Starting qr.refine on Sat Apr 6 11:13:36 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs/regularized_V3a/1x24.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/1x24.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs/regularized_V3a/1x24.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 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 126": "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: 4962 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2481 Classifications: {'peptide': 152} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 7, 'TRANS': 144} Chain: "B" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2481 Classifications: {'peptide': 152} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 7, 'TRANS': 144} Time building chain proxies: 0.65, per 1000 atoms: 0.13 Number of scatterers: 4962 At special positions: 0 Unit cell: (146.891, 146.891, 146.891, 90, 90, 90) Space group: I 21 3 (No. 199) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 434 8.00 N 424 7.00 C 1580 6.00 H 2510 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 104 " distance=2.03 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: 0.98 Adding C-beta torsion restraints... Number of C-beta restraints generated: 572 Time building geometry restraints manager: 1.15 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: 2506 1.14 - 1.31: 402 1.31 - 1.48: 984 1.48 - 1.65: 1104 1.65 - 1.81: 20 Bond restraints: 5016 Sorted by residual: bond pdb=" C ALA B 74 " pdb=" N PRO B 75 " ideal model delta sigma weight residual 1.341 1.329 0.012 1.60e-02 3.91e+03 5.69e-01 bond pdb=" C ALA A 74 " pdb=" O ALA A 74 " ideal model delta sigma weight residual 1.231 1.246 -0.015 2.00e-02 2.50e+03 5.27e-01 bond pdb=" C ALA A 74 " pdb=" N PRO A 75 " ideal model delta sigma weight residual 1.341 1.330 0.011 1.60e-02 3.91e+03 4.56e-01 bond pdb=" C ALA B 111 " pdb=" O ALA B 111 " ideal model delta sigma weight residual 1.231 1.244 -0.013 2.00e-02 2.50e+03 4.12e-01 bond pdb=" C TRP B 68 " pdb=" N PRO B 69 " ideal model delta sigma weight residual 1.341 1.331 0.010 1.60e-02 3.91e+03 3.89e-01 ... (remaining 5011 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.17: 143 107.17 - 113.86: 6041 113.86 - 120.56: 1646 120.56 - 127.25: 1253 127.25 - 133.95: 27 Bond angle restraints: 9110 Sorted by residual: angle pdb=" C LYS B 15 " pdb=" CA LYS B 15 " pdb=" CB LYS B 15 " ideal model delta sigma weight residual 110.10 115.59 -5.49 1.90e+00 2.77e-01 8.35e+00 angle pdb=" C LYS A 15 " pdb=" CA LYS A 15 " pdb=" CB LYS A 15 " ideal model delta sigma weight residual 110.10 115.55 -5.45 1.90e+00 2.77e-01 8.22e+00 angle pdb=" CA ALA B 111 " pdb=" C ALA B 111 " pdb=" N PRO B 112 " ideal model delta sigma weight residual 116.90 121.11 -4.21 1.50e+00 4.44e-01 7.88e+00 angle pdb=" CA ALA A 111 " pdb=" C ALA A 111 " pdb=" N PRO A 112 " ideal model delta sigma weight residual 116.90 121.10 -4.20 1.50e+00 4.44e-01 7.83e+00 angle pdb=" CA ARG A 153 " pdb=" C ARG A 153 " pdb=" N PRO A 154 " ideal model delta sigma weight residual 116.90 119.61 -2.71 1.50e+00 4.44e-01 3.26e+00 ... (remaining 9105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.41: 2019 11.41 - 22.82: 207 22.82 - 34.23: 77 34.23 - 45.64: 23 45.64 - 57.06: 16 Dihedral angle restraints: 2342 sinusoidal: 1294 harmonic: 1048 Sorted by residual: dihedral pdb=" CA ILE A 90 " pdb=" C ILE A 90 " pdb=" N LYS A 91 " pdb=" CA LYS A 91 " ideal model delta harmonic sigma weight residual -180.00 -164.01 -15.99 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA ILE B 90 " pdb=" C ILE B 90 " pdb=" N LYS B 91 " pdb=" CA LYS B 91 " ideal model delta harmonic sigma weight residual -180.00 -164.96 -15.04 0 5.00e+00 4.00e-02 9.05e+00 dihedral pdb=" N CYS B 104 " pdb=" CA CYS B 104 " pdb=" CB CYS B 104 " pdb=" SG CYS B 104 " ideal model delta sinusoidal sigma weight residual 180.00 -129.38 -50.62 3 1.50e+01 4.44e-03 8.92e+00 ... (remaining 2339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 226 0.025 - 0.050: 83 0.050 - 0.075: 43 0.075 - 0.100: 10 0.100 - 0.125: 18 Chirality restraints: 380 Sorted by residual: chirality pdb=" CA ILE B 100 " pdb=" N ILE B 100 " pdb=" C ILE B 100 " pdb=" CB ILE B 100 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA VAL A 102 " pdb=" N VAL A 102 " pdb=" C VAL A 102 " pdb=" CB VAL A 102 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA ILE A 100 " pdb=" N ILE A 100 " pdb=" C ILE A 100 " pdb=" CB ILE A 100 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 377 not shown) Planarity restraints: 718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 111 " 0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO B 112 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 111 " 0.018 5.00e-02 4.00e+02 2.70e-02 1.16e+00 pdb=" N PRO A 112 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 137 " -0.091 9.50e-02 1.11e+02 3.05e-02 1.01e+00 pdb=" NE ARG A 137 " 0.005 2.00e-02 2.50e+03 pdb=" CZ ARG A 137 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 137 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 137 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 137 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 137 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 137 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 137 " -0.000 2.00e-02 2.50e+03 ... (remaining 715 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 335 2.09 - 2.72: 7843 2.72 - 3.34: 15168 3.34 - 3.97: 20486 3.97 - 4.60: 30205 Nonbonded interactions: 74037 Sorted by model distance: nonbonded pdb=" O ARG A 137 " pdb=" H GLY A 139 " model vdw 1.459 1.800 nonbonded pdb=" O ARG B 137 " pdb=" H GLY B 139 " model vdw 1.533 1.800 nonbonded pdb=" O PHE A 70 " pdb="HH12 ARG A 110 " model vdw 1.571 1.800 nonbonded pdb=" OE2 GLU A 127 " pdb="HH22 ARG B 157 " model vdw 1.578 1.800 nonbonded pdb=" HE ARG A 47 " pdb=" OD1 ASP A 67 " model vdw 1.606 1.800 ... (remaining 74032 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 14 15.96 2 O 434 7.97 2 N 424 6.97 2 C 1580 5.97 2 H 2510 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 10 485.8573958873749 Trying rss 9 424.61315298080444 Trying rss 8 371.44483852386475 Trying rss 7 303.0479121208191 Trying rss 6 254.550555229187 Trying rss 5 224.47671246528625 Trying rss 4 194.56912088394165 Trying rss 3 167.2747118473053 Trying rss 2 122.61096668243408 Trying rss 1 108.34928369522095 STOP: /net/cci-gpu-00/raid1/scratch1/pavel/phenix/modules/qrefine/refine.py(128)