Starting qr.refine on Sun May 19 23:11:32 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7un3_26612.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7un3_26612.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/7un3_26612.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7un3_26612.map" model { file = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7un3_26612.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7un3_26612.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 PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1256": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 300": "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: 18922 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1193 Classifications: {'peptide': 73} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "A" Number of atoms: 10424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 10424 Inner-chain residues flagged as termini: ['pdbres="HIS A 83 "', 'pdbres="VAL A 122 "', 'pdbres="TYR A 241 "', 'pdbres="PHE A 260 "', 'pdbres="PHE A 313 "', 'pdbres="VAL A 321 "', 'pdbres="LEU A 339 "', 'pdbres="ASP A 343 "', 'pdbres="PRO A 358 "', 'pdbres="ASP A 542 "', 'pdbres="GLY A 663 "', 'pdbres="GLU A 675 "', 'pdbres="ILE A 710 "', 'pdbres="VAL A 928 "', 'pdbres="THR A1046 "', 'pdbres="ARG A1054 "', 'pdbres="LEU A1152 "', 'pdbres="PRO A1252 "'] Classifications: {'peptide': 649} Modifications used: {'COO': 10, 'NH2': 1, 'NH3': 9} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 611} Chain breaks: 9 Chain: "B" Number of atoms: 3686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3686 Inner-chain residues flagged as termini: ['pdbres="ILE B 121 "', 'pdbres="PRO B 164 "', 'pdbres="VAL B 306 "', 'pdbres="ILE B 319 "'] Classifications: {'peptide': 223} Modifications used: {'COO': 3, 'NH2': 1, 'NH3': 2} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain breaks: 2 Chain: "C" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3619 Inner-chain residues flagged as termini: ['pdbres="ASN C 122 "', 'pdbres="GLY C 166 "', 'pdbres="VAL C 306 "', 'pdbres="ASP C 315 "'] Classifications: {'peptide': 219} Modifications used: {'COO': 3, 'NH3': 3} Link IDs: {'PTRANS': 11, 'TRANS': 207} Chain breaks: 2 Time building chain proxies: 2.08, per 1000 atoms: 0.11 Number of scatterers: 18922 At special positions: 0 Unit cell: (84.975, 114.675, 142.725, 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 41 16.00 O 1738 8.00 N 1605 7.00 C 6056 6.00 H 9482 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: 3.52 Adding C-beta torsion restraints... Number of C-beta restraints generated: 2202 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 9462 1.15 - 1.31: 1597 1.31 - 1.48: 3812 1.48 - 1.65: 4200 1.65 - 1.82: 62 Bond restraints: 19133 Sorted by residual: bond pdb=" C ILE A 195 " pdb=" N TRP A 196 " ideal model delta sigma weight residual 1.329 1.353 -0.024 1.40e-02 5.10e+03 3.01e+00 bond pdb=" N ASN A1030 " pdb=" CA ASN A1030 " ideal model delta sigma weight residual 1.458 1.438 0.020 1.90e-02 2.77e+03 1.12e+00 bond pdb=" C GLN A 219 " pdb=" N ILE A 220 " ideal model delta sigma weight residual 1.329 1.315 0.014 1.40e-02 5.10e+03 1.07e+00 bond pdb=" C THR A 551 " pdb=" N MET A 552 " ideal model delta sigma weight residual 1.329 1.342 -0.013 1.40e-02 5.10e+03 8.95e-01 bond pdb=" C ASP A 207 " pdb=" N CYS A 208 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.40e-02 5.10e+03 6.71e-01 ... (remaining 19128 not shown) Histogram of bond angle deviations from ideal: 100.23 - 106.99: 422 106.99 - 113.74: 22868 113.74 - 120.50: 6186 120.50 - 127.25: 5082 127.25 - 134.01: 112 Bond angle restraints: 34670 Sorted by residual: angle pdb=" C PRO A 149 " pdb=" N ARG A 150 " pdb=" CA ARG A 150 " ideal model delta sigma weight residual 121.70 128.38 -6.68 1.80e+00 3.09e-01 1.38e+01 angle pdb=" CA GLU C 190 " pdb=" C GLU C 190 " pdb=" N PRO C 191 " ideal model delta sigma weight residual 116.90 121.70 -4.80 1.50e+00 4.44e-01 1.02e+01 angle pdb=" CA PHE A1259 " pdb=" C PHE A1259 " pdb=" N PRO A1260 " ideal model delta sigma weight residual 116.90 121.57 -4.67 1.50e+00 4.44e-01 9.68e+00 angle pdb=" C SER A 940 " pdb=" CA SER A 940 " pdb=" CB SER A 940 " ideal model delta sigma weight residual 110.10 115.90 -5.80 1.90e+00 2.77e-01 9.32e+00 angle pdb=" CA GLN C 111 " pdb=" C GLN C 111 " pdb=" N PRO C 112 " ideal model delta sigma weight residual 116.90 121.46 -4.56 1.50e+00 4.44e-01 9.24e+00 ... (remaining 34665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 8160 17.29 - 34.58: 571 34.58 - 51.87: 172 51.87 - 69.16: 46 69.16 - 86.45: 8 Dihedral angle restraints: 8957 sinusoidal: 4897 harmonic: 4060 Sorted by residual: dihedral pdb=" CA PHE B 224 " pdb=" C PHE B 224 " pdb=" N THR B 225 " pdb=" CA THR B 225 " ideal model delta harmonic sigma weight residual -180.00 -163.31 -16.69 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ARG B 333 " pdb=" C ARG B 333 " pdb=" N ILE B 334 " pdb=" CA ILE B 334 " ideal model delta harmonic sigma weight residual -180.00 -163.32 -16.68 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CG LYS A 217 " pdb=" CD LYS A 217 " pdb=" CE LYS A 217 " pdb=" NZ LYS A 217 " ideal model delta sinusoidal sigma weight residual 180.00 124.91 55.09 3 1.50e+01 4.44e-03 9.33e+00 ... (remaining 8954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 924 0.031 - 0.061: 306 0.061 - 0.092: 114 0.092 - 0.123: 81 0.123 - 0.154: 16 Chirality restraints: 1441 Sorted by residual: chirality pdb=" CA ILE A1254 " pdb=" N ILE A1254 " pdb=" C ILE A1254 " pdb=" CB ILE A1254 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA ILE A 660 " pdb=" N ILE A 660 " pdb=" C ILE A 660 " pdb=" CB ILE A 660 " 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 199 " pdb=" N ILE B 199 " pdb=" C ILE B 199 " pdb=" CB ILE B 199 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 1438 not shown) Planarity restraints: 2768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 111 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO B 112 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1256 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.13e+00 pdb=" N PRO A1257 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A1257 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1257 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 190 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO B 191 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 191 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 191 " 0.022 5.00e-02 4.00e+02 ... (remaining 2765 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 1095 2.05 - 2.69: 27749 2.69 - 3.32: 56693 3.32 - 3.96: 73935 3.96 - 4.60: 108567 Nonbonded interactions: 268039 Sorted by model distance: nonbonded pdb=" HH TYR A 643 " pdb=" OE1 GLU A1102 " model vdw 1.412 1.800 nonbonded pdb=" O TYR A 203 " pdb=" H LEU A 339 " model vdw 1.413 1.800 nonbonded pdb=" H GLY A 263 " pdb=" O VAL A 296 " model vdw 1.481 1.800 nonbonded pdb=" OD1 ASN C 226 " pdb=" H ASP C 261 " model vdw 1.487 1.800 nonbonded pdb=" O VAL B 178 " pdb=" H SER B 182 " model vdw 1.502 1.800 ... (remaining 268034 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 41 15.96 2 O 1738 7.97 2 N 1605 6.97 2 C 6056 5.97 2 H 9482 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 : 0.004 0.026 9651 Z= 0.179 ANGLE : 0.941 7.195 13050 Z= 0.440 CHIRALITY : 0.043 0.154 1441 PLANARITY : 0.004 0.046 1682 DIHEDRAL : 12.824 86.452 3630 MIN NONBONDED DISTANCE : 1.791 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 7.31 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 6.46 % FAVORED : 93.54 % ROTAMER: OUTLIERS : 0.09 % ALLOWED : 1.89 % FAVORED : 98.01 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 3.28 % 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: -1.42 (0.24), RESIDUES: 1130 HELIX: 0.05 (0.28), RESIDUES: 308 SHEET: -0.86 (0.32), RESIDUES: 248 LOOP : -1.51 (0.25), RESIDUES: 574 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.003 0.000 ARG D 72 TYR 0.013 0.001 TYR A1100 PHE 0.011 0.001 PHE A 622 TRP 0.008 0.001 TRP B 171 HIS 0.004 0.001 HIS B 328 Resolution of map is: 3.6699 Map-model correlation coefficient (CC) CC_mask : 0.6237 weight= None bond: 0.004 angle: 0.94 clash: 7.3 rota: 0.09 rama: f: 93.54 o: 0.00 Z: -1.42 cb: 0.00 shift=0.0000 cc_mask=0.6237 Initial weight estimate from ratio of grad norms: 0.32770108861144137 cycle: 0 start: weight= 0.3277 bond: 0.004 angle: 0.94 clash: 7.3 rota: 0.09 rama: f: 93.54 o: 0.00 Z: -1.42 cb: 0.00 shift=0.0000 cc_mask=0.6237 final: weight= 0.3277 bond: 0.026 angle: 3.05 clash: 52.6 rota: 6.16 rama: f: 79.03 o: 4.78 Z: -6.24 cb: 6.72 shift=0.6386 cc_mask=0.7205 cycle: 1 start: weight= 0.2294 bond: 0.004 angle: 0.94 clash: 7.3 rota: 0.09 rama: f: 93.54 o: 0.00 Z: -1.42 cb: 0.00 shift=0.0000 cc_mask=0.6237 final: weight= 0.2294 bond: 0.021 angle: 2.58 clash: 32.6 rota: 3.79 rama: f: 82.92 o: 2.48 Z: -5.38 cb: 3.00 shift=0.5604 cc_mask=0.7083 cycle: 2 start: weight= 0.1606 bond: 0.004 angle: 0.94 clash: 7.3 rota: 0.09 rama: f: 93.54 o: 0.00 Z: -1.42 cb: 0.00 shift=0.0000 cc_mask=0.6237 final: weight= 0.1606 bond: 0.017 angle: 2.24 clash: 18.8 rota: 2.37 rama: f: 87.26 o: 1.77 Z: -4.56 cb: 0.82 shift=0.4825 cc_mask=0.6960 cycle: 3 start: weight= 0.0803 bond: 0.004 angle: 0.94 clash: 7.3 rota: 0.09 rama: f: 93.54 o: 0.00 Z: -1.42 cb: 0.00 shift=0.0000 cc_mask=0.6237 final: weight= 0.0803 bond: 0.013 angle: 1.87 clash: 6.7 rota: 0.47 rama: f: 93.36 o: 0.27 Z: -3.26 cb: 0.27 shift=0.3590 cc_mask=0.6725 cycle: 4 start: weight= 0.0562 bond: 0.004 angle: 0.94 clash: 7.3 rota: 0.09 rama: f: 93.54 o: 0.00 Z: -1.42 cb: 0.00 shift=0.0000 cc_mask=0.6237 final: weight= 0.0562 bond: 0.011 angle: 1.77 clash: 3.8 rota: 0.19 rama: f: 94.69 o: 0.27 Z: -2.78 cb: 0.18 shift=0.3122 cc_mask=0.6618 cycle: 5 start: weight= 0.0393 bond: 0.004 angle: 0.94 clash: 7.3 rota: 0.09 rama: f: 93.54 o: 0.00 Z: -1.42 cb: 0.00 shift=0.0000 cc_mask=0.6237 final: weight= 0.0393 bond: 0.010 angle: 1.71 clash: 2.9 rota: 0.09 rama: f: 95.58 o: 0.18 Z: -2.42 cb: 0.09 shift=0.2756 cc_mask=0.6521 cycle: 6 start: weight= 0.0197 bond: 0.004 angle: 0.94 clash: 7.3 rota: 0.09 rama: f: 93.54 o: 0.00 Z: -1.42 cb: 0.00 shift=0.0000 cc_mask=0.6237 final: weight= 0.0197 bond: 0.010 angle: 1.66 clash: 1.3 rota: 0.09 rama: f: 96.19 o: 0.18 Z: -2.05 cb: 0.09 shift=0.2354 cc_mask=0.6367 cycle: 7 start: weight= 0.0138 bond: 0.004 angle: 0.94 clash: 7.3 rota: 0.09 rama: f: 93.54 o: 0.00 Z: -1.42 cb: 0.00 shift=0.0000 cc_mask=0.6237 final: weight= 0.0138 bond: 0.009 angle: 1.65 clash: 1.2 rota: 0.09 rama: f: 96.19 o: 0.09 Z: -1.97 cb: 0.09 shift=0.2334 cc_mask=0.6316 cycle: 8 start: weight= 0.0096 bond: 0.004 angle: 0.94 clash: 7.3 rota: 0.09 rama: f: 93.54 o: 0.00 Z: -1.42 cb: 0.00 shift=0.0000 cc_mask=0.6237 final: weight= 0.0096 bond: 0.009 angle: 1.65 clash: 1.1 rota: 0.09 rama: f: 96.19 o: 0.09 Z: -1.92 cb: 0.09 shift=0.2311 cc_mask=0.6274 cycle: 9 start: weight= 0.0048 bond: 0.004 angle: 0.94 clash: 7.3 rota: 0.09 rama: f: 93.54 o: 0.00 Z: -1.42 cb: 0.00 shift=0.0000 cc_mask=0.6237 final: weight= 0.0048 bond: 0.009 angle: 1.64 clash: 1.1 rota: 0.09 rama: f: 96.28 o: 0.09 Z: -1.85 cb: 0.09 shift=0.2287 cc_mask=0.6220 cycle: 10 start: weight= 0.0034 bond: 0.004 angle: 0.94 clash: 7.3 rota: 0.09 rama: f: 93.54 o: 0.00 Z: -1.42 cb: 0.00 shift=0.0000 cc_mask=0.6237 final: weight= 0.0034 bond: 0.009 angle: 1.65 clash: 1.0 rota: 0.09 rama: f: 96.28 o: 0.09 Z: -1.85 cb: 0.09 shift=0.2300 cc_mask=0.6203 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.003373449220229153 start: weight= 0.0034 bond: 0.009 angle: 1.65 clash: 1.0 rota: 0.09 rama: f: 96.28 o: 0.09 Z: -1.85 cb: 0.09 shift=0.0000 cc_mask=0.6237 final: weight= 0.0034 bond: 0.009 angle: 1.64 clash: 1.0 rota: 0.09 rama: f: 96.37 o: 0.09 Z: -1.84 cb: 0.09 shift=0.2295 cc_mask=0.6203 start: weight= 0.0034 bond: 0.009 angle: 1.64 clash: 1.0 rota: 0.09 rama: f: 96.37 o: 0.09 Z: -1.84 cb: 0.09 shift=0.2295 cc_mask=0.6203 final: weight= 0.0034 bond: 0.009 angle: 1.61 clash: 0.9 rota: 0.38 rama: f: 96.02 o: 0.09 Z: -1.84 cb: 0.09 shift=0.3193 cc_mask=0.6179 start: weight= 0.0034 bond: 0.009 angle: 1.61 clash: 0.9 rota: 0.38 rama: f: 96.02 o: 0.09 Z: -1.84 cb: 0.09 shift=0.3193 cc_mask=0.6179 final: weight= 0.0034 bond: 0.009 angle: 1.63 clash: 0.7 rota: 0.76 rama: f: 96.02 o: 0.18 Z: -2.00 cb: 0.18 shift=0.3764 cc_mask=0.6158 start: weight= 0.0034 bond: 0.009 angle: 1.63 clash: 0.7 rota: 0.76 rama: f: 96.02 o: 0.18 Z: -2.00 cb: 0.18 shift=0.3764 cc_mask=0.6158 final: weight= 0.0034 bond: 0.009 angle: 1.63 clash: 0.7 rota: 0.85 rama: f: 95.84 o: 0.27 Z: -2.03 cb: 0.09 shift=0.4228 cc_mask=0.6149 start: weight= 0.0034 bond: 0.009 angle: 1.63 clash: 0.7 rota: 0.85 rama: f: 95.84 o: 0.27 Z: -2.03 cb: 0.09 shift=0.4228 cc_mask=0.6149 final: weight= 0.0034 bond: 0.009 angle: 1.64 clash: 0.5 rota: 1.04 rama: f: 95.84 o: 0.27 Z: -2.10 cb: 0.09 shift=0.4585 cc_mask=0.6139 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.057 9651 Z= 0.474 ANGLE : 1.636 10.109 13050 Z= 0.864 CHIRALITY : 0.113 0.404 1441 PLANARITY : 0.019 0.258 1682 DIHEDRAL : 14.451 157.028 3630 MIN NONBONDED DISTANCE : 2.554 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.53 RAMACHANDRAN PLOT: OUTLIERS : 0.27 % ALLOWED : 3.89 % FAVORED : 95.84 % ROTAMER: OUTLIERS : 1.04 % ALLOWED : 4.55 % FAVORED : 94.41 % CBETA DEVIATIONS : 0.09 % PEPTIDE PLANE: CIS-PROLINE : 3.28 % 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: -2.10 (0.22), RESIDUES: 1130 HELIX: -1.28 (0.25), RESIDUES: 301 SHEET: -1.83 (0.28), RESIDUES: 249 LOOP : -1.12 (0.24), RESIDUES: 580 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.027 0.005 ARG A1118 TYR 0.141 0.015 TYR A1100 PHE 0.071 0.012 PHE A 929 TRP 0.097 0.026 TRP A1055 HIS 0.011 0.002 HIS A 194 Resolution of map is: 3.6699 Map-model correlation coefficient (CC) CC_mask : 0.6139 =============================================================================== Job complete usr+sys time: 2874.84 seconds wall clock time: 38 minutes 16.47 seconds (2296.47 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)