Starting qr.refine on Mon May 20 18:02:44 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/2fdq.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- mode=opt restraints=qm engine=aimnet2 clustering=false minimizer=lbfgs gradient_only=true use_reduce=False select_within_radius=7 number_of_micro_cycles=3 max_iterations_refine=100 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/2fdq.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/2fdq.pdb" } use_reduce = False cluster { clustering = false select_within_radius = 7 } quantum { engine_name = mopac *aimnet2 torchani terachem turbomole pyscf orca \ gaussian xtb server } refine { mode = *opt refine gtest number_of_micro_cycles = 3 max_iterations_refine = 100 gradient_only = true } Starting job =============================================================================== Validate inputs: ------------------------------------------------------------------------------- Refinement start **************** max_atoms = 50000 debug_rss = False 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 = False 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 = 3 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_angle_rmsd = 1.7 stop_one_found_first_good_weight = True 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 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: 0.53, 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: 0.76 Adding C-beta torsion restraints... Number of C-beta restraints generated: 486 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 - 1.14: 2076 1.14 - 1.31: 375 1.31 - 1.48: 784 1.48 - 1.64: 950 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 1.327 0.014 1.60e-02 3.91e+03 7.50e-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 5.84e-01 bond pdb=" C PHE C 5 " pdb=" N ASP C 6 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.40e-02 5.10e+03 5.72e-01 bond pdb=" C ILE B 39 " pdb=" N ASN B 40 " ideal model delta sigma weight residual 1.329 1.339 -0.010 1.40e-02 5.10e+03 5.58e-01 bond pdb=" C LYS C 18 " pdb=" N PRO C 19 " ideal model delta sigma weight residual 1.341 1.330 0.011 1.60e-02 3.91e+03 4.66e-01 ... (remaining 4198 not shown) Histogram of bond angle deviations from ideal: 99.77 - 106.62: 41 106.62 - 113.47: 5102 113.47 - 120.32: 1315 120.32 - 127.17: 1154 127.17 - 134.01: 23 Bond angle restraints: 7635 Sorted by residual: angle pdb=" C MET A 46 " pdb=" CA MET A 46 " pdb=" CB MET A 46 " ideal model delta sigma weight residual 110.10 114.63 -4.53 1.90e+00 2.77e-01 5.68e+00 angle pdb=" CA ARG A 43 " pdb=" C ARG A 43 " pdb=" N PRO A 44 " ideal model delta sigma weight residual 116.90 119.34 -2.44 1.50e+00 4.44e-01 2.65e+00 angle pdb=" CA TYR A 84 " pdb=" C TYR A 84 " pdb=" N GLY A 85 " ideal model delta sigma weight residual 116.20 119.42 -3.22 2.00e+00 2.50e-01 2.60e+00 angle pdb=" CA LYS B 18 " pdb=" C LYS B 18 " pdb=" N PRO B 19 " ideal model delta sigma weight residual 116.90 119.28 -2.38 1.50e+00 4.44e-01 2.52e+00 angle pdb=" CA ASN A 14 " pdb=" C ASN A 14 " pdb=" N LEU A 15 " ideal model delta sigma weight residual 116.20 119.38 -3.18 2.00e+00 2.50e-01 2.52e+00 ... (remaining 7630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 1795 17.29 - 34.57: 115 34.57 - 51.86: 26 51.86 - 69.15: 9 69.15 - 86.43: 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 81.69 -81.69 1 3.00e+01 1.11e-03 9.12e+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 -105.18 45.18 3 1.50e+01 4.44e-03 8.12e+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 -103.21 43.21 3 1.50e+01 4.44e-03 7.76e+00 ... (remaining 1944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 191 0.021 - 0.043: 62 0.043 - 0.064: 23 0.064 - 0.086: 11 0.086 - 0.107: 4 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 2.54 -0.11 2.00e-01 2.50e+01 2.88e-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 2.53 -0.10 2.00e-01 2.50e+01 2.34e-01 chirality pdb=" CA ILE C 74 " pdb=" N ILE C 74 " pdb=" C ILE C 74 " pdb=" CB ILE C 74 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.09 2.00e-01 2.50e+01 1.91e-01 ... (remaining 288 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 77 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" C VAL B 77 " -0.020 2.00e-02 2.50e+03 pdb=" O VAL B 77 " 0.008 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=" CA LEU B 25 " 0.005 2.00e-02 2.50e+03 1.03e-02 1.07e+00 pdb=" C LEU B 25 " -0.018 2.00e-02 2.50e+03 pdb=" O LEU B 25 " 0.007 2.00e-02 2.50e+03 pdb=" N PHE B 26 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 28 " 0.004 2.00e-02 2.50e+03 8.94e-03 8.00e-01 pdb=" C TYR B 28 " -0.015 2.00e-02 2.50e+03 pdb=" O TYR B 28 " 0.006 2.00e-02 2.50e+03 pdb=" N SER B 29 " 0.005 2.00e-02 2.50e+03 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 497 2.22 - 2.82: 8673 2.82 - 3.41: 11976 3.41 - 4.01: 15737 4.01 - 4.60: 23563 Nonbonded interactions: 60446 Sorted by model distance: nonbonded pdb=" O LEU B 61 " pdb=" HG1 THR B 64 " model vdw 1.627 1.800 nonbonded pdb=" OE1 GLU B 11 " pdb=" HZ2 LYS B 81 " model vdw 1.646 1.800 nonbonded pdb=" OD1 ASP A 38 " pdb=" H GLY A 63 " model vdw 1.656 1.800 nonbonded pdb=" OE2 GLU B 23 " pdb=" HZ3 LYS B 83 " model vdw 1.685 1.800 nonbonded pdb=" O GLU A 11 " pdb=" H ASN A 14 " model vdw 1.690 1.800 ... (remaining 60441 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- 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 start: bond: 0.004 angle: 0.83 clash: 1.2 rota: 0.46 rama: f: 94.44 o: 0.00 Z: -1.46 cb: 0.00 shift start/prev: 0.000 0.000 LBFGS: function start/end, n_calls: -652.710092 -704.865472 101 cycle 0: bond: 0.008 angle: 1.33 clash: 0.0 rota: 0.00 rama: f: 97.22 o: 0.00 Z: 0.03 cb: 0.00 shift start/prev: 0.194 0.194 LBFGS: function start/end, n_calls: -704.865472 -708.018368 102 cycle 1: bond: 0.008 angle: 1.32 clash: 0.0 rota: 0.00 rama: f: 97.62 o: 0.00 Z: 0.10 cb: 0.00 shift start/prev: 0.257 0.099 LBFGS: function start/end, n_calls: -708.018368 -709.444363 102 cycle 2: bond: 0.008 angle: 1.33 clash: 0.0 rota: 0.00 rama: f: 97.62 o: 0.00 Z: 0.28 cb: 0.00 shift start/prev: 0.295 0.061 calculator(opt), total_time (target_and_gradients) 49.68297791481018 calculator(opt), number_of_target_and_gradients_calls (target_and_gradients) 305 See 2fdq_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 123.87 seconds wall clock time: 2 minutes 9.48 seconds (129.48 seconds total) /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)