Starting qr.refine on Sun May 19 14:14:26 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8qk3_18455.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8qk3_18455.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/8qk3_18455.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8qk3_18455.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8qk3_18455.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8qk3_18455.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 None 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: 3038 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3038 Classifications: {'peptide': 197} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Time building chain proxies: 0.44, per 1000 atoms: 0.14 Number of scatterers: 3038 At special positions: 0 Unit cell: (54.6, 57.12, 62.16, 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 9 16.00 O 310 8.00 N 258 7.00 C 971 6.00 H 1490 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: 0.57 Adding C-beta torsion restraints... Number of C-beta restraints generated: 376 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.14: 1486 1.14 - 1.31: 262 1.31 - 1.48: 661 1.48 - 1.64: 648 1.64 - 1.81: 14 Bond restraints: 3071 Sorted by residual: bond pdb=" C TYR A 242 " pdb=" N PRO A 243 " ideal model delta sigma weight residual 1.341 1.329 0.012 1.60e-02 3.91e+03 5.30e-01 bond pdb=" C SER A 153 " pdb=" N ASN A 154 " ideal model delta sigma weight residual 1.329 1.338 -0.009 1.40e-02 5.10e+03 3.84e-01 bond pdb=" C PHE A 269 " pdb=" O PHE A 269 " ideal model delta sigma weight residual 1.231 1.243 -0.012 2.00e-02 2.50e+03 3.69e-01 bond pdb=" C SER A 314 " pdb=" N PRO A 315 " ideal model delta sigma weight residual 1.341 1.332 0.009 1.60e-02 3.91e+03 3.38e-01 bond pdb=" C PHE A 269 " pdb=" N PRO A 270 " ideal model delta sigma weight residual 1.341 1.332 0.009 1.60e-02 3.91e+03 3.33e-01 ... (remaining 3066 not shown) Histogram of bond angle deviations from ideal: 100.63 - 107.29: 86 107.29 - 113.94: 3572 113.94 - 120.60: 980 120.60 - 127.26: 852 127.26 - 133.91: 15 Bond angle restraints: 5505 Sorted by residual: angle pdb=" CA PHE A 269 " pdb=" C PHE A 269 " pdb=" N PRO A 270 " ideal model delta sigma weight residual 116.90 119.87 -2.97 1.50e+00 4.44e-01 3.92e+00 angle pdb=" C SER A 153 " pdb=" N ASN A 154 " pdb=" CA ASN A 154 " ideal model delta sigma weight residual 121.70 124.94 -3.24 1.80e+00 3.09e-01 3.23e+00 angle pdb=" C LEU A 277 " pdb=" N ASN A 278 " pdb=" CA ASN A 278 " ideal model delta sigma weight residual 121.70 124.86 -3.16 1.80e+00 3.09e-01 3.09e+00 angle pdb=" N PHE A 172 " pdb=" CA PHE A 172 " pdb=" C PHE A 172 " ideal model delta sigma weight residual 111.00 106.09 4.91 2.80e+00 1.28e-01 3.08e+00 angle pdb=" N THR A 165 " pdb=" CA THR A 165 " pdb=" C THR A 165 " ideal model delta sigma weight residual 111.00 106.09 4.91 2.80e+00 1.28e-01 3.08e+00 ... (remaining 5500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.21: 1378 13.21 - 26.43: 58 26.43 - 39.64: 23 39.64 - 52.86: 10 52.86 - 66.07: 6 Dihedral angle restraints: 1475 sinusoidal: 784 harmonic: 691 Sorted by residual: dihedral pdb=" CA PHE A 172 " pdb=" C PHE A 172 " pdb=" N VAL A 173 " pdb=" CA VAL A 173 " ideal model delta harmonic sigma weight residual -180.00 -164.64 -15.36 0 5.00e+00 4.00e-02 9.43e+00 dihedral pdb=" CA ASN A 154 " pdb=" C ASN A 154 " pdb=" N ASP A 155 " pdb=" CA ASP A 155 " ideal model delta harmonic sigma weight residual 180.00 -164.84 -15.16 0 5.00e+00 4.00e-02 9.19e+00 dihedral pdb=" N ASN A 149 " pdb=" CA ASN A 149 " pdb=" CB ASN A 149 " pdb=" CG ASN A 149 " ideal model delta sinusoidal sigma weight residual -180.00 -134.58 -45.42 3 1.50e+01 4.44e-03 8.17e+00 ... (remaining 1472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 140 0.027 - 0.054: 79 0.054 - 0.081: 13 0.081 - 0.108: 7 0.108 - 0.134: 12 Chirality restraints: 251 Sorted by residual: chirality pdb=" CA ILE A 292 " pdb=" N ILE A 292 " pdb=" C ILE A 292 " pdb=" CB ILE A 292 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE A 255 " pdb=" N ILE A 255 " pdb=" C ILE A 255 " pdb=" CB ILE A 255 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 248 not shown) Planarity restraints: 467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 139 " 0.014 5.00e-02 4.00e+02 2.11e-02 7.13e-01 pdb=" N PRO A 140 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 140 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 140 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 242 " 0.014 5.00e-02 4.00e+02 2.05e-02 6.71e-01 pdb=" N PRO A 243 " -0.035 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 172 " 0.009 2.00e-02 2.50e+03 4.61e-03 6.39e-01 pdb=" CG PHE A 172 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE A 172 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 172 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 172 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 172 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 172 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE A 172 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE A 172 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE A 172 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE A 172 " 0.000 2.00e-02 2.50e+03 pdb=" HZ PHE A 172 " 0.001 2.00e-02 2.50e+03 ... (remaining 464 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.08: 150 2.08 - 2.71: 4628 2.71 - 3.34: 8359 3.34 - 3.97: 11724 3.97 - 4.60: 16850 Nonbonded interactions: 41711 Sorted by model distance: nonbonded pdb=" H ASN A 278 " pdb=" O CYS A 289 " model vdw 1.456 1.800 nonbonded pdb=" H TYR A 260 " pdb=" OG SER A 314 " model vdw 1.552 1.800 nonbonded pdb=" HG SER A 264 " pdb=" OE2 GLU A 303 " model vdw 1.577 1.800 nonbonded pdb=" O TYR A 260 " pdb=" H SER A 314 " model vdw 1.589 1.800 nonbonded pdb=" O PHE A 235 " pdb=" HH TYR A 320 " model vdw 1.593 1.800 ... (remaining 41706 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 9 15.96 2 O 310 7.97 2 N 258 6.97 2 C 971 5.97 2 H 1490 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 : 0.003 0.014 1581 Z= 0.162 ANGLE : 0.935 4.912 2158 Z= 0.430 CHIRALITY : 0.042 0.134 251 PLANARITY : 0.003 0.021 278 DIHEDRAL : 9.849 66.071 559 MIN NONBONDED DISTANCE : 2.188 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 2.64 RAMACHANDRAN PLOT: OUTLIERS : 0.51 % ALLOWED : 4.62 % FAVORED : 94.87 % ROTAMER: OUTLIERS : 0.00 % ALLOWED : 4.00 % FAVORED : 96.00 % 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: -0.91 (0.58), RESIDUES: 195 HELIX: -3.13 (0.81), RESIDUES: 12 SHEET: 0.03 (0.61), RESIDUES: 70 LOOP : -0.68 (0.58), RESIDUES: 113 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.001 0.000 ARG A 291 TYR 0.008 0.001 TYR A 320 PHE 0.013 0.001 PHE A 172 TRP 0.010 0.001 TRP A 296 HIS 0.002 0.001 HIS A 218 Resolution of map is: 3.5437 Map-model correlation coefficient (CC) CC_mask : 0.8301 weight= None bond: 0.003 angle: 0.94 clash: 2.6 rota: 0.00 rama: f: 94.87 o: 0.51 Z: -0.91 cb: 0.00 shift=0.0000 cc_mask=0.8301 Initial weight estimate from ratio of grad norms: 0.5921534183466741 cycle: 0 start: weight= 0.5922 bond: 0.003 angle: 0.94 clash: 2.6 rota: 0.00 rama: f: 94.87 o: 0.51 Z: -0.91 cb: 0.00 shift=0.0000 cc_mask=0.8301 final: weight= 0.5922 bond: 0.029 angle: 2.38 clash: 17.5 rota: 1.71 rama: f: 90.26 o: 1.54 Z: -3.84 cb: 1.06 shift=0.4118 cc_mask=0.8785 cycle: 1 start: weight= 0.4145 bond: 0.003 angle: 0.94 clash: 2.6 rota: 0.00 rama: f: 94.87 o: 0.51 Z: -0.91 cb: 0.00 shift=0.0000 cc_mask=0.8301 final: weight= 0.4145 bond: 0.023 angle: 2.04 clash: 9.6 rota: 0.57 rama: f: 92.31 o: 1.54 Z: -2.83 cb: 0.00 shift=0.3562 cc_mask=0.8716 cycle: 2 start: weight= 0.2902 bond: 0.003 angle: 0.94 clash: 2.6 rota: 0.00 rama: f: 94.87 o: 0.51 Z: -0.91 cb: 0.00 shift=0.0000 cc_mask=0.8301 final: weight= 0.2902 bond: 0.019 angle: 1.83 clash: 5.3 rota: 0.57 rama: f: 94.87 o: 1.54 Z: -2.11 cb: 0.00 shift=0.3102 cc_mask=0.8652 cycle: 3 start: weight= 0.1451 bond: 0.003 angle: 0.94 clash: 2.6 rota: 0.00 rama: f: 94.87 o: 0.51 Z: -0.91 cb: 0.00 shift=0.0000 cc_mask=0.8301 final: weight= 0.1451 bond: 0.014 angle: 1.62 clash: 3.3 rota: 0.57 rama: f: 96.41 o: 1.03 Z: -0.83 cb: 0.00 shift=0.2474 cc_mask=0.8531 cycle: 4 start: weight= 0.1016 bond: 0.003 angle: 0.94 clash: 2.6 rota: 0.00 rama: f: 94.87 o: 0.51 Z: -0.91 cb: 0.00 shift=0.0000 cc_mask=0.8301 final: weight= 0.1016 bond: 0.012 angle: 1.58 clash: 1.3 rota: 0.00 rama: f: 96.92 o: 1.03 Z: -0.57 cb: 0.00 shift=0.2257 cc_mask=0.8476 cycle: 5 start: weight= 0.0711 bond: 0.003 angle: 0.94 clash: 2.6 rota: 0.00 rama: f: 94.87 o: 0.51 Z: -0.91 cb: 0.00 shift=0.0000 cc_mask=0.8301 final: weight= 0.0711 bond: 0.011 angle: 1.56 clash: 1.0 rota: 0.00 rama: f: 96.92 o: 1.03 Z: -0.48 cb: 0.00 shift=0.2160 cc_mask=0.8432 cycle: 6 start: weight= 0.0355 bond: 0.003 angle: 0.94 clash: 2.6 rota: 0.00 rama: f: 94.87 o: 0.51 Z: -0.91 cb: 0.00 shift=0.0000 cc_mask=0.8301 final: weight= 0.0355 bond: 0.010 angle: 1.55 clash: 0.3 rota: 0.00 rama: f: 96.92 o: 1.03 Z: -0.53 cb: 0.00 shift=0.2091 cc_mask=0.8369 cycle: 7 start: weight= 0.0249 bond: 0.003 angle: 0.94 clash: 2.6 rota: 0.00 rama: f: 94.87 o: 0.51 Z: -0.91 cb: 0.00 shift=0.0000 cc_mask=0.8301 final: weight= 0.0249 bond: 0.010 angle: 1.55 clash: 0.3 rota: 0.00 rama: f: 96.92 o: 1.03 Z: -0.54 cb: 0.00 shift=0.2046 cc_mask=0.8348 cycle: 8 start: weight= 0.0174 bond: 0.003 angle: 0.94 clash: 2.6 rota: 0.00 rama: f: 94.87 o: 0.51 Z: -0.91 cb: 0.00 shift=0.0000 cc_mask=0.8301 final: weight= 0.0174 bond: 0.010 angle: 1.55 clash: 0.3 rota: 0.00 rama: f: 97.44 o: 1.03 Z: -0.56 cb: 0.00 shift=0.2032 cc_mask=0.8331 cycle: 9 start: weight= 0.0087 bond: 0.003 angle: 0.94 clash: 2.6 rota: 0.00 rama: f: 94.87 o: 0.51 Z: -0.91 cb: 0.00 shift=0.0000 cc_mask=0.8301 final: weight= 0.0087 bond: 0.009 angle: 1.55 clash: 0.3 rota: 0.00 rama: f: 97.44 o: 0.51 Z: -0.57 cb: 0.00 shift=0.2113 cc_mask=0.8309 cycle: 10 start: weight= 0.0061 bond: 0.003 angle: 0.94 clash: 2.6 rota: 0.00 rama: f: 94.87 o: 0.51 Z: -0.91 cb: 0.00 shift=0.0000 cc_mask=0.8301 final: weight= 0.0061 bond: 0.009 angle: 1.55 clash: 0.3 rota: 0.00 rama: f: 97.44 o: 0.51 Z: -0.57 cb: 0.00 shift=0.2075 cc_mask=0.8304 cycle: 11 start: weight= 0.0043 bond: 0.003 angle: 0.94 clash: 2.6 rota: 0.00 rama: f: 94.87 o: 0.51 Z: -0.91 cb: 0.00 shift=0.0000 cc_mask=0.8301 final: weight= 0.0043 bond: 0.009 angle: 1.56 clash: 0.3 rota: 0.00 rama: f: 97.44 o: 0.51 Z: -0.59 cb: 0.00 shift=0.2107 cc_mask=0.8299 cycle: 12 start: weight= 0.0021 bond: 0.003 angle: 0.94 clash: 2.6 rota: 0.00 rama: f: 94.87 o: 0.51 Z: -0.91 cb: 0.00 shift=0.0000 cc_mask=0.8301 final: weight= 0.0021 bond: 0.009 angle: 1.56 clash: 0.3 rota: 0.00 rama: f: 97.44 o: 0.51 Z: -0.59 cb: 0.00 shift=0.2107 cc_mask=0.8294 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.0021335291363989537 start: weight= 0.0021 bond: 0.009 angle: 1.56 clash: 0.3 rota: 0.00 rama: f: 97.44 o: 0.51 Z: -0.59 cb: 0.00 shift=0.0000 cc_mask=0.8301 final: weight= 0.0021 bond: 0.009 angle: 1.55 clash: 0.3 rota: 0.00 rama: f: 97.44 o: 0.51 Z: -0.59 cb: 0.00 shift=0.2098 cc_mask=0.8295 start: weight= 0.0021 bond: 0.009 angle: 1.55 clash: 0.3 rota: 0.00 rama: f: 97.44 o: 0.51 Z: -0.59 cb: 0.00 shift=0.2098 cc_mask=0.8295 final: weight= 0.0021 bond: 0.009 angle: 1.58 clash: 0.0 rota: 0.00 rama: f: 97.44 o: 0.00 Z: -0.48 cb: 0.00 shift=0.2966 cc_mask=0.8256 start: weight= 0.0021 bond: 0.009 angle: 1.58 clash: 0.0 rota: 0.00 rama: f: 97.44 o: 0.00 Z: -0.48 cb: 0.00 shift=0.2966 cc_mask=0.8256 final: weight= 0.0021 bond: 0.009 angle: 1.56 clash: 0.0 rota: 0.00 rama: f: 96.41 o: 0.51 Z: -0.85 cb: 0.00 shift=0.3352 cc_mask=0.8223 start: weight= 0.0021 bond: 0.009 angle: 1.56 clash: 0.0 rota: 0.00 rama: f: 96.41 o: 0.51 Z: -0.85 cb: 0.00 shift=0.3352 cc_mask=0.8223 final: weight= 0.0021 bond: 0.009 angle: 1.57 clash: 0.0 rota: 0.00 rama: f: 96.92 o: 0.51 Z: -0.83 cb: 0.00 shift=0.3603 cc_mask=0.8205 start: weight= 0.0021 bond: 0.009 angle: 1.57 clash: 0.0 rota: 0.00 rama: f: 96.92 o: 0.51 Z: -0.83 cb: 0.00 shift=0.3603 cc_mask=0.8205 final: weight= 0.0021 bond: 0.009 angle: 1.57 clash: 0.0 rota: 0.00 rama: f: 96.41 o: 0.00 Z: -0.88 cb: 0.00 shift=0.4028 cc_mask=0.8166 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.033 1581 Z= 0.488 ANGLE : 1.568 9.328 2158 Z= 0.817 CHIRALITY : 0.110 0.413 251 PLANARITY : 0.011 0.065 278 DIHEDRAL : 10.786 78.136 559 MIN NONBONDED DISTANCE : 2.565 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.00 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 3.59 % FAVORED : 96.41 % ROTAMER: OUTLIERS : 0.00 % ALLOWED : 2.86 % FAVORED : 97.14 % 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: -0.88 (0.58), RESIDUES: 195 HELIX: -1.93 (1.64), RESIDUES: 6 SHEET: -0.89 (0.54), RESIDUES: 72 LOOP : -0.18 (0.60), RESIDUES: 117 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.016 0.003 ARG A 249 TYR 0.051 0.013 TYR A 256 PHE 0.045 0.015 PHE A 244 TRP 0.132 0.029 TRP A 296 HIS 0.001 0.000 HIS A 218 Resolution of map is: 3.5437 Map-model correlation coefficient (CC) CC_mask : 0.8166 =============================================================================== Job complete usr+sys time: 354.08 seconds wall clock time: 6 minutes 41.88 seconds (401.88 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)