Starting qr.refine on Sun May 19 22:34:41 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8g94_29861.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8g94_29861.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 { model { file = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8g94_29861.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8g94_29861.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8g94_29861.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8g94_29861.map" } 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 "B PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 200": "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: 18682 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 4812 Inner-chain residues flagged as termini: ['pdbres="ILE A 37 "', 'pdbres="LYS A 46 "', 'pdbres="LYS A 239 "', 'pdbres="LYS A 250 "'] Classifications: {'peptide': 288} Modifications used: {'COO': 3, 'NH3': 3} Link IDs: {'PTRANS': 6, 'TRANS': 281} Chain breaks: 2 Chain: "B" Number of atoms: 3574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3574 Inner-chain residues flagged as termini: ['pdbres="ILE B 55 "', 'pdbres="THR B 182 "', 'pdbres="ALA B 235 "', 'pdbres="MET B 240 "'] Classifications: {'peptide': 221} Modifications used: {'COO': 3, 'NH3': 3} Link IDs: {'PTRANS': 2, 'TRANS': 218} Chain breaks: 2 Chain: "C" Number of atoms: 5095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 5095 Classifications: {'peptide': 337} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "D" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 902 Classifications: {'peptide': 58} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 3500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3500 Inner-chain residues flagged as termini: ['pdbres="SER E 120 "', 'pdbres="SER E 124 "'] Classifications: {'peptide': 231} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "F" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 392 Classifications: {'peptide': 25} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'TRANS': 24} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 407 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 26} Time building chain proxies: 2.05, per 1000 atoms: 0.11 Number of scatterers: 18682 At special positions: 0 Unit cell: (90.47, 119.52, 129.48, 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 67 16.00 O 1727 8.00 N 1575 7.00 C 5939 6.00 H 9374 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " 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: 3.52 Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.14: 9338 1.14 - 1.31: 1534 1.31 - 1.48: 3851 1.48 - 1.65: 4042 1.65 - 1.82: 96 Bond restraints: 18861 Sorted by residual: bond pdb=" CD LYS G 58 " pdb=" CE LYS G 58 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.33e+00 bond pdb=" CB LYS G 58 " pdb=" CG LYS G 58 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.90e+00 bond pdb=" CB PHE G 62 " pdb=" CG PHE G 62 " ideal model delta sigma weight residual 1.502 1.527 -0.025 2.30e-02 1.89e+03 1.16e+00 bond pdb=" C ARG C 304 " pdb=" N ALA C 305 " ideal model delta sigma weight residual 1.329 1.343 -0.014 1.40e-02 5.10e+03 9.72e-01 bond pdb=" C GLN E 167 " pdb=" N ARG E 168 " ideal model delta sigma weight residual 1.329 1.342 -0.013 1.40e-02 5.10e+03 8.50e-01 ... (remaining 18856 not shown) Histogram of bond angle deviations from ideal: 99.97 - 106.78: 279 106.78 - 113.59: 22369 113.59 - 120.41: 6110 120.41 - 127.22: 5172 127.22 - 134.03: 86 Bond angle restraints: 34016 Sorted by residual: angle pdb=" CA ALA A 270 " pdb=" C ALA A 270 " pdb=" N PRO A 271 " ideal model delta sigma weight residual 116.90 121.51 -4.61 1.50e+00 4.44e-01 9.44e+00 angle pdb=" CA ASP E 74 " pdb=" C ASP E 74 " pdb=" N PRO E 75 " ideal model delta sigma weight residual 116.90 121.30 -4.40 1.50e+00 4.44e-01 8.60e+00 angle pdb=" CA LEU A 177 " pdb=" C LEU A 177 " pdb=" N PRO A 178 " ideal model delta sigma weight residual 116.90 121.29 -4.39 1.50e+00 4.44e-01 8.56e+00 angle pdb=" CA ASN A 307 " pdb=" C ASN A 307 " pdb=" N PRO A 308 " ideal model delta sigma weight residual 116.90 121.05 -4.15 1.50e+00 4.44e-01 7.66e+00 angle pdb=" C ASP C 291 " pdb=" N PHE C 292 " pdb=" CA PHE C 292 " ideal model delta sigma weight residual 121.70 126.35 -4.65 1.80e+00 3.09e-01 6.68e+00 ... (remaining 34011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 8163 16.96 - 33.92: 458 33.92 - 50.88: 175 50.88 - 67.84: 42 67.84 - 84.80: 11 Dihedral angle restraints: 8849 sinusoidal: 4750 harmonic: 4099 Sorted by residual: dihedral pdb=" CA GLN C 75 " pdb=" C GLN C 75 " pdb=" N ASP C 76 " pdb=" CA ASP C 76 " ideal model delta harmonic sigma weight residual 180.00 160.03 19.97 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ARG E 179 " pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 8846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 911 0.029 - 0.058: 400 0.058 - 0.087: 102 0.087 - 0.115: 59 0.115 - 0.144: 14 Chirality restraints: 1486 Sorted by residual: chirality pdb=" CA ILE B 265 " pdb=" N ILE B 265 " pdb=" C ILE B 265 " pdb=" CB ILE B 265 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA VAL C 327 " pdb=" N VAL C 327 " pdb=" C VAL C 327 " pdb=" CB VAL C 327 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA ILE C 58 " pdb=" N ILE C 58 " pdb=" C ILE C 58 " pdb=" CB ILE C 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1483 not shown) Planarity restraints: 2756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 270 " -0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO A 271 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 58 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C LYS G 58 " 0.023 2.00e-02 2.50e+03 pdb=" O LYS G 58 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP G 59 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 281 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO B 282 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO B 282 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 282 " -0.015 5.00e-02 4.00e+02 ... (remaining 2753 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.08: 1332 2.08 - 2.71: 29252 2.71 - 3.34: 54497 3.34 - 3.97: 73983 3.97 - 4.60: 108739 Nonbonded interactions: 267803 Sorted by model distance: nonbonded pdb=" OE2 GLU B 8 " pdb=" HH TYR E 163 " model vdw 1.456 1.800 nonbonded pdb=" O LEU A 174 " pdb=" HH TYR A 202 " model vdw 1.463 1.800 nonbonded pdb=" O LYS B 277 " pdb=" H SER B 281 " model vdw 1.479 1.800 nonbonded pdb=" HG1 THR C 274 " pdb=" O VAL C 315 " model vdw 1.482 1.800 nonbonded pdb=" HZ1 LYS B 210 " pdb=" OD1 ASN C 230 " model vdw 1.498 1.800 ... (remaining 267798 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 67 15.96 2 O 1727 7.97 2 N 1575 6.97 2 C 5939 5.97 2 H 9374 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 0.055 9487 Z= 0.188 ANGLE : 0.944 6.148 12842 Z= 0.452 CHIRALITY : 0.039 0.144 1486 PLANARITY : 0.003 0.034 1608 DIHEDRAL : 12.278 84.300 3417 MIN NONBONDED DISTANCE : 2.077 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 3.27 RAMACHANDRAN PLOT: OUTLIERS : 0.09 % ALLOWED : 5.16 % FAVORED : 94.75 % ROTAMER: OUTLIERS : 0.49 % ALLOWED : 2.45 % FAVORED : 97.06 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 3.70 % 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: -1.85 (0.22), RESIDUES: 1163 HELIX: -0.10 (0.23), RESIDUES: 421 SHEET: -1.69 (0.29), RESIDUES: 271 LOOP : -1.88 (0.25), RESIDUES: 471 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.003 0.000 ARG A 159 TYR 0.010 0.001 TYR E 95 PHE 0.011 0.001 PHE B 189 TRP 0.010 0.001 TRP C 339 HIS 0.002 0.001 HIS C 142 Resolution of map is: 3.2100 Map-model correlation coefficient (CC) CC_mask : 0.8521 weight= None bond: 0.004 angle: 0.94 clash: 3.3 rota: 0.49 rama: f: 94.75 o: 0.09 Z: -1.85 cb: 0.00 shift=0.0000 cc_mask=0.8521 Initial weight estimate from ratio of grad norms: 0.27174346545854094 cycle: 0 start: weight= 0.2717 bond: 0.004 angle: 0.94 clash: 3.3 rota: 0.49 rama: f: 94.75 o: 0.09 Z: -1.85 cb: 0.00 shift=0.0000 cc_mask=0.8521 final: weight= 0.2717 bond: 0.026 angle: 2.30 clash: 8.2 rota: 1.76 rama: f: 92.26 o: 0.69 Z: -3.89 cb: 0.99 shift=0.3098 cc_mask=0.8752 cycle: 1 start: weight= 0.1902 bond: 0.004 angle: 0.94 clash: 3.3 rota: 0.49 rama: f: 94.75 o: 0.09 Z: -1.85 cb: 0.00 shift=0.0000 cc_mask=0.8521 final: weight= 0.1902 bond: 0.020 angle: 2.01 clash: 4.3 rota: 1.17 rama: f: 93.72 o: 0.60 Z: -3.27 cb: 0.63 shift=0.2761 cc_mask=0.8713 cycle: 2 start: weight= 0.1332 bond: 0.004 angle: 0.94 clash: 3.3 rota: 0.49 rama: f: 94.75 o: 0.09 Z: -1.85 cb: 0.00 shift=0.0000 cc_mask=0.8521 final: weight= 0.1332 bond: 0.017 angle: 1.83 clash: 2.8 rota: 0.88 rama: f: 95.10 o: 0.52 Z: -2.71 cb: 0.36 shift=0.2554 cc_mask=0.8676 cycle: 3 start: weight= 0.0666 bond: 0.004 angle: 0.94 clash: 3.3 rota: 0.49 rama: f: 94.75 o: 0.09 Z: -1.85 cb: 0.00 shift=0.0000 cc_mask=0.8521 final: weight= 0.0666 bond: 0.012 angle: 1.64 clash: 1.2 rota: 0.39 rama: f: 96.04 o: 0.43 Z: -1.92 cb: 0.27 shift=0.2242 cc_mask=0.8613 cycle: 4 start: weight= 0.0466 bond: 0.004 angle: 0.94 clash: 3.3 rota: 0.49 rama: f: 94.75 o: 0.09 Z: -1.85 cb: 0.00 shift=0.0000 cc_mask=0.8521 final: weight= 0.0466 bond: 0.011 angle: 1.61 clash: 0.7 rota: 0.39 rama: f: 96.22 o: 0.26 Z: -1.73 cb: 0.09 shift=0.2179 cc_mask=0.8585 cycle: 5 start: weight= 0.0326 bond: 0.004 angle: 0.94 clash: 3.3 rota: 0.49 rama: f: 94.75 o: 0.09 Z: -1.85 cb: 0.00 shift=0.0000 cc_mask=0.8521 final: weight= 0.0326 bond: 0.010 angle: 1.59 clash: 0.7 rota: 0.39 rama: f: 96.39 o: 0.26 Z: -1.65 cb: 0.09 shift=0.2155 cc_mask=0.8561 cycle: 6 start: weight= 0.0163 bond: 0.004 angle: 0.94 clash: 3.3 rota: 0.49 rama: f: 94.75 o: 0.09 Z: -1.85 cb: 0.00 shift=0.0000 cc_mask=0.8521 final: weight= 0.0163 bond: 0.010 angle: 1.57 clash: 0.6 rota: 0.39 rama: f: 96.39 o: 0.17 Z: -1.58 cb: 0.09 shift=0.2144 cc_mask=0.8525 cycle: 7 start: weight= 0.0114 bond: 0.004 angle: 0.94 clash: 3.3 rota: 0.49 rama: f: 94.75 o: 0.09 Z: -1.85 cb: 0.00 shift=0.0000 cc_mask=0.8521 final: weight= 0.0114 bond: 0.009 angle: 1.57 clash: 0.5 rota: 0.39 rama: f: 96.39 o: 0.17 Z: -1.56 cb: 0.09 shift=0.2165 cc_mask=0.8512 cycle: 8 start: weight= 0.0080 bond: 0.004 angle: 0.94 clash: 3.3 rota: 0.49 rama: f: 94.75 o: 0.09 Z: -1.85 cb: 0.00 shift=0.0000 cc_mask=0.8521 final: weight= 0.0080 bond: 0.009 angle: 1.57 clash: 0.5 rota: 0.39 rama: f: 96.47 o: 0.17 Z: -1.56 cb: 0.09 shift=0.2163 cc_mask=0.8501 cycle: 9 start: weight= 0.0040 bond: 0.004 angle: 0.94 clash: 3.3 rota: 0.49 rama: f: 94.75 o: 0.09 Z: -1.85 cb: 0.00 shift=0.0000 cc_mask=0.8521 final: weight= 0.0040 bond: 0.009 angle: 1.57 clash: 0.5 rota: 0.39 rama: f: 96.56 o: 0.17 Z: -1.55 cb: 0.09 shift=0.2175 cc_mask=0.8488 cycle: 10 start: weight= 0.0028 bond: 0.004 angle: 0.94 clash: 3.3 rota: 0.49 rama: f: 94.75 o: 0.09 Z: -1.85 cb: 0.00 shift=0.0000 cc_mask=0.8521 final: weight= 0.0028 bond: 0.009 angle: 1.57 clash: 0.5 rota: 0.29 rama: f: 96.47 o: 0.17 Z: -1.54 cb: 0.09 shift=0.2167 cc_mask=0.8485 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.0027974053596765396 start: weight= 0.0028 bond: 0.009 angle: 1.57 clash: 0.5 rota: 0.29 rama: f: 96.47 o: 0.17 Z: -1.54 cb: 0.09 shift=0.0000 cc_mask=0.8521 final: weight= 0.0028 bond: 0.009 angle: 1.57 clash: 0.5 rota: 0.29 rama: f: 96.56 o: 0.17 Z: -1.54 cb: 0.09 shift=0.2166 cc_mask=0.8485 start: weight= 0.0028 bond: 0.009 angle: 1.57 clash: 0.5 rota: 0.29 rama: f: 96.56 o: 0.17 Z: -1.54 cb: 0.09 shift=0.2166 cc_mask=0.8485 final: weight= 0.0028 bond: 0.009 angle: 1.54 clash: 0.6 rota: 0.29 rama: f: 96.39 o: 0.34 Z: -1.37 cb: 0.09 shift=0.2881 cc_mask=0.8449 start: weight= 0.0028 bond: 0.009 angle: 1.54 clash: 0.6 rota: 0.29 rama: f: 96.39 o: 0.34 Z: -1.37 cb: 0.09 shift=0.2881 cc_mask=0.8449 final: weight= 0.0028 bond: 0.009 angle: 1.55 clash: 0.4 rota: 0.59 rama: f: 96.47 o: 0.17 Z: -1.32 cb: 0.09 shift=0.3356 cc_mask=0.8418 start: weight= 0.0028 bond: 0.009 angle: 1.55 clash: 0.4 rota: 0.59 rama: f: 96.47 o: 0.17 Z: -1.32 cb: 0.09 shift=0.3356 cc_mask=0.8418 final: weight= 0.0028 bond: 0.009 angle: 1.55 clash: 0.3 rota: 0.59 rama: f: 96.22 o: 0.09 Z: -1.41 cb: 0.09 shift=0.3725 cc_mask=0.8393 start: weight= 0.0028 bond: 0.009 angle: 1.55 clash: 0.3 rota: 0.59 rama: f: 96.22 o: 0.09 Z: -1.41 cb: 0.09 shift=0.3725 cc_mask=0.8393 final: weight= 0.0028 bond: 0.009 angle: 1.56 clash: 0.2 rota: 0.59 rama: f: 96.30 o: 0.09 Z: -1.38 cb: 0.09 shift=0.4036 cc_mask=0.8371 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.146 9487 Z= 0.475 ANGLE : 1.558 9.366 12842 Z= 0.828 CHIRALITY : 0.118 0.491 1486 PLANARITY : 0.016 0.152 1608 DIHEDRAL : 12.954 108.204 3417 MIN NONBONDED DISTANCE : 2.590 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.21 RAMACHANDRAN PLOT: OUTLIERS : 0.09 % ALLOWED : 3.61 % FAVORED : 96.30 % ROTAMER: OUTLIERS : 0.59 % ALLOWED : 3.33 % FAVORED : 96.09 % CBETA DEVIATIONS : 0.09 % PEPTIDE PLANE: CIS-PROLINE : 3.70 % 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: -1.38 (0.22), RESIDUES: 1163 HELIX: -1.06 (0.20), RESIDUES: 431 SHEET: -1.03 (0.29), RESIDUES: 290 LOOP : -0.35 (0.29), RESIDUES: 442 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.022 0.005 ARG E 72 TYR 0.140 0.020 TYR E 50 PHE 0.088 0.011 PHE A 210 TRP 0.091 0.021 TRP C 339 HIS 0.009 0.002 HIS A 199 Resolution of map is: 3.2100 Map-model correlation coefficient (CC) CC_mask : 0.8371 =============================================================================== Job complete usr+sys time: 2785.05 seconds wall clock time: 36 minutes 47.93 seconds (2207.93 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)