Starting qr.refine on Sat Apr 6 07:45:56 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs/regularized_V3a/4xcr.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/4xcr.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs/regularized_V3a/4xcr.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 None 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: 3086 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1543 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1543 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Time building chain proxies: 0.43, per 1000 atoms: 0.14 Number of scatterers: 3086 At special positions: 0 Unit cell: (70.82, 70.82, 70.01, 90, 90, 120) Space group: P 65 (No. 170) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 308 8.00 N 280 7.00 C 954 6.00 H 1544 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: 360 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.09: 1532 1.09 - 1.21: 12 1.21 - 1.32: 283 1.32 - 1.43: 354 1.43 - 1.55: 925 Bond restraints: 3106 Sorted by residual: bond pdb=" C GLY B 27 " pdb=" N PRO B 28 " ideal model delta sigma weight residual 1.341 1.329 0.012 1.60e-02 3.91e+03 5.55e-01 bond pdb=" C ALA A 93 " pdb=" N GLY A 94 " ideal model delta sigma weight residual 1.329 1.319 0.010 1.40e-02 5.10e+03 5.54e-01 bond pdb=" C SER A 77 " pdb=" O SER A 77 " ideal model delta sigma weight residual 1.231 1.244 -0.013 2.00e-02 2.50e+03 4.44e-01 bond pdb=" CA SER B 68 " pdb=" CB SER B 68 " ideal model delta sigma weight residual 1.530 1.517 0.013 2.00e-02 2.50e+03 4.32e-01 bond pdb=" C ASP A 60 " pdb=" N LYS A 61 " ideal model delta sigma weight residual 1.329 1.338 -0.009 1.40e-02 5.10e+03 3.96e-01 ... (remaining 3101 not shown) Histogram of bond angle deviations from ideal: 102.68 - 108.93: 1477 108.93 - 115.18: 2673 115.18 - 121.43: 690 121.43 - 127.68: 775 127.68 - 133.93: 17 Bond angle restraints: 5632 Sorted by residual: angle pdb=" C SER A 77 " pdb=" CA SER A 77 " pdb=" CB SER A 77 " ideal model delta sigma weight residual 110.10 113.64 -3.54 1.90e+00 2.77e-01 3.48e+00 angle pdb=" C LEU A 76 " pdb=" N SER A 77 " pdb=" CA SER A 77 " ideal model delta sigma weight residual 121.70 124.78 -3.08 1.80e+00 3.09e-01 2.92e+00 angle pdb=" N SER A 68 " pdb=" CA SER A 68 " pdb=" C SER A 68 " ideal model delta sigma weight residual 111.00 106.26 4.74 2.80e+00 1.28e-01 2.86e+00 angle pdb=" C GLY A 33 " pdb=" N SER A 34 " pdb=" CA SER A 34 " ideal model delta sigma weight residual 121.70 118.88 2.82 1.80e+00 3.09e-01 2.45e+00 angle pdb=" CA THR A 2 " pdb=" C THR A 2 " pdb=" N LYS A 3 " ideal model delta sigma weight residual 116.20 119.30 -3.10 2.00e+00 2.50e-01 2.40e+00 ... (remaining 5627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 1319 16.94 - 33.87: 60 33.87 - 50.81: 40 50.81 - 67.75: 9 67.75 - 84.69: 2 Dihedral angle restraints: 1430 sinusoidal: 788 harmonic: 642 Sorted by residual: dihedral pdb=" CA ILE A 69 " pdb=" C ILE A 69 " pdb=" N GLU A 70 " pdb=" CA GLU A 70 " ideal model delta harmonic sigma weight residual 180.00 164.40 15.60 0 5.00e+00 4.00e-02 9.74e+00 dihedral pdb=" CA ARG A 85 " pdb=" C ARG A 85 " pdb=" N THR A 86 " pdb=" CA THR A 86 " ideal model delta harmonic sigma weight residual 180.00 -164.45 -15.55 0 5.00e+00 4.00e-02 9.67e+00 dihedral pdb=" CA LEU A 101 " pdb=" C LEU A 101 " pdb=" N ALA A 102 " pdb=" CA ALA A 102 " ideal model delta harmonic sigma weight residual 180.00 164.63 15.37 0 5.00e+00 4.00e-02 9.45e+00 ... (remaining 1427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 134 0.031 - 0.062: 61 0.062 - 0.092: 22 0.092 - 0.123: 21 0.123 - 0.154: 6 Chirality restraints: 244 Sorted by residual: chirality pdb=" CA ILE A 18 " pdb=" N ILE A 18 " pdb=" C ILE A 18 " pdb=" CB ILE A 18 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA VAL B 88 " pdb=" N VAL B 88 " pdb=" C VAL B 88 " pdb=" CB VAL B 88 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA ILE B 17 " pdb=" N ILE B 17 " pdb=" C ILE B 17 " pdb=" CB ILE B 17 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 241 not shown) Planarity restraints: 494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 12 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO B 13 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 13 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 13 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 27 " 0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO A 28 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 28 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 28 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 45 " 0.006 2.00e-02 2.50e+03 4.19e-03 5.26e-01 pdb=" CG PHE B 45 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE B 45 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 45 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 45 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 45 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 45 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE B 45 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE B 45 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE B 45 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE B 45 " 0.001 2.00e-02 2.50e+03 pdb=" HZ PHE B 45 " -0.000 2.00e-02 2.50e+03 ... (remaining 491 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.21: 318 2.21 - 2.78: 5834 2.78 - 3.35: 7750 3.35 - 3.93: 11115 3.93 - 4.50: 15632 Nonbonded interactions: 40649 Sorted by model distance: nonbonded pdb=" OE2 GLU A 21 " pdb=" HE1 TRP A 32 " model vdw 1.633 1.800 nonbonded pdb=" HZ3 LYS A 30 " pdb=" OG SER A 68 " model vdw 1.634 1.800 nonbonded pdb=" HG1 THR A 2 " pdb=" O GLN A 22 " model vdw 1.641 1.800 nonbonded pdb=" H GLY B 84 " pdb=" O ILE B 106 " model vdw 1.657 1.800 nonbonded pdb=" H GLY A 96 " pdb="HD21 ASN B 26 " model vdw sym.op. 1.675 2.000 -x+1,-y+1,z+1/2 ... (remaining 40644 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: 4 Type Number sf(0) Gaussians O 308 7.97 2 N 280 6.97 2 C 954 5.97 2 H 1544 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 10 301.0385890007019 Trying rss 9 243.80677151679993 Trying rss 8 205.23100471496582 Trying rss 7 161.71592950820923 Trying rss 6 134.00687313079834 Trying rss 5 106.19614338874817 Trying rss 4 89.96482825279236 Trying rss 3 76.73279166221619 Trying rss 2 54.37219786643982 Trying rss 1 46.25046753883362 STOP: /net/cci-gpu-00/raid1/scratch1/pavel/phenix/modules/qrefine/refine.py(128)