Starting qr.refine on Sun May 19 18:40:02 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8dl8_27499.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8dl8_27499.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/8dl8_27499.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8dl8_27499.map" model { file = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8dl8_27499.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8dl8_27499.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 "C PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 190": "OD1" <-> "OD2" Residue "C TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 200": "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: 13419 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 6914 Inner-chain residues flagged as termini: ['pdbres="GLY A 238 "', 'pdbres="CYS A 284 "', 'pdbres="PRO A 397 "', 'pdbres="PRO A 451 "'] Classifications: {'peptide': 445} Modifications used: {'COO': 3, 'NH2': 1, 'NH3': 2} Link IDs: {'PTRANS': 11, 'TRANS': 433} Chain breaks: 2 Chain: "C" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3220 Classifications: {'peptide': 213} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Chain: "D" Number of atoms: 3285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3285 Classifications: {'peptide': 219} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 204} Time building chain proxies: 1.54, per 1000 atoms: 0.11 Number of scatterers: 13419 At special positions: 0 Unit cell: (73.44, 76.68, 146.88, 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 42 16.00 O 1269 8.00 N 1096 7.00 C 4311 6.00 H 6701 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 553 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " 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: 2.39 Adding C-beta torsion restraints... Number of C-beta restraints generated: 1612 Time building geometry restraints manager: 2.75 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: 6692 1.14 - 1.31: 1079 1.31 - 1.48: 2839 1.48 - 1.65: 2896 1.65 - 1.82: 65 Bond restraints: 13571 Sorted by residual: bond pdb=" C PHE D 171 " pdb=" N PRO D 172 " ideal model delta sigma weight residual 1.341 1.367 -0.026 1.60e-02 3.91e+03 2.65e+00 bond pdb=" CG PRO D 144 " pdb=" CD PRO D 144 " ideal model delta sigma weight residual 1.503 1.450 0.053 3.40e-02 8.65e+02 2.43e+00 bond pdb=" CB PHE D 171 " pdb=" CG PHE D 171 " ideal model delta sigma weight residual 1.502 1.538 -0.036 2.30e-02 1.89e+03 2.39e+00 bond pdb=" CG PRO D 172 " pdb=" CD PRO D 172 " ideal model delta sigma weight residual 1.503 1.547 -0.044 3.40e-02 8.65e+02 1.67e+00 bond pdb=" CG2 THR D 209 " pdb="HG22 THR D 209 " ideal model delta sigma weight residual 1.090 1.064 0.026 2.00e-02 2.50e+03 1.65e+00 ... (remaining 13566 not shown) Histogram of bond angle deviations from ideal: 95.82 - 103.54: 76 103.54 - 111.25: 15074 111.25 - 118.97: 3530 118.97 - 126.68: 5708 126.68 - 134.40: 120 Bond angle restraints: 24508 Sorted by residual: angle pdb=" CB THR D 142 " pdb=" CG2 THR D 142 " pdb="HG22 THR D 142 " ideal model delta sigma weight residual 110.00 101.72 8.28 3.00e+00 1.11e-01 7.61e+00 angle pdb=" CA ALA A 188 " pdb=" C ALA A 188 " pdb=" N PRO A 189 " ideal model delta sigma weight residual 116.90 120.89 -3.99 1.50e+00 4.44e-01 7.08e+00 angle pdb=" N GLY D 169 " pdb=" CA GLY D 169 " pdb=" C GLY D 169 " ideal model delta sigma weight residual 113.30 105.99 7.31 2.90e+00 1.19e-01 6.35e+00 angle pdb=" CA TYR D 170 " pdb=" CB TYR D 170 " pdb=" CG TYR D 170 " ideal model delta sigma weight residual 113.90 118.38 -4.48 1.80e+00 3.09e-01 6.18e+00 angle pdb=" CA GLU A 290 " pdb=" C GLU A 290 " pdb=" N PRO A 291 " ideal model delta sigma weight residual 116.90 120.60 -3.70 1.50e+00 4.44e-01 6.09e+00 ... (remaining 24503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 5693 17.39 - 34.78: 489 34.78 - 52.17: 196 52.17 - 69.56: 59 69.56 - 86.95: 5 Dihedral angle restraints: 6442 sinusoidal: 3443 harmonic: 2999 Sorted by residual: dihedral pdb=" CA GLY D 169 " pdb=" C GLY D 169 " pdb=" N TYR D 170 " pdb=" CA TYR D 170 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA SER C 194 " pdb=" C SER C 194 " pdb=" N MET C 195 " pdb=" CA MET C 195 " ideal model delta harmonic sigma weight residual 180.00 -159.10 -20.90 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA SER C 228 " pdb=" C SER C 228 " pdb=" N PHE C 229 " pdb=" CA PHE C 229 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 6439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 756 0.036 - 0.071: 236 0.071 - 0.107: 69 0.107 - 0.143: 26 0.143 - 0.179: 3 Chirality restraints: 1090 Sorted by residual: chirality pdb=" CA ILE C 164 " pdb=" N ILE C 164 " pdb=" C ILE C 164 " pdb=" CB ILE C 164 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.98e-01 chirality pdb=" CA PRO D 172 " pdb=" N PRO D 172 " pdb=" C PRO D 172 " pdb=" CB PRO D 172 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CB ILE D 235 " pdb=" CA ILE D 235 " pdb=" CG1 ILE D 235 " pdb=" CG2 ILE D 235 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.23e-01 ... (remaining 1087 not shown) Planarity restraints: 2005 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 143 " -0.042 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO D 144 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 144 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 144 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 516 " 0.039 5.00e-02 4.00e+02 5.90e-02 5.57e+00 pdb=" N PRO A 517 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 517 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 517 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 213 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO D 214 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 214 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 214 " -0.029 5.00e-02 4.00e+02 ... (remaining 2002 not shown) Histogram of nonbonded interaction distances: 1.29 - 1.95: 442 1.95 - 2.61: 14329 2.61 - 3.28: 40764 3.28 - 3.94: 52985 3.94 - 4.60: 78058 Nonbonded interactions: 186578 Sorted by model distance: nonbonded pdb=" O SER C 141 " pdb=" H LEU C 145 " model vdw 1.288 1.800 nonbonded pdb=" HG1 THR C 184 " pdb=" O SER C 194 " model vdw 1.375 1.800 nonbonded pdb=" OG SER C 141 " pdb=" H GLN C 144 " model vdw 1.457 1.800 nonbonded pdb=" O GLY A 368 " pdb=" HG1 THR A 372 " model vdw 1.520 1.800 nonbonded pdb=" O ILE A 354 " pdb=" HG1 THR A 357 " model vdw 1.556 1.800 ... (remaining 186573 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 42 15.96 2 O 1269 7.97 2 N 1096 6.97 2 C 4311 5.97 2 H 6701 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 0.053 6870 Z= 0.231 ANGLE : 0.962 7.308 9354 Z= 0.461 CHIRALITY : 0.041 0.179 1090 PLANARITY : 0.006 0.065 1166 DIHEDRAL : 14.872 86.950 2413 MIN NONBONDED DISTANCE : 1.918 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 5.37 RAMACHANDRAN PLOT: OUTLIERS : 0.12 % ALLOWED : 5.19 % FAVORED : 94.69 % ROTAMER: OUTLIERS : 2.15 % ALLOWED : 19.92 % FAVORED : 77.93 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 3.03 % 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: 0.69 (0.29), RESIDUES: 867 HELIX: 1.66 (0.25), RESIDUES: 394 SHEET: 0.46 (0.38), RESIDUES: 207 LOOP : -1.38 (0.37), RESIDUES: 266 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.003 0.001 ARG C 74 TYR 0.014 0.001 TYR D 170 PHE 0.019 0.002 PHE D 191 TRP 0.015 0.001 TRP D 213 HIS 0.007 0.001 HIS D 224 Resolution of map is: 4.1017 Map-model correlation coefficient (CC) CC_mask : 0.8278 weight= None bond: 0.004 angle: 0.96 clash: 5.4 rota: 2.15 rama: f: 94.69 o: 0.12 Z: 0.69 cb: 0.00 shift=0.0000 cc_mask=0.8278 Initial weight estimate from ratio of grad norms: 0.40536517063509986 cycle: 0 start: weight= 0.4054 bond: 0.004 angle: 0.96 clash: 5.4 rota: 2.15 rama: f: 94.69 o: 0.12 Z: 0.69 cb: 0.00 shift=0.0000 cc_mask=0.8278 final: weight= 0.4054 bond: 0.029 angle: 2.52 clash: 29.8 rota: 4.04 rama: f: 92.39 o: 0.46 Z: -3.98 cb: 1.12 shift=0.4576 cc_mask=0.8698 cycle: 1 start: weight= 0.2838 bond: 0.004 angle: 0.96 clash: 5.4 rota: 2.15 rama: f: 94.69 o: 0.12 Z: 0.69 cb: 0.00 shift=0.0000 cc_mask=0.8278 final: weight= 0.2838 bond: 0.023 angle: 2.16 clash: 17.7 rota: 3.10 rama: f: 95.16 o: 0.23 Z: -3.19 cb: 0.25 shift=0.4089 cc_mask=0.8645 cycle: 2 start: weight= 0.1986 bond: 0.004 angle: 0.96 clash: 5.4 rota: 2.15 rama: f: 94.69 o: 0.12 Z: 0.69 cb: 0.00 shift=0.0000 cc_mask=0.8278 final: weight= 0.1986 bond: 0.019 angle: 1.90 clash: 7.5 rota: 2.69 rama: f: 95.62 o: 0.23 Z: -2.51 cb: 0.37 shift=0.3494 cc_mask=0.8590 cycle: 3 start: weight= 0.0993 bond: 0.004 angle: 0.96 clash: 5.4 rota: 2.15 rama: f: 94.69 o: 0.12 Z: 0.69 cb: 0.00 shift=0.0000 cc_mask=0.8278 final: weight= 0.0993 bond: 0.013 angle: 1.65 clash: 2.6 rota: 1.62 rama: f: 96.08 o: 0.35 Z: -1.46 cb: 0.37 shift=0.3112 cc_mask=0.8498 cycle: 4 start: weight= 0.0695 bond: 0.004 angle: 0.96 clash: 5.4 rota: 2.15 rama: f: 94.69 o: 0.12 Z: 0.69 cb: 0.00 shift=0.0000 cc_mask=0.8278 final: weight= 0.0695 bond: 0.012 angle: 1.59 clash: 1.9 rota: 1.62 rama: f: 96.42 o: 0.23 Z: -1.07 cb: 0.37 shift=0.2773 cc_mask=0.8453 cycle: 5 start: weight= 0.0487 bond: 0.004 angle: 0.96 clash: 5.4 rota: 2.15 rama: f: 94.69 o: 0.12 Z: 0.69 cb: 0.00 shift=0.0000 cc_mask=0.8278 final: weight= 0.0487 bond: 0.011 angle: 1.56 clash: 1.5 rota: 1.35 rama: f: 96.54 o: 0.23 Z: -0.92 cb: 0.50 shift=0.2664 cc_mask=0.8414 cycle: 6 start: weight= 0.0243 bond: 0.004 angle: 0.96 clash: 5.4 rota: 2.15 rama: f: 94.69 o: 0.12 Z: 0.69 cb: 0.00 shift=0.0000 cc_mask=0.8278 final: weight= 0.0243 bond: 0.010 angle: 1.53 clash: 1.0 rota: 1.35 rama: f: 96.77 o: 0.23 Z: -0.76 cb: 0.50 shift=0.2399 cc_mask=0.8355 cycle: 7 start: weight= 0.0170 bond: 0.004 angle: 0.96 clash: 5.4 rota: 2.15 rama: f: 94.69 o: 0.12 Z: 0.69 cb: 0.00 shift=0.0000 cc_mask=0.8278 final: weight= 0.0170 bond: 0.010 angle: 1.51 clash: 1.0 rota: 1.35 rama: f: 96.89 o: 0.23 Z: -0.69 cb: 0.50 shift=0.2313 cc_mask=0.8335 cycle: 8 start: weight= 0.0119 bond: 0.004 angle: 0.96 clash: 5.4 rota: 2.15 rama: f: 94.69 o: 0.12 Z: 0.69 cb: 0.00 shift=0.0000 cc_mask=0.8278 final: weight= 0.0119 bond: 0.009 angle: 1.53 clash: 1.0 rota: 1.21 rama: f: 96.89 o: 0.23 Z: -0.82 cb: 0.50 shift=0.2448 cc_mask=0.8319 cycle: 9 start: weight= 0.0060 bond: 0.004 angle: 0.96 clash: 5.4 rota: 2.15 rama: f: 94.69 o: 0.12 Z: 0.69 cb: 0.00 shift=0.0000 cc_mask=0.8278 final: weight= 0.0060 bond: 0.009 angle: 1.52 clash: 0.8 rota: 1.35 rama: f: 97.00 o: 0.23 Z: -0.75 cb: 0.50 shift=0.2380 cc_mask=0.8300 cycle: 10 start: weight= 0.0042 bond: 0.004 angle: 0.96 clash: 5.4 rota: 2.15 rama: f: 94.69 o: 0.12 Z: 0.69 cb: 0.00 shift=0.0000 cc_mask=0.8278 final: weight= 0.0042 bond: 0.009 angle: 1.51 clash: 0.9 rota: 1.35 rama: f: 96.89 o: 0.23 Z: -0.68 cb: 0.50 shift=0.2289 cc_mask=0.8294 cycle: 11 start: weight= 0.0029 bond: 0.004 angle: 0.96 clash: 5.4 rota: 2.15 rama: f: 94.69 o: 0.12 Z: 0.69 cb: 0.00 shift=0.0000 cc_mask=0.8278 final: weight= 0.0029 bond: 0.009 angle: 1.52 clash: 0.9 rota: 1.21 rama: f: 97.00 o: 0.23 Z: -0.76 cb: 0.50 shift=0.2386 cc_mask=0.8289 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.0029210619263029926 start: weight= 0.0029 bond: 0.009 angle: 1.52 clash: 0.9 rota: 1.21 rama: f: 97.00 o: 0.23 Z: -0.76 cb: 0.50 shift=0.0000 cc_mask=0.8278 final: weight= 0.0029 bond: 0.009 angle: 1.52 clash: 0.9 rota: 1.48 rama: f: 97.12 o: 0.23 Z: -0.74 cb: 0.50 shift=0.2340 cc_mask=0.8290 start: weight= 0.0029 bond: 0.009 angle: 1.52 clash: 0.9 rota: 1.48 rama: f: 97.12 o: 0.23 Z: -0.74 cb: 0.50 shift=0.2340 cc_mask=0.8290 final: weight= 0.0029 bond: 0.009 angle: 1.48 clash: 1.0 rota: 1.21 rama: f: 96.89 o: 0.23 Z: -0.95 cb: 0.50 shift=0.3325 cc_mask=0.8263 start: weight= 0.0029 bond: 0.009 angle: 1.48 clash: 1.0 rota: 1.21 rama: f: 96.89 o: 0.23 Z: -0.95 cb: 0.50 shift=0.3325 cc_mask=0.8263 final: weight= 0.0029 bond: 0.009 angle: 1.50 clash: 0.8 rota: 0.94 rama: f: 97.12 o: 0.23 Z: -1.08 cb: 0.37 shift=0.4007 cc_mask=0.8230 start: weight= 0.0029 bond: 0.009 angle: 1.50 clash: 0.8 rota: 0.94 rama: f: 97.12 o: 0.23 Z: -1.08 cb: 0.37 shift=0.4007 cc_mask=0.8230 final: weight= 0.0029 bond: 0.009 angle: 1.49 clash: 0.7 rota: 0.94 rama: f: 97.23 o: 0.23 Z: -1.10 cb: 0.37 shift=0.4482 cc_mask=0.8199 start: weight= 0.0029 bond: 0.009 angle: 1.49 clash: 0.7 rota: 0.94 rama: f: 97.23 o: 0.23 Z: -1.10 cb: 0.37 shift=0.4482 cc_mask=0.8199 final: weight= 0.0029 bond: 0.009 angle: 1.50 clash: 0.6 rota: 1.08 rama: f: 97.00 o: 0.23 Z: -1.10 cb: 0.37 shift=0.4810 cc_mask=0.8175 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.164 6870 Z= 0.479 ANGLE : 1.500 9.510 9354 Z= 0.783 CHIRALITY : 0.113 0.566 1090 PLANARITY : 0.015 0.178 1166 DIHEDRAL : 13.683 126.452 2413 MIN NONBONDED DISTANCE : 2.599 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.60 RAMACHANDRAN PLOT: OUTLIERS : 0.23 % ALLOWED : 2.77 % FAVORED : 97.00 % ROTAMER: OUTLIERS : 1.08 % ALLOWED : 4.71 % FAVORED : 94.21 % CBETA DEVIATIONS : 0.37 % PEPTIDE PLANE: CIS-PROLINE : 3.03 % 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: -1.10 (0.26), RESIDUES: 867 HELIX: -0.73 (0.21), RESIDUES: 397 SHEET: -0.74 (0.34), RESIDUES: 199 LOOP : -0.28 (0.38), RESIDUES: 271 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.017 0.005 ARG A 40 TYR 0.132 0.015 TYR D 170 PHE 0.056 0.011 PHE C 91 TRP 0.150 0.022 TRP D 179 HIS 0.003 0.001 HIS D 54 Resolution of map is: 4.1017 Map-model correlation coefficient (CC) CC_mask : 0.8175 =============================================================================== Job complete usr+sys time: 2186.76 seconds wall clock time: 25 minutes 18.13 seconds (1518.13 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)