Starting qr.refine on Sun May 19 19:30:58 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7vxz_32189.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7vxz_32189.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/7vxz_32189.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7vxz_32189.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7vxz_32189.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7vxz_32189.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 "1 TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 PHE 213": "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: 14348 Number of models: 1 Model: "" Number of chains: 5 Chain: "0" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 3851 Classifications: {'peptide': 255} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 238} Chain: "1" Number of atoms: 3592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3592 Classifications: {'peptide': 237} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 220} Chain: "2" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 864 Inner-chain residues flagged as termini: ['pdbres="HIS 2 13 "', 'pdbres="ILE 2 25 "'] Classifications: {'peptide': 56} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain breaks: 1 Chain: "3" Number of atoms: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1849 Classifications: {'peptide': 118} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 110} Chain: "4" Number of atoms: 4192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 4192 Classifications: {'peptide': 268} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 248} Time building chain proxies: 1.63, per 1000 atoms: 0.11 Number of scatterers: 14348 At special positions: 0 Unit cell: (128.52, 98.28, 92.88, 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 45 16.00 O 1399 8.00 N 1223 7.00 C 4610 6.00 H 7071 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 3 22 " - pdb=" SG CYS 3 101 " distance=2.04 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: 2.46 Adding C-beta torsion restraints... Number of C-beta restraints generated: 1738 Time building geometry restraints manager: 2.86 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: 7052 1.15 - 1.31: 1218 1.31 - 1.48: 3095 1.48 - 1.65: 3102 1.65 - 1.81: 69 Bond restraints: 14536 Sorted by residual: bond pdb=" C THR 4 163 " pdb=" N ASN 4 164 " ideal model delta sigma weight residual 1.329 1.353 -0.024 1.40e-02 5.10e+03 2.93e+00 bond pdb=" C LEU 3 20 " pdb=" N PRO 3 21 " ideal model delta sigma weight residual 1.341 1.360 -0.019 1.60e-02 3.91e+03 1.35e+00 bond pdb=" C LEU 3 20 " pdb=" O LEU 3 20 " ideal model delta sigma weight residual 1.231 1.251 -0.020 2.00e-02 2.50e+03 9.92e-01 bond pdb=" C ASP 1 227 " pdb=" N THR 1 228 " ideal model delta sigma weight residual 1.329 1.342 -0.013 1.40e-02 5.10e+03 9.09e-01 bond pdb=" C GLN 2 44 " pdb=" N ASP 2 45 " ideal model delta sigma weight residual 1.329 1.342 -0.013 1.40e-02 5.10e+03 8.67e-01 ... (remaining 14531 not shown) Histogram of bond angle deviations from ideal: 100.22 - 106.98: 370 106.98 - 113.74: 17170 113.74 - 120.50: 4438 120.50 - 127.26: 4122 127.26 - 134.02: 106 Bond angle restraints: 26206 Sorted by residual: angle pdb=" CA LEU 0 82 " pdb=" C LEU 0 82 " pdb=" N PRO 0 83 " ideal model delta sigma weight residual 116.90 121.16 -4.26 1.50e+00 4.44e-01 8.06e+00 angle pdb=" CA TRP 4 159 " pdb=" C TRP 4 159 " pdb=" N GLN 4 160 " ideal model delta sigma weight residual 116.20 121.27 -5.07 2.00e+00 2.50e-01 6.44e+00 angle pdb=" CA ILE 0 226 " pdb=" C ILE 0 226 " pdb=" N PRO 0 227 " ideal model delta sigma weight residual 116.90 120.01 -3.11 1.50e+00 4.44e-01 4.29e+00 angle pdb=" C ASN 0 95 " pdb=" N MET 0 96 " pdb=" CA MET 0 96 " ideal model delta sigma weight residual 121.70 118.08 3.62 1.80e+00 3.09e-01 4.05e+00 angle pdb=" C LEU 1 132 " pdb=" N ALA 1 133 " pdb=" CA ALA 1 133 " ideal model delta sigma weight residual 121.70 118.10 3.60 1.80e+00 3.09e-01 4.01e+00 ... (remaining 26201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.22: 6339 15.22 - 30.44: 413 30.44 - 45.67: 148 45.67 - 60.89: 79 60.89 - 76.11: 3 Dihedral angle restraints: 6982 sinusoidal: 3753 harmonic: 3229 Sorted by residual: dihedral pdb=" CA TYR 0 106 " pdb=" C TYR 0 106 " pdb=" N THR 0 107 " pdb=" CA THR 0 107 " 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=" N ASN 4 55 " pdb=" CA ASN 4 55 " pdb=" CB ASN 4 55 " pdb=" CG ASN 4 55 " ideal model delta sinusoidal sigma weight residual -180.00 -120.58 -59.42 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA MET 1 211 " pdb=" CB MET 1 211 " pdb=" CG MET 1 211 " pdb=" SD MET 1 211 " ideal model delta sinusoidal sigma weight residual -60.00 -118.28 58.28 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 6979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 722 0.034 - 0.067: 282 0.067 - 0.101: 65 0.101 - 0.134: 55 0.134 - 0.168: 7 Chirality restraints: 1131 Sorted by residual: chirality pdb=" CA VAL 0 124 " pdb=" N VAL 0 124 " pdb=" C VAL 0 124 " pdb=" CB VAL 0 124 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA ILE 0 243 " pdb=" N ILE 0 243 " pdb=" C ILE 0 243 " pdb=" CB ILE 0 243 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CA ILE 1 190 " pdb=" N ILE 1 190 " pdb=" C ILE 1 190 " pdb=" CB ILE 1 190 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 1128 not shown) Planarity restraints: 2190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL 0 127 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO 0 128 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO 0 128 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO 0 128 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU 2 55 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.22e+00 pdb=" N PRO 2 56 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO 2 56 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO 2 56 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER 0 75 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO 0 76 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO 0 76 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO 0 76 " 0.021 5.00e-02 4.00e+02 ... (remaining 2187 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1003 2.17 - 2.78: 25160 2.78 - 3.38: 36167 3.38 - 3.99: 49707 3.99 - 4.60: 71777 Nonbonded interactions: 183814 Sorted by model distance: nonbonded pdb=" O THR 1 98 " pdb=" H GLU 1 102 " model vdw 1.560 1.800 nonbonded pdb=" O GLU 0 27 " pdb="HD22 ASN 0 198 " model vdw 1.611 1.800 nonbonded pdb=" OD1 ASP 0 44 " pdb="HH21 ARG 4 51 " model vdw 1.616 1.800 nonbonded pdb=" HG1 THR 3 17 " pdb=" O THR 3 89 " model vdw 1.618 1.800 nonbonded pdb=" HG1 THR 0 136 " pdb=" O ASN 0 165 " model vdw 1.646 1.800 ... (remaining 183809 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 45 15.96 2 O 1399 7.97 2 N 1223 6.97 2 C 4610 5.97 2 H 7071 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 0.031 7465 Z= 0.188 ANGLE : 0.936 5.075 10184 Z= 0.432 CHIRALITY : 0.044 0.168 1131 PLANARITY : 0.004 0.038 1323 DIHEDRAL : 10.882 75.509 2691 MIN NONBONDED DISTANCE : 2.424 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.91 RAMACHANDRAN PLOT: OUTLIERS : 0.43 % ALLOWED : 5.10 % FAVORED : 94.47 % ROTAMER: OUTLIERS : 2.47 % ALLOWED : 5.07 % FAVORED : 92.46 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 1.64 % 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: -1.69 (0.24), RESIDUES: 922 HELIX: -2.98 (0.45), RESIDUES: 67 SHEET: 0.18 (0.30), RESIDUES: 270 LOOP : -1.60 (0.22), RESIDUES: 585 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.002 0.000 ARG 4 102 TYR 0.015 0.001 TYR 0 173 PHE 0.008 0.001 PHE 1 120 TRP 0.010 0.001 TRP 0 79 HIS 0.003 0.001 HIS 4 220 Resolution of map is: 3.1950 Map-model correlation coefficient (CC) CC_mask : 0.8407 weight= None bond: 0.004 angle: 0.94 clash: 0.9 rota: 2.47 rama: f: 94.47 o: 0.43 Z: -1.69 cb: 0.00 shift=0.0000 cc_mask=0.8407 Initial weight estimate from ratio of grad norms: 0.38488790082349705 cycle: 0 start: weight= 0.3849 bond: 0.004 angle: 0.94 clash: 0.9 rota: 2.47 rama: f: 94.47 o: 0.43 Z: -1.69 cb: 0.00 shift=0.0000 cc_mask=0.8407 final: weight= 0.3849 bond: 0.022 angle: 2.23 clash: 1.7 rota: 2.97 rama: f: 92.84 o: 0.43 Z: -3.59 cb: 1.04 shift=0.3259 cc_mask=0.8766 cycle: 1 start: weight= 0.2694 bond: 0.004 angle: 0.94 clash: 0.9 rota: 2.47 rama: f: 94.47 o: 0.43 Z: -1.69 cb: 0.00 shift=0.0000 cc_mask=0.8407 final: weight= 0.2694 bond: 0.018 angle: 1.98 clash: 0.9 rota: 2.72 rama: f: 93.82 o: 0.43 Z: -3.20 cb: 0.46 shift=0.3136 cc_mask=0.8740 cycle: 2 start: weight= 0.1886 bond: 0.004 angle: 0.94 clash: 0.9 rota: 2.47 rama: f: 94.47 o: 0.43 Z: -1.69 cb: 0.00 shift=0.0000 cc_mask=0.8407 final: weight= 0.1886 bond: 0.015 angle: 1.83 clash: 0.6 rota: 2.10 rama: f: 94.90 o: 0.33 Z: -2.77 cb: 0.23 shift=0.3103 cc_mask=0.8717 cycle: 3 start: weight= 0.0943 bond: 0.004 angle: 0.94 clash: 0.9 rota: 2.47 rama: f: 94.47 o: 0.43 Z: -1.69 cb: 0.00 shift=0.0000 cc_mask=0.8407 final: weight= 0.0943 bond: 0.011 angle: 1.67 clash: 0.2 rota: 1.36 rama: f: 95.23 o: 0.22 Z: -2.11 cb: 0.12 shift=0.2805 cc_mask=0.8659 cycle: 4 start: weight= 0.0660 bond: 0.004 angle: 0.94 clash: 0.9 rota: 2.47 rama: f: 94.47 o: 0.43 Z: -1.69 cb: 0.00 shift=0.0000 cc_mask=0.8407 final: weight= 0.0660 bond: 0.011 angle: 1.63 clash: 0.2 rota: 1.48 rama: f: 95.55 o: 0.11 Z: -1.90 cb: 0.12 shift=0.2620 cc_mask=0.8623 cycle: 5 start: weight= 0.0462 bond: 0.004 angle: 0.94 clash: 0.9 rota: 2.47 rama: f: 94.47 o: 0.43 Z: -1.69 cb: 0.00 shift=0.0000 cc_mask=0.8407 final: weight= 0.0462 bond: 0.010 angle: 1.60 clash: 0.1 rota: 1.61 rama: f: 95.66 o: 0.11 Z: -1.73 cb: 0.12 shift=0.2461 cc_mask=0.8588 cycle: 6 start: weight= 0.0231 bond: 0.004 angle: 0.94 clash: 0.9 rota: 2.47 rama: f: 94.47 o: 0.43 Z: -1.69 cb: 0.00 shift=0.0000 cc_mask=0.8407 final: weight= 0.0231 bond: 0.010 angle: 1.58 clash: 0.1 rota: 1.48 rama: f: 95.55 o: 0.22 Z: -1.60 cb: 0.00 shift=0.2313 cc_mask=0.8525 cycle: 7 start: weight= 0.0162 bond: 0.004 angle: 0.94 clash: 0.9 rota: 2.47 rama: f: 94.47 o: 0.43 Z: -1.69 cb: 0.00 shift=0.0000 cc_mask=0.8407 final: weight= 0.0162 bond: 0.010 angle: 1.57 clash: 0.1 rota: 1.48 rama: f: 95.66 o: 0.22 Z: -1.55 cb: 0.00 shift=0.2218 cc_mask=0.8499 cycle: 8 start: weight= 0.0113 bond: 0.004 angle: 0.94 clash: 0.9 rota: 2.47 rama: f: 94.47 o: 0.43 Z: -1.69 cb: 0.00 shift=0.0000 cc_mask=0.8407 final: weight= 0.0113 bond: 0.009 angle: 1.57 clash: 0.1 rota: 1.48 rama: f: 95.66 o: 0.22 Z: -1.53 cb: 0.00 shift=0.2202 cc_mask=0.8479 cycle: 9 start: weight= 0.0057 bond: 0.004 angle: 0.94 clash: 0.9 rota: 2.47 rama: f: 94.47 o: 0.43 Z: -1.69 cb: 0.00 shift=0.0000 cc_mask=0.8407 final: weight= 0.0057 bond: 0.009 angle: 1.57 clash: 0.1 rota: 1.48 rama: f: 95.88 o: 0.22 Z: -1.53 cb: 0.00 shift=0.2191 cc_mask=0.8449 cycle: 10 start: weight= 0.0040 bond: 0.004 angle: 0.94 clash: 0.9 rota: 2.47 rama: f: 94.47 o: 0.43 Z: -1.69 cb: 0.00 shift=0.0000 cc_mask=0.8407 final: weight= 0.0040 bond: 0.009 angle: 1.57 clash: 0.1 rota: 1.48 rama: f: 95.88 o: 0.22 Z: -1.52 cb: 0.00 shift=0.2210 cc_mask=0.8440 cycle: 11 start: weight= 0.0028 bond: 0.004 angle: 0.94 clash: 0.9 rota: 2.47 rama: f: 94.47 o: 0.43 Z: -1.69 cb: 0.00 shift=0.0000 cc_mask=0.8407 final: weight= 0.0028 bond: 0.009 angle: 1.57 clash: 0.1 rota: 1.48 rama: f: 95.77 o: 0.22 Z: -1.51 cb: 0.00 shift=0.2195 cc_mask=0.8434 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.0027735026944439964 start: weight= 0.0028 bond: 0.009 angle: 1.57 clash: 0.1 rota: 1.48 rama: f: 95.77 o: 0.22 Z: -1.51 cb: 0.00 shift=0.0000 cc_mask=0.8407 final: weight= 0.0028 bond: 0.009 angle: 1.57 clash: 0.1 rota: 1.48 rama: f: 95.77 o: 0.22 Z: -1.51 cb: 0.00 shift=0.2195 cc_mask=0.8434 start: weight= 0.0028 bond: 0.009 angle: 1.57 clash: 0.1 rota: 1.48 rama: f: 95.77 o: 0.22 Z: -1.51 cb: 0.00 shift=0.2195 cc_mask=0.8434 final: weight= 0.0028 bond: 0.009 angle: 1.53 clash: 0.1 rota: 1.48 rama: f: 95.66 o: 0.11 Z: -1.35 cb: 0.00 shift=0.2915 cc_mask=0.8410 start: weight= 0.0028 bond: 0.009 angle: 1.53 clash: 0.1 rota: 1.48 rama: f: 95.66 o: 0.11 Z: -1.35 cb: 0.00 shift=0.2915 cc_mask=0.8410 final: weight= 0.0028 bond: 0.009 angle: 1.56 clash: 0.1 rota: 1.48 rama: f: 95.77 o: 0.11 Z: -1.46 cb: 0.00 shift=0.3548 cc_mask=0.8365 start: weight= 0.0028 bond: 0.009 angle: 1.56 clash: 0.1 rota: 1.48 rama: f: 95.77 o: 0.11 Z: -1.46 cb: 0.00 shift=0.3548 cc_mask=0.8365 final: weight= 0.0028 bond: 0.009 angle: 1.56 clash: 0.1 rota: 1.48 rama: f: 95.66 o: 0.00 Z: -1.44 cb: 0.00 shift=0.3982 cc_mask=0.8320 start: weight= 0.0028 bond: 0.009 angle: 1.56 clash: 0.1 rota: 1.48 rama: f: 95.66 o: 0.00 Z: -1.44 cb: 0.00 shift=0.3982 cc_mask=0.8320 final: weight= 0.0028 bond: 0.009 angle: 1.57 clash: 0.1 rota: 1.24 rama: f: 95.77 o: 0.00 Z: -1.49 cb: 0.00 shift=0.4373 cc_mask=0.8272 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.033 7465 Z= 0.500 ANGLE : 1.570 9.349 10184 Z= 0.823 CHIRALITY : 0.101 0.352 1131 PLANARITY : 0.015 0.197 1323 DIHEDRAL : 11.785 115.806 2691 MIN NONBONDED DISTANCE : 2.599 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.14 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 4.23 % FAVORED : 95.77 % ROTAMER: OUTLIERS : 1.24 % ALLOWED : 1.85 % FAVORED : 96.91 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 1.64 % 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: -1.49 (0.25), RESIDUES: 922 HELIX: -3.01 (0.48), RESIDUES: 70 SHEET: -0.51 (0.30), RESIDUES: 243 LOOP : -0.94 (0.23), RESIDUES: 609 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.021 0.004 ARG 0 258 TYR 0.099 0.013 TYR 4 217 PHE 0.051 0.009 PHE 4 192 TRP 0.096 0.024 TRP 1 193 HIS 0.005 0.001 HIS 4 139 Resolution of map is: 3.1950 Map-model correlation coefficient (CC) CC_mask : 0.8272 =============================================================================== Job complete usr+sys time: 2316.02 seconds wall clock time: 27 minutes 22.75 seconds (1642.75 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)