01 2.50e-03 9.90e+00 ... (remaining 1595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 159 0.028 - 0.056: 56 0.056 - 0.084: 27 0.084 - 0.112: 20 0.112 - 0.140: 9 Chirality restraints: 271 Sorted by residual: chirality pdb=" CA ILE A 120 " pdb=" N ILE A 120 " pdb=" C ILE A 120 " pdb=" CB ILE A 120 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA ILE A 208 " pdb=" N ILE A 208 " pdb=" C ILE A 208 " pdb=" CB ILE A 208 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA VAL A 291 " pdb=" N VAL A 291 " pdb=" C VAL A 291 " pdb=" CB VAL A 291 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 268 not shown) Planarity restraints: 524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 249 " -0.004 2.00e-02 2.50e+03 8.85e-03 7.83e-01 pdb=" C ALA A 249 " 0.015 2.00e-02 2.50e+03 pdb=" O ALA A 249 " -0.006 2.00e-02 2.50e+03 pdb=" N MET A 250 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 267 " -0.014 5.00e-02 4.00e+02 2.12e-02 7.17e-01 pdb=" N PRO A 268 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 268 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 268 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 237 " 0.004 2.00e-02 2.50e+03 7.92e-03 6.27e-01 pdb=" C ARG A 237 " -0.014 2.00e-02 2.50e+03 pdb=" O ARG A 237 " 0.005 2.00e-02 2.50e+03 pdb=" N LEU A 238 " 0.005 2.00e-02 2.50e+03 ... (remaining 521 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 201 2.06 - 2.69: 5265 2.69 - 3.33: 10584 3.33 - 3.96: 14032 3.96 - 4.60: 21069 Nonbonded interactions: 51151 Sorted by model distance: nonbonded pdb=" O GLY A 246 " pdb=" H MET A 250 " model vdw 1.421 1.800 nonbonded pdb=" O SER A 126 " pdb=" H CYS A 130 " model vdw 1.484 1.800 nonbonded pdb="HH12 ARG A 206 " pdb=" O SER A 242 " model vdw sym.op. 1.569 1.800 -x+2,-x+y+1,-z+1 nonbonded pdb="HH11 ARG A 206 " pdb=" O ILE A 243 " model vdw sym.op. 1.592 1.800 -x+2,-x+y+1,-z+1 nonbonded pdb=" H GLY A 297 " pdb=" O ILE A 317 " model vdw 1.595 1.800 ... (remaining 51146 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- /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) Number of scattering types: 5 Type Number sf(0) Gaussians S 7 15.96 2 O 338 7.97 2 N 305 6.97 2 C 1069 5.97 2 H 1729 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 Trying rss 10 268.53177857398987 Trying rss 9 245.32200384140015 Trying rss 8 233.58461141586304 Trying rss 7 200.49271035194397 Trying rss 6 167.21272158622742 Trying rss 5 146.45313453674316 Trying rss 4 128.75554418563843 Trying rss 3 113.0652346611023 Trying rss 2 76.7381272315979 Trying rss 1 61.08809494972229 STOP: /net/cci-gpu-00/raid1/scratch1/pavel/phenix/modules/qrefine/refine.py(128)