Starting qr.refine on Sat Apr 6 09:01:19 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs/regularized_V3a/2fdq.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/2fdq.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs/regularized_V3a/2fdq.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 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 73": "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: 4164 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1388 Classifications: {'peptide': 86} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "B" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1388 Classifications: {'peptide': 86} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "C" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1388 Classifications: {'peptide': 86} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 83} Time building chain proxies: 0.54, per 1000 atoms: 0.13 Number of scatterers: 4164 At special positions: 0 Unit cell: (49.11, 49.11, 130.48, 90, 90, 90) Space group: P 41 (No. 76) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 411 8.00 N 342 7.00 C 1326 6.00 H 2076 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: 0.77 Adding C-beta torsion restraints... Number of C-beta restraints generated: 486 Time building geometry restraints manager: 0.91 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: 2076 1.14 - 1.31: 375 1.31 - 1.48: 783 1.48 - 1.64: 951 1.64 - 1.81: 18 Bond restraints: 4203 Sorted by residual: bond pdb=" C LYS A 18 " pdb=" N PRO A 19 " ideal model delta sigma weight residual 1.341 1.326 0.015 1.60e-02 3.91e+03 8.55e-01 bond pdb=" C ILE B 39 " pdb=" N ASN B 40 " ideal model delta sigma weight residual 1.329 1.341 -0.012 1.40e-02 5.10e+03 7.91e-01 bond pdb=" C ILE C 39 " pdb=" N ASN C 40 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.40e-02 5.10e+03 6.40e-01 bond pdb=" C MET C 46 " pdb=" N LEU C 47 " ideal model delta sigma weight residual 1.329 1.339 -0.010 1.40e-02 5.10e+03 4.66e-01 bond pdb=" C ARG A 43 " pdb=" N PRO A 44 " ideal model delta sigma weight residual 1.341 1.330 0.011 1.60e-02 3.91e+03 4.56e-01 ... (remaining 4198 not shown) Histogram of bond angle deviations from ideal: 99.77 - 106.62: 40 106.62 - 113.47: 5112 113.47 - 120.32: 1311 120.32 - 127.16: 1148 127.16 - 134.01: 24 Bond angle restraints: 7635 Sorted by residual: angle pdb=" CA LYS A 18 " pdb=" C LYS A 18 " pdb=" N PRO A 19 " ideal model delta sigma weight residual 116.90 119.44 -2.54 1.50e+00 4.44e-01 2.86e+00 angle pdb=" CA TYR A 84 " pdb=" C TYR A 84 " pdb=" N GLY A 85 " ideal model delta sigma weight residual 116.20 119.44 -3.24 2.00e+00 2.50e-01 2.62e+00 angle pdb=" CA ARG B 43 " pdb=" C ARG B 43 " pdb=" N PRO B 44 " ideal model delta sigma weight residual 116.90 119.21 -2.31 1.50e+00 4.44e-01 2.36e+00 angle pdb=" CA ASN A 14 " pdb=" C ASN A 14 " pdb=" N LEU A 15 " ideal model delta sigma weight residual 116.20 119.26 -3.06 2.00e+00 2.50e-01 2.34e+00 angle pdb=" CA ARG C 43 " pdb=" C ARG C 43 " pdb=" N PRO C 44 " ideal model delta sigma weight residual 116.90 119.19 -2.29 1.50e+00 4.44e-01 2.34e+00 ... (remaining 7630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 1788 17.55 - 35.10: 118 35.10 - 52.65: 30 52.65 - 70.20: 9 70.20 - 87.75: 2 Dihedral angle restraints: 1947 sinusoidal: 1056 harmonic: 891 Sorted by residual: dihedral pdb=" CB GLU C 42 " pdb=" CG GLU C 42 " pdb=" CD GLU C 42 " pdb=" OE1 GLU C 42 " ideal model delta sinusoidal sigma weight residual 0.00 80.22 -80.22 1 3.00e+01 1.11e-03 8.86e+00 dihedral pdb=" CB MET C 24 " pdb=" CG MET C 24 " pdb=" SD MET C 24 " pdb=" CE MET C 24 " ideal model delta sinusoidal sigma weight residual -60.00 -104.30 44.30 3 1.50e+01 4.44e-03 7.97e+00 dihedral pdb=" N GLU A 67 " pdb=" CA GLU A 67 " pdb=" CB GLU A 67 " pdb=" CG GLU A 67 " ideal model delta sinusoidal sigma weight residual -60.00 -100.65 40.65 3 1.50e+01 4.44e-03 7.25e+00 ... (remaining 1944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 196 0.023 - 0.045: 60 0.045 - 0.068: 22 0.068 - 0.090: 10 0.090 - 0.113: 3 Chirality restraints: 291 Sorted by residual: chirality pdb=" CA ILE B 86 " pdb=" N ILE B 86 " pdb=" C ILE B 86 " pdb=" CB ILE B 86 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.18e-01 chirality pdb=" CA VAL C 36 " pdb=" N VAL C 36 " pdb=" C VAL C 36 " pdb=" CB VAL C 36 " both_signs ideal model delta sigma weight residual False 2.44 2.53 -0.09 2.00e-01 2.50e+01 2.18e-01 chirality pdb=" CA ILE A 27 " pdb=" N ILE A 27 " pdb=" C ILE A 27 " pdb=" CB ILE A 27 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.09 2.00e-01 2.50e+01 2.09e-01 ... (remaining 288 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 6 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" C ASP C 6 " -0.026 2.00e-02 2.50e+03 pdb=" O ASP C 6 " 0.010 2.00e-02 2.50e+03 pdb=" N LYS C 7 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 77 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.27e+00 pdb=" C VAL B 77 " 0.020 2.00e-02 2.50e+03 pdb=" O VAL B 77 " -0.007 2.00e-02 2.50e+03 pdb=" N GLU B 78 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 6 " 0.006 2.00e-02 2.50e+03 1.08e-02 1.16e+00 pdb=" N LYS C 7 " -0.019 2.00e-02 2.50e+03 pdb=" CA LYS C 7 " 0.005 2.00e-02 2.50e+03 pdb=" H LYS C 7 " 0.007 2.00e-02 2.50e+03 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 534 2.23 - 2.82: 8820 2.82 - 3.42: 11897 3.42 - 4.01: 15696 4.01 - 4.60: 23439 Nonbonded interactions: 60386 Sorted by model distance: nonbonded pdb=" OD1 ASP A 38 " pdb=" H GLY A 63 " model vdw 1.640 1.800 nonbonded pdb=" OE1 GLU A 23 " pdb=" HH TYR A 84 " model vdw 1.668 1.800 nonbonded pdb=" O LEU B 61 " pdb=" HG1 THR B 64 " model vdw 1.673 1.800 nonbonded pdb=" OE1 GLU B 11 " pdb=" HZ2 LYS B 81 " model vdw 1.676 1.800 nonbonded pdb="HE22 GLN A 33 " pdb=" OD1 ASP A 38 " model vdw 1.724 1.800 ... (remaining 60381 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 411 7.97 2 N 342 6.97 2 C 1326 5.97 2 H 2076 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 10 394.2099757194519 Trying rss 9 302.76676082611084 Trying rss 8 261.7577385902405 Trying rss 7 209.28586769104004 Trying rss 6 171.48324966430664 Trying rss 5 146.06912660598755 Trying rss 4 124.02189564704895 Trying rss 3 109.28427124023438 Trying rss 2 89.10278415679932 Trying rss 1 82.4141354560852 STOP: /net/cci-gpu-00/raid1/scratch1/pavel/phenix/modules/qrefine/refine.py(128)