Starting qr.refine on Sat Apr 6 10:07:46 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs/regularized_V3a/1xgo.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/1xgo.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs/regularized_V3a/1xgo.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 TYR 206": "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: 4719 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 4719 Classifications: {'peptide': 295} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 280} Time building chain proxies: 0.60, per 1000 atoms: 0.13 Number of scatterers: 4719 At special positions: 0 Unit cell: (138.916, 138.916, 63.907, 90, 90, 120) Space group: P 62 (No. 171) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 423 8.00 N 390 7.00 C 1490 6.00 H 2407 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: 1.35 Adding C-beta torsion restraints... Number of C-beta restraints generated: 546 Time building geometry restraints manager: 1.51 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: 2407 1.14 - 1.31: 392 1.31 - 1.48: 863 1.48 - 1.64: 1080 1.64 - 1.81: 18 Bond restraints: 4760 Sorted by residual: bond pdb=" CB VAL A 16 " pdb=" CG2 VAL A 16 " ideal model delta sigma weight residual 1.521 1.561 -0.040 3.30e-02 9.18e+02 1.48e+00 bond pdb=" CB GLU A 136 " pdb=" CG GLU A 136 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.55e-01 bond pdb=" CB ILE A 291 " pdb=" CG2 ILE A 291 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.43e-01 bond pdb=" CB LYS A 39 " pdb=" CG LYS A 39 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.79e-01 bond pdb=" CB LYS A 8 " pdb=" CG LYS A 8 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 5.02e-01 ... (remaining 4755 not shown) Histogram of bond angle deviations from ideal: 100.33 - 107.04: 148 107.04 - 113.74: 5930 113.74 - 120.45: 1352 120.45 - 127.15: 1236 127.15 - 133.86: 23 Bond angle restraints: 8689 Sorted by residual: angle pdb=" C ARG A 157 " pdb=" N TYR A 158 " pdb=" CA TYR A 158 " ideal model delta sigma weight residual 121.70 125.62 -3.92 1.80e+00 3.09e-01 4.74e+00 angle pdb=" C ALA A 252 " pdb=" N LEU A 253 " pdb=" CA LEU A 253 " ideal model delta sigma weight residual 121.70 118.02 3.68 1.80e+00 3.09e-01 4.18e+00 angle pdb=" CA LYS A 145 " pdb=" C LYS A 145 " pdb=" N PRO A 146 " ideal model delta sigma weight residual 116.90 119.87 -2.97 1.50e+00 4.44e-01 3.93e+00 angle pdb=" CA LEU A 256 " pdb=" CB LEU A 256 " pdb=" CG LEU A 256 " ideal model delta sigma weight residual 116.30 123.20 -6.90 3.50e+00 8.16e-02 3.88e+00 angle pdb=" CA ILE A 166 " pdb=" C ILE A 166 " pdb=" N PRO A 167 " ideal model delta sigma weight residual 116.90 119.85 -2.95 1.50e+00 4.44e-01 3.86e+00 ... (remaining 8684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 1927 17.43 - 34.87: 194 34.87 - 52.30: 60 52.30 - 69.74: 15 69.74 - 87.17: 2 Dihedral angle restraints: 2198 sinusoidal: 1234 harmonic: 964 Sorted by residual: dihedral pdb=" CB GLU A 138 " pdb=" CG GLU A 138 " pdb=" CD GLU A 138 " pdb=" OE1 GLU A 138 " ideal model delta sinusoidal sigma weight residual 0.00 -87.17 87.17 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CA LYS A 67 " pdb=" C LYS A 67 " pdb=" N GLY A 68 " pdb=" CA GLY A 68 " ideal model delta harmonic sigma weight residual 180.00 -164.34 -15.66 0 5.00e+00 4.00e-02 9.81e+00 dihedral pdb=" CA ARG A 17 " pdb=" CB ARG A 17 " pdb=" CG ARG A 17 " pdb=" CD ARG A 17 " ideal model delta sinusoidal sigma weight residual -180.00 -122.03 -57.97 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 2195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 212 0.029 - 0.059: 89 0.059 - 0.088: 30 0.088 - 0.118: 29 0.118 - 0.147: 5 Chirality restraints: 365 Sorted by residual: chirality pdb=" CA ILE A 166 " pdb=" N ILE A 166 " pdb=" C ILE A 166 " pdb=" CB ILE A 166 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CA VAL A 290 " pdb=" N VAL A 290 " pdb=" C VAL A 290 " pdb=" CB VAL A 290 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA VAL A 212 " pdb=" N VAL A 212 " pdb=" C VAL A 212 " pdb=" CB VAL A 212 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 362 not shown) Planarity restraints: 685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 187 " -0.021 5.00e-02 4.00e+02 3.15e-02 1.58e+00 pdb=" N PRO A 188 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 166 " -0.019 5.00e-02 4.00e+02 2.81e-02 1.26e+00 pdb=" N PRO A 167 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 167 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 167 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 39 " -0.005 2.00e-02 2.50e+03 1.06e-02 1.12e+00 pdb=" C LYS A 39 " 0.018 2.00e-02 2.50e+03 pdb=" O LYS A 39 " -0.007 2.00e-02 2.50e+03 pdb=" N MET A 40 " -0.006 2.00e-02 2.50e+03 ... (remaining 682 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 443 2.13 - 2.74: 8610 2.74 - 3.36: 14282 3.36 - 3.98: 19988 3.98 - 4.60: 29332 Nonbonded interactions: 72655 Sorted by model distance: nonbonded pdb=" O LYS A 47 " pdb=" H HIS A 86 " model vdw 1.506 1.800 nonbonded pdb=" O ASP A 93 " pdb=" HG1 THR A 282 " model vdw 1.509 1.800 nonbonded pdb=" O LYS A 250 " pdb=" H LYS A 254 " model vdw 1.549 1.800 nonbonded pdb=" H ALA A 60 " pdb=" O LEU A 268 " model vdw 1.551 1.800 nonbonded pdb=" OE1 GLU A 58 " pdb=" H GLU A 58 " model vdw 1.567 1.800 ... (remaining 72650 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 9 15.96 2 O 423 7.97 2 N 390 6.97 2 C 1490 5.97 2 H 2407 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 10 313.3132905960083 Trying rss 9 277.1818902492523 Trying rss 8 249.51048398017883 Trying rss 7 217.3849458694458 Trying rss 6 194.48793363571167 Trying rss 5 169.05232048034668 Trying rss 4 149.6235179901123 Trying rss 3 133.78022146224976 Trying rss 2 108.83967447280884 Trying rss 1 102.31676006317139 STOP: /net/cci-gpu-00/raid1/scratch1/pavel/phenix/modules/qrefine/refine.py(128)