Starting qr.refine on Sat Apr 6 07:30:57 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs/regularized_V3a/1yab.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/1yab.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs/regularized_V3a/1yab.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 84": "OE1" <-> "OE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "B ASP 69": "OD1" <-> "OD2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B GLU 154": "OE1" <-> "OE2" 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: 2831 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1401 Classifications: {'peptide': 85} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "B" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1430 Classifications: {'peptide': 87} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 82} Time building chain proxies: 0.39, per 1000 atoms: 0.14 Number of scatterers: 2831 At special positions: 0 Unit cell: (100.173, 100.173, 87.853, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 4 16.00 O 257 8.00 N 229 7.00 C 865 6.00 H 1476 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: 0.80 Adding C-beta torsion restraints... Number of C-beta restraints generated: 320 Time building geometry restraints manager: 0.89 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: 1476 1.14 - 1.31: 241 1.31 - 1.48: 435 1.48 - 1.64: 679 1.64 - 1.81: 8 Bond restraints: 2839 Sorted by residual: bond pdb=" CB VAL B 143 " pdb=" CG1 VAL B 143 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.02e+00 bond pdb=" CB VAL B 114 " pdb=" CG2 VAL B 114 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.58e+00 bond pdb=" C PRO B 113 " pdb=" N VAL B 114 " ideal model delta sigma weight residual 1.329 1.345 -0.016 1.40e-02 5.10e+03 1.36e+00 bond pdb=" C ASN B 153 " pdb=" N GLU B 154 " ideal model delta sigma weight residual 1.329 1.344 -0.015 1.40e-02 5.10e+03 1.15e+00 bond pdb=" CG LEU A 152 " pdb=" CD1 LEU A 152 " ideal model delta sigma weight residual 1.521 1.556 -0.035 3.30e-02 9.18e+02 1.11e+00 ... (remaining 2834 not shown) Histogram of bond angle deviations from ideal: 99.37 - 105.81: 35 105.81 - 112.24: 3626 112.24 - 118.67: 617 118.67 - 125.11: 897 125.11 - 131.54: 46 Bond angle restraints: 5221 Sorted by residual: angle pdb=" C GLY A 111 " pdb=" N GLU A 112 " pdb=" CA GLU A 112 " ideal model delta sigma weight residual 121.70 114.44 7.26 1.80e+00 3.09e-01 1.63e+01 angle pdb=" C ASN B 153 " pdb=" N GLU B 154 " pdb=" CA GLU B 154 " ideal model delta sigma weight residual 121.70 128.95 -7.25 1.80e+00 3.09e-01 1.62e+01 angle pdb=" C VAL B 114 " pdb=" N ASP B 115 " pdb=" CA ASP B 115 " ideal model delta sigma weight residual 121.70 117.46 4.24 1.80e+00 3.09e-01 5.56e+00 angle pdb=" C ILE A 123 " pdb=" N ALA A 124 " pdb=" CA ALA A 124 " ideal model delta sigma weight residual 121.70 117.54 4.16 1.80e+00 3.09e-01 5.35e+00 angle pdb=" N GLU B 154 " pdb=" CA GLU B 154 " pdb=" C GLU B 154 " ideal model delta sigma weight residual 111.00 117.44 -6.44 2.80e+00 1.28e-01 5.28e+00 ... (remaining 5216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 1077 17.77 - 35.53: 142 35.53 - 53.30: 34 53.30 - 71.06: 12 71.06 - 88.83: 5 Dihedral angle restraints: 1270 sinusoidal: 764 harmonic: 506 Sorted by residual: dihedral pdb=" CA LEU A 75 " pdb=" C LEU A 75 " pdb=" N ASP A 76 " pdb=" CA ASP A 76 " ideal model delta harmonic sigma weight residual 180.00 -156.39 -23.61 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA ASP B 69 " pdb=" C ASP B 69 " pdb=" N LYS B 70 " pdb=" CA LYS B 70 " ideal model delta harmonic sigma weight residual 180.00 157.31 22.69 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA LEU B 106 " pdb=" C LEU B 106 " pdb=" N ASP B 107 " pdb=" CA ASP B 107 " ideal model delta harmonic sigma weight residual -180.00 -158.83 -21.17 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 1267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 135 0.035 - 0.070: 58 0.070 - 0.104: 23 0.104 - 0.139: 14 0.139 - 0.174: 8 Chirality restraints: 238 Sorted by residual: chirality pdb=" CA VAL B 129 " pdb=" N VAL B 129 " pdb=" C VAL B 129 " pdb=" CB VAL B 129 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CA VAL A 81 " pdb=" N VAL A 81 " pdb=" C VAL A 81 " pdb=" CB VAL A 81 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" CA ILE A 116 " pdb=" N ILE A 116 " pdb=" C ILE A 116 " pdb=" CB ILE A 116 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 235 not shown) Planarity restraints: 394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 94 " -0.208 9.50e-02 1.11e+02 6.95e-02 5.25e+00 pdb=" NE ARG B 94 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 94 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 94 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 94 " -0.004 2.00e-02 2.50e+03 pdb="HH11 ARG B 94 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG B 94 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG B 94 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG B 94 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 94 " -0.178 9.50e-02 1.11e+02 5.93e-02 3.85e+00 pdb=" NE ARG A 94 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 94 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 94 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 94 " -0.004 2.00e-02 2.50e+03 pdb="HH11 ARG A 94 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 94 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 94 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 94 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 144 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO B 145 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 145 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 145 " -0.026 5.00e-02 4.00e+02 ... (remaining 391 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 205 2.09 - 2.72: 4783 2.72 - 3.35: 8554 3.35 - 3.97: 11710 3.97 - 4.60: 16926 Nonbonded interactions: 42178 Sorted by model distance: nonbonded pdb=" O LEU A 74 " pdb=" H ASP A 76 " model vdw 1.464 1.800 nonbonded pdb=" H ASP A 76 " pdb=" H ILE A 77 " model vdw 1.542 2.000 nonbonded pdb=" H ILE A 104 " pdb=" O VAL B 137 " model vdw 1.604 1.800 nonbonded pdb=" OD1 ASP B 132 " pdb=" H GLU B 133 " model vdw 1.640 1.800 nonbonded pdb=" O VAL B 129 " pdb=" H GLY B 136 " model vdw 1.645 1.800 ... (remaining 42173 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 4 15.96 2 O 257 7.97 2 N 229 6.97 2 C 865 5.97 2 H 1476 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 10 132.18658018112183 Trying rss 9 123.729820728302 Trying rss 8 121.87450408935547 Trying rss 7 97.07333159446716 Trying rss 6 84.30957388877869 Trying rss 5 74.55456447601318 Trying rss 4 69.15147376060486 Trying rss 3 66.04756307601929 Trying rss 2 48.49017405509949 Trying rss 1 43.93315649032593 STOP: /net/cci-gpu-00/raid1/scratch1/pavel/phenix/modules/qrefine/refine.py(128)