Starting qr.refine on Sun May 19 21:26:34 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7vvn_32145.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7vvn_32145.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- mode=refine restraints=qm engine=aimnet2 clustering=false minimizer=lbfgsb max_bond_rmsd=0.0001 gradient_only=false Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7vvn_32145.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7vvn_32145.map" model { file = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7vvn_32145.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7vvn_32145.pdb" } cluster { clustering = false } quantum { engine_name = mopac *aimnet2 torchani terachem turbomole pyscf orca \ gaussian xtb server } refine { max_bond_rmsd = 0.0001 minimizer = lbfgs *lbfgsb } Starting job =============================================================================== Validate inputs: ------------------------------------------------------------------------------- Refinement start **************** max_atoms = 50000 debug_rss = False debug = False scattering_table = wk1995 it1992 *n_gaussian electron neutron use_reduce = True cluster { charge_cutoff = 8 clustering = False charge_embedding = False two_buffers = False maxnum_residues_in_cluster = 15 bcc_threshold = 9 select_within_radius = 10 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 = 50 data_weight = None skip_weight_search = False adjust_restraints_weight_scale_value = 2 max_iterations_weight = 50 max_iterations_refine = 50 use_ase_lbfgs = False line_search = True stpmax = 0.2 gradient_only = False refine_sites = True refine_adp = False restraints_weight_scale = 1 shake_sites = False use_convergence_test = True max_bond_rmsd = 0.0001 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 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 30": "OD1" <-> "OD2" Residue "P PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-gpu-00/raid1/scratch1/pavel/phenix/modules/chem_data/mon_lib" Total number of atoms: 17338 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3832 Inner-chain residues flagged as termini: ['pdbres="ILE A 62 "', 'pdbres="GLY A 206 "'] Classifications: {'peptide': 230} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Chain: "B" Number of atoms: 5107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5107 Classifications: {'peptide': 338} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 874 Classifications: {'peptide': 56} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1912 Classifications: {'peptide': 128} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "P" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 578 Classifications: {'peptide': 34} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 33} Chain: "R" Number of atoms: 5035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 5035 Inner-chain residues flagged as termini: ['pdbres="GLU R 49 "', 'pdbres="GLU R 111 "', 'pdbres="CYS R 117 "', 'pdbres="VAL R 129 "', 'pdbres="ILE R 135 "', 'pdbres="PHE R 138 "', 'pdbres="ARG R 146 "', 'pdbres="ARG R 162 "', 'pdbres="LEU R 174 "', 'pdbres="ARG R 181 "', 'pdbres="LEU R 244 "', 'pdbres="TYR R 278 "', 'pdbres="TRP R 352 "', 'pdbres="TRP R 361 "', 'pdbres="THR R 392 "', 'pdbres="ARG R 400 "', 'pdbres="THR R 430 "', 'pdbres="LEU R 436 "'] Classifications: {'peptide': 300} Modifications used: {'COO': 10, 'NH3': 10} Link IDs: {'PTRANS': 6, 'TRANS': 293} Chain breaks: 9 Time building chain proxies: 1.92, per 1000 atoms: 0.11 Number of scatterers: 17338 At special positions: 0 Unit cell: (123.947, 108.454, 117.307, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 O 1595 8.00 N 1528 7.00 C 5549 6.00 H 8610 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.02 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " 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: 3.24 Adding C-beta torsion restraints... Number of C-beta restraints generated: 2048 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.16: 8590 1.16 - 1.34: 2860 1.34 - 1.52: 3548 1.52 - 1.70: 2447 1.70 - 1.89: 80 Bond restraints: 17525 Sorted by residual: bond pdb=" CB CYS R 117 " pdb=" SG CYS R 117 " ideal model delta sigma weight residual 1.808 1.886 -0.078 3.30e-02 9.18e+02 5.58e+00 bond pdb=" C THR R 430 " pdb=" O THR R 430 " ideal model delta sigma weight residual 1.231 1.198 0.033 2.00e-02 2.50e+03 2.73e+00 bond pdb=" SD MET R 425 " pdb=" CE MET R 425 " ideal model delta sigma weight residual 1.791 1.753 0.038 2.50e-02 1.60e+03 2.34e+00 bond pdb=" CA CYS R 48 " pdb=" CB CYS R 48 " ideal model delta sigma weight residual 1.530 1.560 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" CB TYR R 421 " pdb=" CG TYR R 421 " ideal model delta sigma weight residual 1.512 1.483 0.029 2.20e-02 2.07e+03 1.74e+00 ... (remaining 17520 not shown) Histogram of bond angle deviations from ideal: 96.44 - 104.04: 82 104.04 - 111.64: 19081 111.64 - 119.24: 4624 119.24 - 126.84: 7576 126.84 - 134.44: 135 Bond angle restraints: 31498 Sorted by residual: angle pdb=" C GLN R 47 " pdb=" N CYS R 48 " pdb=" CA CYS R 48 " ideal model delta sigma weight residual 121.70 114.15 7.55 1.80e+00 3.09e-01 1.76e+01 angle pdb=" C ALA R 347 " pdb=" N ASN R 348 " pdb=" CA ASN R 348 " ideal model delta sigma weight residual 121.70 127.80 -6.10 1.80e+00 3.09e-01 1.15e+01 angle pdb=" C GLU A 360 " pdb=" N ASN A 361 " pdb=" CA ASN A 361 " ideal model delta sigma weight residual 121.70 127.30 -5.60 1.80e+00 3.09e-01 9.68e+00 angle pdb=" C GLU R 317 " pdb=" N LYS R 318 " pdb=" CA LYS R 318 " ideal model delta sigma weight residual 121.70 127.07 -5.37 1.80e+00 3.09e-01 8.90e+00 angle pdb=" CA MET R 414 " pdb=" C MET R 414 " pdb=" N PRO R 415 " ideal model delta sigma weight residual 116.90 121.09 -4.19 1.50e+00 4.44e-01 7.79e+00 ... (remaining 31493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7452 17.93 - 35.86: 559 35.86 - 53.79: 168 53.79 - 71.72: 40 71.72 - 89.65: 8 Dihedral angle restraints: 8227 sinusoidal: 4377 harmonic: 3850 Sorted by residual: dihedral pdb=" CA ASN R 220 " pdb=" C ASN R 220 " pdb=" N TYR R 221 " pdb=" CA TYR R 221 " ideal model delta harmonic sigma weight residual 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA TYR R 421 " pdb=" C TYR R 421 " pdb=" N ILE R 422 " pdb=" CA ILE R 422 " ideal model delta harmonic sigma weight residual 180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 8224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 847 0.032 - 0.065: 346 0.065 - 0.097: 86 0.097 - 0.129: 41 0.129 - 0.161: 8 Chirality restraints: 1328 Sorted by residual: chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE B 123 " pdb=" N ILE B 123 " pdb=" C ILE B 123 " pdb=" CB ILE B 123 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 1325 not shown) Planarity restraints: 2582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 343 " 0.200 9.50e-02 1.11e+02 8.21e-02 5.39e+00 pdb=" NE ARG R 343 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG R 343 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG R 343 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG R 343 " 0.004 2.00e-02 2.50e+03 pdb="HH21 ARG R 343 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 315 " 0.018 2.00e-02 2.50e+03 1.13e-02 3.82e+00 pdb=" CG PHE R 315 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE R 315 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE R 315 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE R 315 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE R 315 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE R 315 " 0.008 2.00e-02 2.50e+03 pdb=" HD1 PHE R 315 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE R 315 " -0.005 2.00e-02 2.50e+03 pdb=" HE1 PHE R 315 " -0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE R 315 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE R 315 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS R 48 " 0.011 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" N GLU R 49 " -0.032 2.00e-02 2.50e+03 pdb=" CA GLU R 49 " 0.008 2.00e-02 2.50e+03 pdb=" H GLU R 49 " 0.013 2.00e-02 2.50e+03 ... (remaining 2579 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 1184 2.08 - 2.71: 26832 2.71 - 3.34: 50263 3.34 - 3.97: 67135 3.97 - 4.60: 98526 Nonbonded interactions: 243940 Sorted by model distance: nonbonded pdb=" O GLN B 75 " pdb=" HG SER B 98 " model vdw 1.452 1.800 nonbonded pdb=" HG1 THR B 29 " pdb=" OE1 GLN B 32 " model vdw 1.459 1.800 nonbonded pdb=" O SER N 30 " pdb="HE22 GLN N 53 " model vdw 1.459 1.800 nonbonded pdb=" O VAL R 326 " pdb=" H GLY R 330 " model vdw 1.497 1.800 nonbonded pdb=" O VAL R 384 " pdb=" HG1 THR R 387 " model vdw 1.533 1.800 ... (remaining 243935 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 56 15.96 2 O 1595 7.97 2 N 1528 6.97 2 C 5549 5.97 2 H 8610 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 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.005 0.078 8915 Z= 0.244 ANGLE : 0.971 7.551 12061 Z= 0.470 CHIRALITY : 0.041 0.161 1328 PLANARITY : 0.005 0.088 1539 DIHEDRAL : 13.845 86.012 3220 MIN NONBONDED DISTANCE : 2.006 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 9.59 RAMACHANDRAN PLOT: OUTLIERS : 0.19 % ALLOWED : 6.26 % FAVORED : 93.55 % ROTAMER: OUTLIERS : 1.28 % ALLOWED : 7.58 % FAVORED : 91.14 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 0.00 % CIS-GENERAL : 0.00 % TWISTED PROLINE : 0.00 % TWISTED GENERAL : 0.00 % RAMA-Z (RAMACHANDRAN PLOT Z-SCORE): INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD |RAMA-Z| < 2. SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY; THEREFORE, THE VALUES ARE NOT RELATED IN A SIMPLE MANNER. WHOLE: -2.89 (0.22), RESIDUES: 1054 HELIX: -1.78 (0.21), RESIDUES: 410 SHEET: -1.87 (0.35), RESIDUES: 192 LOOP : -1.90 (0.26), RESIDUES: 452 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.012 0.001 ARG R 343 TYR 0.017 0.001 TYR R 421 PHE 0.028 0.002 PHE R 315 TRP 0.027 0.002 TRP R 352 HIS 0.005 0.001 HIS R 140 Resolution of map is: 3.2427 Map-model correlation coefficient (CC) CC_mask : 0.7007 weight= None bond: 0.005 angle: 0.97 clash: 9.6 rota: 1.28 rama: f: 93.55 o: 0.19 Z: -2.89 cb: 0.00 shift=0.0000 cc_mask=0.7007 Initial weight estimate from ratio of grad norms: 0.26295850966305356 cycle: 0 start: weight= 0.2630 bond: 0.005 angle: 0.97 clash: 9.6 rota: 1.28 rama: f: 93.55 o: 0.19 Z: -2.89 cb: 0.00 shift=0.0000 cc_mask=0.7007 final: weight= 0.2630 bond: 0.024 angle: 2.90 clash: 33.7 rota: 8.43 rama: f: 81.69 o: 3.89 Z: -6.03 cb: 4.49 shift=0.5388 cc_mask=0.7342 cycle: 1 start: weight= 0.1841 bond: 0.005 angle: 0.97 clash: 9.6 rota: 1.28 rama: f: 93.55 o: 0.19 Z: -2.89 cb: 0.00 shift=0.0000 cc_mask=0.7007 final: weight= 0.1841 bond: 0.019 angle: 2.45 clash: 20.5 rota: 5.12 rama: f: 87.38 o: 1.23 Z: -5.24 cb: 1.95 shift=0.4661 cc_mask=0.7289 cycle: 2 start: weight= 0.1288 bond: 0.005 angle: 0.97 clash: 9.6 rota: 1.28 rama: f: 93.55 o: 0.19 Z: -2.89 cb: 0.00 shift=0.0000 cc_mask=0.7007 final: weight= 0.1288 bond: 0.016 angle: 2.14 clash: 11.1 rota: 3.74 rama: f: 90.99 o: 0.47 Z: -4.47 cb: 0.88 shift=0.3867 cc_mask=0.7235 cycle: 3 start: weight= 0.0644 bond: 0.005 angle: 0.97 clash: 9.6 rota: 1.28 rama: f: 93.55 o: 0.19 Z: -2.89 cb: 0.00 shift=0.0000 cc_mask=0.7007 final: weight= 0.0644 bond: 0.012 angle: 1.80 clash: 4.6 rota: 1.92 rama: f: 94.12 o: 0.28 Z: -3.44 cb: 0.39 shift=0.2916 cc_mask=0.7142 cycle: 4 start: weight= 0.0451 bond: 0.005 angle: 0.97 clash: 9.6 rota: 1.28 rama: f: 93.55 o: 0.19 Z: -2.89 cb: 0.00 shift=0.0000 cc_mask=0.7007 final: weight= 0.0451 bond: 0.011 angle: 1.72 clash: 2.9 rota: 1.71 rama: f: 94.02 o: 0.28 Z: -3.01 cb: 0.20 shift=0.2578 cc_mask=0.7098 cycle: 5 start: weight= 0.0316 bond: 0.005 angle: 0.97 clash: 9.6 rota: 1.28 rama: f: 93.55 o: 0.19 Z: -2.89 cb: 0.00 shift=0.0000 cc_mask=0.7007 final: weight= 0.0316 bond: 0.010 angle: 1.68 clash: 2.8 rota: 1.28 rama: f: 94.59 o: 0.19 Z: -2.71 cb: 0.20 shift=0.2369 cc_mask=0.7064 cycle: 6 start: weight= 0.0158 bond: 0.005 angle: 0.97 clash: 9.6 rota: 1.28 rama: f: 93.55 o: 0.19 Z: -2.89 cb: 0.00 shift=0.0000 cc_mask=0.7007 final: weight= 0.0158 bond: 0.010 angle: 1.65 clash: 2.2 rota: 1.07 rama: f: 94.97 o: 0.19 Z: -2.45 cb: 0.20 shift=0.2207 cc_mask=0.7010 cycle: 7 start: weight= 0.0110 bond: 0.005 angle: 0.97 clash: 9.6 rota: 1.28 rama: f: 93.55 o: 0.19 Z: -2.89 cb: 0.00 shift=0.0000 cc_mask=0.7007 final: weight= 0.0110 bond: 0.010 angle: 1.64 clash: 2.2 rota: 1.07 rama: f: 95.07 o: 0.19 Z: -2.37 cb: 0.10 shift=0.2205 cc_mask=0.6990 cycle: 8 start: weight= 0.0077 bond: 0.005 angle: 0.97 clash: 9.6 rota: 1.28 rama: f: 93.55 o: 0.19 Z: -2.89 cb: 0.00 shift=0.0000 cc_mask=0.7007 final: weight= 0.0077 bond: 0.009 angle: 1.65 clash: 1.9 rota: 1.28 rama: f: 95.16 o: 0.19 Z: -2.41 cb: 0.10 shift=0.2247 cc_mask=0.6974 cycle: 9 start: weight= 0.0039 bond: 0.005 angle: 0.97 clash: 9.6 rota: 1.28 rama: f: 93.55 o: 0.19 Z: -2.89 cb: 0.00 shift=0.0000 cc_mask=0.7007 final: weight= 0.0039 bond: 0.009 angle: 1.64 clash: 2.0 rota: 1.07 rama: f: 95.26 o: 0.19 Z: -2.36 cb: 0.10 shift=0.2099 cc_mask=0.6964 cycle: 10 start: weight= 0.0027 bond: 0.005 angle: 0.97 clash: 9.6 rota: 1.28 rama: f: 93.55 o: 0.19 Z: -2.89 cb: 0.00 shift=0.0000 cc_mask=0.7007 final: weight= 0.0027 bond: 0.009 angle: 1.65 clash: 2.0 rota: 1.07 rama: f: 94.97 o: 0.28 Z: -2.39 cb: 0.10 shift=0.2157 cc_mask=0.6956 cycle: 11 start: weight= 0.0019 bond: 0.005 angle: 0.97 clash: 9.6 rota: 1.28 rama: f: 93.55 o: 0.19 Z: -2.89 cb: 0.00 shift=0.0000 cc_mask=0.7007 final: weight= 0.0019 bond: 0.009 angle: 1.64 clash: 1.8 rota: 1.07 rama: f: 95.16 o: 0.19 Z: -2.39 cb: 0.00 shift=0.2158 cc_mask=0.6953 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.0018948793493301012 start: weight= 0.0019 bond: 0.009 angle: 1.64 clash: 1.8 rota: 1.07 rama: f: 95.16 o: 0.19 Z: -2.39 cb: 0.00 shift=0.0000 cc_mask=0.7007 final: weight= 0.0019 bond: 0.009 angle: 1.64 clash: 1.9 rota: 1.07 rama: f: 94.97 o: 0.19 Z: -2.41 cb: 0.00 shift=0.2242 cc_mask=0.6949 start: weight= 0.0019 bond: 0.009 angle: 1.64 clash: 1.9 rota: 1.07 rama: f: 94.97 o: 0.19 Z: -2.41 cb: 0.00 shift=0.2242 cc_mask=0.6949 final: weight= 0.0019 bond: 0.009 angle: 1.60 clash: 1.4 rota: 1.07 rama: f: 95.83 o: 0.09 Z: -2.18 cb: 0.00 shift=0.3008 cc_mask=0.6904 start: weight= 0.0019 bond: 0.009 angle: 1.60 clash: 1.4 rota: 1.07 rama: f: 95.83 o: 0.09 Z: -2.18 cb: 0.00 shift=0.3008 cc_mask=0.6904 final: weight= 0.0019 bond: 0.009 angle: 1.61 clash: 0.8 rota: 1.39 rama: f: 96.11 o: 0.09 Z: -2.15 cb: 0.00 shift=0.3688 cc_mask=0.6863 start: weight= 0.0019 bond: 0.009 angle: 1.61 clash: 0.8 rota: 1.39 rama: f: 96.11 o: 0.09 Z: -2.15 cb: 0.00 shift=0.3688 cc_mask=0.6863 final: weight= 0.0019 bond: 0.009 angle: 1.60 clash: 0.6 rota: 1.49 rama: f: 96.58 o: 0.09 Z: -2.02 cb: 0.00 shift=0.4160 cc_mask=0.6831 start: weight= 0.0019 bond: 0.009 angle: 1.60 clash: 0.6 rota: 1.49 rama: f: 96.58 o: 0.09 Z: -2.02 cb: 0.00 shift=0.4160 cc_mask=0.6831 final: weight= 0.0019 bond: 0.009 angle: 1.60 clash: 0.6 rota: 1.60 rama: f: 96.49 o: 0.09 Z: -1.93 cb: 0.00 shift=0.4448 cc_mask=0.6808 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.104 8915 Z= 0.484 ANGLE : 1.600 12.346 12061 Z= 0.873 CHIRALITY : 0.121 0.413 1328 PLANARITY : 0.020 0.229 1539 DIHEDRAL : 14.438 119.306 3220 MIN NONBONDED DISTANCE : 2.565 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.64 RAMACHANDRAN PLOT: OUTLIERS : 0.09 % ALLOWED : 3.42 % FAVORED : 96.49 % ROTAMER: OUTLIERS : 1.60 % ALLOWED : 5.76 % FAVORED : 92.64 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 0.00 % CIS-GENERAL : 0.00 % TWISTED PROLINE : 0.00 % TWISTED GENERAL : 0.10 % RAMA-Z (RAMACHANDRAN PLOT Z-SCORE): INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD |RAMA-Z| < 2. SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY; THEREFORE, THE VALUES ARE NOT RELATED IN A SIMPLE MANNER. WHOLE: -1.93 (0.23), RESIDUES: 1054 HELIX: -1.44 (0.20), RESIDUES: 420 SHEET: -1.31 (0.32), RESIDUES: 212 LOOP : -0.80 (0.29), RESIDUES: 422 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.024 0.005 ARG B 304 TYR 0.119 0.017 TYR R 459 PHE 0.078 0.011 PHE R 315 TRP 0.111 0.022 TRP R 352 HIS 0.011 0.002 HIS B 54 Resolution of map is: 3.2427 Map-model correlation coefficient (CC) CC_mask : 0.6808 =============================================================================== Job complete usr+sys time: 2685.31 seconds wall clock time: 34 minutes 29.02 seconds (2069.02 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)