Starting qr.refine on Mon May 20 17:57:13 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/4xcr.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/4xcr.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/pairs_cp/regularized/4xcr.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 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: 0.42, 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: 0.59 Adding C-beta torsion restraints... Number of C-beta restraints generated: 360 Time building geometry restraints manager: 0.69 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: 1537 1.09 - 1.21: 7 1.21 - 1.32: 282 1.32 - 1.43: 361 1.43 - 1.55: 919 Bond restraints: 3106 Sorted by residual: bond pdb=" C ASP A 60 " pdb=" N LYS A 61 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.40e-02 5.10e+03 5.65e-01 bond pdb=" C GLY B 27 " pdb=" N PRO B 28 " ideal model delta sigma weight residual 1.341 1.331 0.010 1.60e-02 3.91e+03 4.11e-01 bond pdb=" N GLY A 27 " pdb=" CA GLY A 27 " ideal model delta sigma weight residual 1.451 1.441 0.010 1.60e-02 3.91e+03 3.86e-01 bond pdb=" C GLU A 40 " pdb=" N GLY A 41 " ideal model delta sigma weight residual 1.329 1.338 -0.009 1.40e-02 5.10e+03 3.80e-01 bond pdb=" C TRP A 32 " pdb=" N GLY A 33 " ideal model delta sigma weight residual 1.329 1.321 0.008 1.40e-02 5.10e+03 3.59e-01 ... (remaining 3101 not shown) Histogram of bond angle deviations from ideal: 102.84 - 109.07: 1758 109.07 - 115.29: 2400 115.29 - 121.52: 700 121.52 - 127.74: 756 127.74 - 133.97: 18 Bond angle restraints: 5632 Sorted by residual: angle pdb=" N SER A 68 " pdb=" CA SER A 68 " pdb=" C SER A 68 " ideal model delta sigma weight residual 111.00 106.30 4.70 2.80e+00 1.28e-01 2.82e+00 angle pdb=" C GLY A 33 " pdb=" N SER A 34 " pdb=" CA SER A 34 " ideal model delta sigma weight residual 121.70 118.91 2.79 1.80e+00 3.09e-01 2.41e+00 angle pdb=" N VAL B 7 " pdb=" CA VAL B 7 " pdb=" C VAL B 7 " ideal model delta sigma weight residual 111.00 106.82 4.18 2.80e+00 1.28e-01 2.23e+00 angle pdb=" N PHE A 45 " pdb=" CA PHE A 45 " pdb=" C PHE A 45 " ideal model delta sigma weight residual 111.00 106.93 4.07 2.80e+00 1.28e-01 2.11e+00 angle pdb=" N PHE B 45 " pdb=" CA PHE B 45 " pdb=" C PHE B 45 " ideal model delta sigma weight residual 111.00 107.02 3.98 2.80e+00 1.28e-01 2.02e+00 ... (remaining 5627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 1332 16.93 - 33.87: 54 33.87 - 50.80: 31 50.80 - 67.74: 11 67.74 - 84.67: 2 Dihedral angle restraints: 1430 sinusoidal: 788 harmonic: 642 Sorted by residual: dihedral pdb=" CA HIS B 46 " pdb=" C HIS B 46 " pdb=" N VAL B 47 " pdb=" CA VAL B 47 " ideal model delta harmonic sigma weight residual 180.00 164.93 15.07 0 5.00e+00 4.00e-02 9.08e+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 180.00 164.98 15.02 0 5.00e+00 4.00e-02 9.02e+00 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 180.00 165.54 14.46 0 5.00e+00 4.00e-02 8.36e+00 ... (remaining 1427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 133 0.029 - 0.058: 58 0.058 - 0.087: 18 0.087 - 0.116: 29 0.116 - 0.145: 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 2.58 -0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA VAL A 31 " pdb=" N VAL A 31 " pdb=" C VAL A 31 " pdb=" CB VAL A 31 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.23e-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 4.03e-01 ... (remaining 241 not shown) Planarity restraints: 494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 12 " 0.012 5.00e-02 4.00e+02 1.83e-02 5.34e-01 pdb=" N PRO B 13 " -0.032 5.00e-02 4.00e+02 pdb=" CA PRO B 13 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO B 13 " 0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 59 " -0.004 2.00e-02 2.50e+03 6.88e-03 4.73e-01 pdb=" N ASP A 60 " 0.012 2.00e-02 2.50e+03 pdb=" CA ASP A 60 " -0.003 2.00e-02 2.50e+03 pdb=" H ASP A 60 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 59 " -0.003 2.00e-02 2.50e+03 6.73e-03 4.53e-01 pdb=" C ALA A 59 " 0.012 2.00e-02 2.50e+03 pdb=" O ALA A 59 " -0.004 2.00e-02 2.50e+03 pdb=" N ASP A 60 " -0.004 2.00e-02 2.50e+03 ... (remaining 491 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.18: 260 2.18 - 2.76: 5598 2.76 - 3.34: 7891 3.34 - 3.92: 10993 3.92 - 4.50: 15834 Nonbonded interactions: 40576 Sorted by model distance: nonbonded pdb=" OE2 GLU A 21 " pdb=" HE1 TRP A 32 " model vdw 1.600 1.800 nonbonded pdb=" O THR B 39 " pdb=" HE2 HIS B 43 " model vdw 1.629 1.800 nonbonded pdb=" OD1 ASP A 71 " pdb=" H VAL A 73 " model vdw 1.647 1.800 nonbonded pdb=" H HIS A 48 " pdb=" O THR A 86 " model vdw 1.662 1.800 nonbonded pdb=" H VAL A 47 " pdb=" O GLY A 52 " model vdw 1.675 1.800 ... (remaining 40571 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: 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 start: bond: 0.003 angle: 0.90 clash: 2.6 rota: 3.85 rama: f: 90.74 o: 1.39 Z: -4.28 cb: 0.00 shift start/prev: 0.000 0.000 LBFGS: function start/end, n_calls: -523.124005 -566.125240 102 cycle 0: bond: 0.009 angle: 1.55 clash: 0.0 rota: 1.92 rama: f: 94.91 o: 0.46 Z: -2.41 cb: 0.00 shift start/prev: 0.233 0.233 LBFGS: function start/end, n_calls: -566.125240 -569.509143 102 cycle 1: bond: 0.009 angle: 1.54 clash: 0.3 rota: 1.28 rama: f: 95.83 o: 0.46 Z: -2.39 cb: 0.00 shift start/prev: 0.334 0.151 LBFGS: function start/end, n_calls: -569.509143 -571.099948 102 cycle 2: bond: 0.009 angle: 1.54 clash: 0.3 rota: 1.28 rama: f: 96.76 o: 0.46 Z: -2.42 cb: 0.00 shift start/prev: 0.398 0.107 calculator(opt), total_time (target_and_gradients) 43.371800899505615 calculator(opt), number_of_target_and_gradients_calls (target_and_gradients) 306 See 4xcr_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 94.43 seconds wall clock time: 99.29 seconds /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)