Starting phenix.real_space_refine on Sat Oct 24 09:15:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tj6_25917/10_2026/7tj6_25917.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tj6_25917/10_2026/7tj6_25917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tj6_25917/10_2026/7tj6_25917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tj6_25917/10_2026/7tj6_25917.map" model { file = "/net/cci-nas-00/data/ceres_data/7tj6_25917/10_2026/7tj6_25917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tj6_25917/10_2026/7tj6_25917.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tj6_25917/10_2026/7tj6_25917.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tj6_25917/10_2026/7tj6_25917.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 28 5.16 5 C 8616 2.51 5 N 2108 2.21 5 O 2252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13008 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3117 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 23, 'TRANS': 367} Chain breaks: 1 Chain: "B" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3117 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 23, 'TRANS': 367} Chain breaks: 1 Chain: "C" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3117 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 23, 'TRANS': 367} Chain breaks: 1 Chain: "D" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3117 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 23, 'TRANS': 367} Chain breaks: 1 Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 101 Unusual residues: {'D21': 5} Classifications: {'RNAv2': 1, 'undetermined': 5} Modifications used: {'rna3p': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'D21:plan-1': 4, 'D21:plan-2': 4, 'D21:plan-3': 5} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 135 Unusual residues: {'D21': 6} Classifications: {'RNAv2': 1, 'undetermined': 6} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'D21:plan-1': 4, 'D21:plan-2': 4, 'D21:plan-3': 5} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 135 Unusual residues: {'D21': 6} Classifications: {'RNAv2': 1, 'undetermined': 6} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'D21:plan-1': 4, 'D21:plan-2': 4, 'D21:plan-3': 5} Unresolved non-hydrogen planarities: 47 Chain: "D" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 169 Unusual residues: {'D21': 7} Classifications: {'RNAv2': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'D21:plan-1': 4, 'D21:plan-2': 4, 'D21:plan-3': 5} Unresolved non-hydrogen planarities: 47 Time building chain proxies: 3.36, per 1000 atoms: 0.26 Number of scatterers: 13008 At special positions: 0 Unit cell: (104.796, 104.796, 116.298, 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 28 16.00 P 4 15.00 O 2252 8.00 N 2108 7.00 C 8616 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.00 Conformation dependent library (CDL) restraints added in 596.8 milliseconds 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2968 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 8 sheets defined 69.1% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 11 through 36 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 48 through 58 removed outlier: 3.565A pdb=" N ILE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 88 Processing helix chain 'A' and resid 90 through 99 removed outlier: 4.227A pdb=" N LEU A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 113 through 127 removed outlier: 4.150A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 159 removed outlier: 3.772A pdb=" N LEU A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 159 " --> pdb=" O TRP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 193 through 224 removed outlier: 4.033A pdb=" N ALA A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 246 Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.566A pdb=" N VAL A 275 " --> pdb=" O GLU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 299 removed outlier: 3.702A pdb=" N ALA A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASP A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 314 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 393 through 404 Processing helix chain 'A' and resid 404 through 418 removed outlier: 4.148A pdb=" N ALA A 408 " --> pdb=" O TYR A 404 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 36 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 48 through 58 removed outlier: 3.566A pdb=" N ILE B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 88 Processing helix chain 'B' and resid 90 through 99 removed outlier: 4.227A pdb=" N LEU B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 113 through 127 removed outlier: 4.150A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B 127 " --> pdb=" O THR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 159 removed outlier: 3.772A pdb=" N LEU B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN B 159 " --> pdb=" O TRP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 193 through 224 removed outlier: 4.033A pdb=" N ALA B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 246 Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.566A pdb=" N VAL B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 299 removed outlier: 3.702A pdb=" N ALA B 286 " --> pdb=" O PRO B 282 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASP B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 314 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 393 through 404 Processing helix chain 'B' and resid 404 through 418 removed outlier: 4.148A pdb=" N ALA B 408 " --> pdb=" O TYR B 404 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 36 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 48 through 58 removed outlier: 3.566A pdb=" N ILE C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 88 Processing helix chain 'C' and resid 90 through 99 removed outlier: 4.227A pdb=" N LEU C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 113 through 127 removed outlier: 4.150A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER C 127 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 159 removed outlier: 3.772A pdb=" N LEU C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN C 159 " --> pdb=" O TRP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 182 Processing helix chain 'C' and resid 193 through 224 removed outlier: 4.033A pdb=" N ALA C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 246 Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 256 through 268 Processing helix chain 'C' and resid 271 through 277 removed outlier: 3.567A pdb=" N VAL C 275 " --> pdb=" O GLU C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 299 removed outlier: 3.702A pdb=" N ALA C 286 " --> pdb=" O PRO C 282 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASP C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 314 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 393 through 404 Processing helix chain 'C' and resid 404 through 418 removed outlier: 4.149A pdb=" N ALA C 408 " --> pdb=" O TYR C 404 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 36 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 48 through 58 removed outlier: 3.565A pdb=" N ILE D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 88 Processing helix chain 'D' and resid 90 through 99 removed outlier: 4.228A pdb=" N LEU D 94 " --> pdb=" O PRO D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 107 through 112 Processing helix chain 'D' and resid 113 through 127 removed outlier: 4.150A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER D 127 " --> pdb=" O THR D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 159 removed outlier: 3.772A pdb=" N LEU D 158 " --> pdb=" O GLY D 154 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN D 159 " --> pdb=" O TRP D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 182 Processing helix chain 'D' and resid 193 through 224 removed outlier: 4.033A pdb=" N ALA D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 246 Processing helix chain 'D' and resid 249 through 254 Processing helix chain 'D' and resid 256 through 268 Processing helix chain 'D' and resid 271 through 277 removed outlier: 3.566A pdb=" N VAL D 275 " --> pdb=" O GLU D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 299 removed outlier: 3.703A pdb=" N ALA D 286 " --> pdb=" O PRO D 282 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASP D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL D 295 " --> pdb=" O ILE D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 314 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 404 through 418 removed outlier: 4.148A pdb=" N ALA D 408 " --> pdb=" O TYR D 404 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 317 through 322 removed outlier: 6.717A pdb=" N ASP A 388 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 6.923A pdb=" N TYR A 327 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA A 383 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 322 removed outlier: 6.717A pdb=" N ASP B 388 " --> pdb=" O ASN B 342 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 329 removed outlier: 6.923A pdb=" N TYR B 327 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA B 383 " --> pdb=" O TYR B 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.716A pdb=" N ASP C 388 " --> pdb=" O ASN C 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 329 removed outlier: 6.924A pdb=" N TYR C 327 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA C 383 " --> pdb=" O TYR C 327 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 317 through 322 removed outlier: 6.716A pdb=" N ASP D 388 " --> pdb=" O ASN D 342 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 329 removed outlier: 6.924A pdb=" N TYR D 327 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA D 383 " --> pdb=" O TYR D 327 " (cutoff:3.500A) 796 hydrogen bonds defined for protein. 2304 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.59 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1944 1.30 - 1.43: 3365 1.43 - 1.56: 7871 1.56 - 1.68: 48 1.68 - 1.81: 48 Bond restraints: 13276 Sorted by residual: bond pdb=" C08 D21 D 508 " pdb=" C09 D21 D 508 " ideal model delta sigma weight residual 1.527 1.304 0.223 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C08 D21 B 507 " pdb=" C09 D21 B 507 " ideal model delta sigma weight residual 1.527 1.304 0.223 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C08 D21 C 507 " pdb=" C09 D21 C 507 " ideal model delta sigma weight residual 1.527 1.305 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C08 D21 A 506 " pdb=" C09 D21 A 506 " ideal model delta sigma weight residual 1.527 1.305 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C09 D21 B 504 " pdb=" C10 D21 B 504 " ideal model delta sigma weight residual 1.526 1.306 0.220 2.00e-02 2.50e+03 1.21e+02 ... (remaining 13271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.61: 17872 8.61 - 17.21: 44 17.21 - 25.82: 0 25.82 - 34.43: 8 34.43 - 43.03: 24 Bond angle restraints: 17948 Sorted by residual: angle pdb=" C09 D21 C 504 " pdb=" C10 D21 C 504 " pdb=" C11 D21 C 504 " ideal model delta sigma weight residual 112.06 155.09 -43.03 3.00e+00 1.11e-01 2.06e+02 angle pdb=" C09 D21 D 505 " pdb=" C10 D21 D 505 " pdb=" C11 D21 D 505 " ideal model delta sigma weight residual 112.06 155.07 -43.01 3.00e+00 1.11e-01 2.06e+02 angle pdb=" C09 D21 B 504 " pdb=" C10 D21 B 504 " pdb=" C11 D21 B 504 " ideal model delta sigma weight residual 112.06 155.05 -42.99 3.00e+00 1.11e-01 2.05e+02 angle pdb=" C09 D21 A 503 " pdb=" C10 D21 A 503 " pdb=" C11 D21 A 503 " ideal model delta sigma weight residual 112.06 155.04 -42.98 3.00e+00 1.11e-01 2.05e+02 angle pdb=" C07 D21 B 507 " pdb=" C08 D21 B 507 " pdb=" C09 D21 B 507 " ideal model delta sigma weight residual 115.05 157.12 -42.07 3.00e+00 1.11e-01 1.97e+02 ... (remaining 17943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 7784 35.43 - 70.86: 300 70.86 - 106.28: 24 106.28 - 141.71: 12 141.71 - 177.14: 24 Dihedral angle restraints: 8144 sinusoidal: 3544 harmonic: 4600 Sorted by residual: dihedral pdb=" C4' CMP B 502 " pdb=" C5' CMP B 502 " pdb=" O5' CMP B 502 " pdb=" P CMP B 502 " ideal model delta sinusoidal sigma weight residual 60.00 -54.92 114.92 1 2.00e+01 2.50e-03 3.41e+01 dihedral pdb=" C4' CMP D 502 " pdb=" C5' CMP D 502 " pdb=" O5' CMP D 502 " pdb=" P CMP D 502 " ideal model delta sinusoidal sigma weight residual 60.00 -54.92 114.92 1 2.00e+01 2.50e-03 3.41e+01 dihedral pdb=" C4' CMP A 501 " pdb=" C5' CMP A 501 " pdb=" O5' CMP A 501 " pdb=" P CMP A 501 " ideal model delta sinusoidal sigma weight residual 60.00 -54.91 114.91 1 2.00e+01 2.50e-03 3.41e+01 ... (remaining 8141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1745 0.096 - 0.191: 283 0.191 - 0.287: 52 0.287 - 0.383: 4 0.383 - 0.479: 8 Chirality restraints: 2092 Sorted by residual: chirality pdb=" C20 D21 A 505 " pdb=" C19 D21 A 505 " pdb=" C21 D21 A 505 " pdb=" O30 D21 A 505 " both_signs ideal model delta sigma weight residual False 2.18 2.65 -0.48 2.00e-01 2.50e+01 5.73e+00 chirality pdb=" C20 D21 C 506 " pdb=" C19 D21 C 506 " pdb=" C21 D21 C 506 " pdb=" O30 D21 C 506 " both_signs ideal model delta sigma weight residual False 2.18 2.65 -0.48 2.00e-01 2.50e+01 5.69e+00 chirality pdb=" C20 D21 D 507 " pdb=" C19 D21 D 507 " pdb=" C21 D21 D 507 " pdb=" O30 D21 D 507 " both_signs ideal model delta sigma weight residual False 2.18 2.65 -0.48 2.00e-01 2.50e+01 5.68e+00 ... (remaining 2089 not shown) Planarity restraints: 2176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 269 " 0.022 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C GLY C 269 " -0.073 2.00e-02 2.50e+03 pdb=" O GLY C 269 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR C 270 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 269 " 0.022 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C GLY D 269 " -0.073 2.00e-02 2.50e+03 pdb=" O GLY D 269 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR D 270 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 269 " 0.021 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" C GLY A 269 " -0.073 2.00e-02 2.50e+03 pdb=" O GLY A 269 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR A 270 " 0.025 2.00e-02 2.50e+03 ... (remaining 2173 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1123 2.74 - 3.28: 13062 3.28 - 3.82: 20941 3.82 - 4.36: 25568 4.36 - 4.90: 42188 Nonbonded interactions: 102882 Sorted by model distance: nonbonded pdb=" OH TYR A 186 " pdb=" OG1 THR B 180 " model vdw 2.198 3.040 nonbonded pdb=" O SER A 220 " pdb=" OG SER A 223 " model vdw 2.302 3.040 nonbonded pdb=" O SER C 220 " pdb=" OG SER C 223 " model vdw 2.302 3.040 nonbonded pdb=" O SER B 220 " pdb=" OG SER B 223 " model vdw 2.302 3.040 nonbonded pdb=" O SER D 220 " pdb=" OG SER D 223 " model vdw 2.303 3.040 ... (remaining 102877 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 418 or resid 503 through 504 or (resid 506 and \ (name C08 or name C09 or name C10 or name C11 or name C12 or name C13)))) selection = (chain 'B' and (resid 10 through 418 or (resid 503 and (name C02 or name C03 or \ name C04 or name C05 or name C06 or name C07 or name C08 or name C09 or name C10 \ or name C11 or name C12 or name C13 or name C14 or name C15)) or (resid 504 and \ (name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C \ 08 or name C09 or name C10 or name C11 or name C12 or name C13)) or (resid 506 a \ nd (name C08 or name C09 or name C10 or name C11 or name C12 or name C13)))) selection = (chain 'C' and (resid 10 through 418 or (resid 503 and (name C02 or name C03 or \ name C04 or name C05 or name C06 or name C07 or name C08 or name C09 or name C10 \ or name C11 or name C12 or name C13 or name C14 or name C15)) or (resid 504 and \ (name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C \ 08 or name C09 or name C10 or name C11 or name C12 or name C13)) or (resid 506 a \ nd (name C08 or name C09 or name C10 or name C11 or name C12 or name C13)))) selection = (chain 'D' and (resid 10 through 418 or (resid 503 and (name C02 or name C03 or \ name C04 or name C05 or name C06 or name C07 or name C08 or name C09 or name C10 \ or name C11 or name C12 or name C13 or name C14 or name C15)) or (resid 504 and \ (name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C \ 08 or name C09 or name C10 or name C11 or name C12 or name C13)) or (resid 506 a \ nd (name C08 or name C09 or name C10 or name C11 or name C12 or name C13)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.080 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.223 13276 Z= 0.574 Angle : 2.160 43.031 17948 Z= 0.962 Chirality : 0.076 0.479 2092 Planarity : 0.008 0.080 2176 Dihedral : 20.809 177.140 5176 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.08 % Allowed : 3.35 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.22), residues: 1548 helix: 1.16 (0.17), residues: 980 sheet: 0.27 (0.47), residues: 88 loop : -0.72 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 418 TYR 0.023 0.003 TYR D 25 PHE 0.026 0.003 PHE A 309 TRP 0.051 0.005 TRP A 18 HIS 0.006 0.002 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.01049 / 0.57 (13276) covalent geometry : angle 2.16016 / 0.96 (17948) hydrogen bonds : bond 0.16793 / 10.93 ( 796) hydrogen bonds : angle 5.89706 / 4.19 ( 2304) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 2 residues processed: 154 average time/residue: 0.6104 time to fit residues: 101.9628 Evaluate side-chains 44 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain D residue 404 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.0870 chunk 149 optimal weight: 2.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 ASN B 217 ASN C 217 ASN D 217 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.085516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.059870 restraints weight = 52722.328| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.11 r_work: 0.3169 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13276 Z= 0.201 Angle : 0.848 11.025 17948 Z= 0.391 Chirality : 0.043 0.180 2092 Planarity : 0.006 0.057 2176 Dihedral : 21.735 167.110 2212 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.46 % Allowed : 9.08 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.22), residues: 1548 helix: 1.47 (0.17), residues: 980 sheet: 0.22 (0.49), residues: 88 loop : -0.92 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 343 TYR 0.023 0.002 TYR C 404 PHE 0.011 0.002 PHE C 242 TRP 0.016 0.002 TRP C 18 HIS 0.003 0.001 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (13276) covalent geometry : angle 0.84812 / 0.39 (17948) hydrogen bonds : bond 0.05143 / 3.34 ( 796) hydrogen bonds : angle 4.63299 / 3.25 ( 2304) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 49 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 137 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8348 (pp) REVERT: B 255 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8703 (ptm160) REVERT: B 343 ARG cc_start: 0.9189 (mtt180) cc_final: 0.8909 (ppt170) REVERT: C 255 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8554 (ptm160) REVERT: C 303 LYS cc_start: 0.9056 (tppt) cc_final: 0.8833 (tppt) REVERT: D 52 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9212 (pp) REVERT: D 54 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8514 (tp) REVERT: D 114 LYS cc_start: 0.9090 (mmmt) cc_final: 0.8888 (mmmt) outliers start: 33 outliers final: 6 residues processed: 76 average time/residue: 0.6674 time to fit residues: 54.9864 Evaluate side-chains 42 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 255 ARG Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 54 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [72, 117, 151, 83, 141, 60, 64, 43, 121, 2, 111] chunk 72 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 151 optimal weight: 20.0000 chunk 83 optimal weight: 0.0870 chunk 141 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 2 optimal weight: 0.0270 chunk 111 optimal weight: 10.0000 overall best weight: 2.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.082829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.056953 restraints weight = 53287.298| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.06 r_work: 0.3107 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13276 Z= 0.208 Angle : 0.763 10.910 17948 Z= 0.352 Chirality : 0.041 0.135 2092 Planarity : 0.005 0.041 2176 Dihedral : 20.926 170.589 2208 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.53 % Allowed : 11.53 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.22), residues: 1548 helix: 1.60 (0.17), residues: 972 sheet: -0.10 (0.51), residues: 96 loop : -1.03 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 343 TYR 0.024 0.002 TYR D 211 PHE 0.009 0.001 PHE C 242 TRP 0.016 0.002 TRP A 18 HIS 0.002 0.001 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 (13276) covalent geometry : angle 0.76274 / 0.35 (17948) hydrogen bonds : bond 0.04775 / 3.11 ( 796) hydrogen bonds : angle 4.47470 / 3.12 ( 2304) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 39 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 LYS cc_start: 0.9032 (tppp) cc_final: 0.8664 (tptp) REVERT: B 215 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8261 (pp) REVERT: C 255 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8602 (ptm160) REVERT: C 303 LYS cc_start: 0.9107 (tppt) cc_final: 0.8900 (tppt) REVERT: D 52 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9257 (pp) REVERT: D 392 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7690 (tm) outliers start: 34 outliers final: 5 residues processed: 66 average time/residue: 0.7243 time to fit residues: 51.6337 Evaluate side-chains 39 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 392 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [42, 71, 137, 133, 3, 101, 5, 37, 12, 31, 61] chunk 42 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 342 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.083374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.057731 restraints weight = 52749.460| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.08 r_work: 0.3130 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13276 Z= 0.141 Angle : 0.711 8.878 17948 Z= 0.324 Chirality : 0.040 0.139 2092 Planarity : 0.005 0.081 2176 Dihedral : 19.564 172.012 2208 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.98 % Allowed : 12.50 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.22), residues: 1548 helix: 1.76 (0.17), residues: 972 sheet: -0.18 (0.51), residues: 96 loop : -1.00 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 343 TYR 0.014 0.001 TYR A 128 PHE 0.011 0.001 PHE D 386 TRP 0.009 0.001 TRP B 18 HIS 0.002 0.000 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (13276) covalent geometry : angle 0.71141 / 0.32 (17948) hydrogen bonds : bond 0.04053 / 2.64 ( 796) hydrogen bonds : angle 4.33557 / 3.01 ( 2304) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 38 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 LYS cc_start: 0.9028 (tppp) cc_final: 0.8670 (tptp) REVERT: B 215 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8294 (pp) REVERT: B 386 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8906 (t80) REVERT: C 52 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9211 (mm) REVERT: C 303 LYS cc_start: 0.9127 (tppt) cc_final: 0.8881 (tppp) REVERT: C 392 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7524 (tm) REVERT: D 52 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9300 (pp) REVERT: D 386 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7949 (t80) REVERT: D 392 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7879 (tm) outliers start: 40 outliers final: 3 residues processed: 72 average time/residue: 0.5297 time to fit residues: 42.1510 Evaluate side-chains 42 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 386 PHE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 392 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [71, 14, 128, 60, 8, 79, 123, 92, 48, 50, 35] chunk 71 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.083571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.058089 restraints weight = 52878.490| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.11 r_work: 0.3141 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13276 Z= 0.128 Angle : 0.722 11.535 17948 Z= 0.324 Chirality : 0.039 0.146 2092 Planarity : 0.004 0.038 2176 Dihedral : 18.299 174.470 2208 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.90 % Allowed : 13.39 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.22), residues: 1548 helix: 1.83 (0.17), residues: 972 sheet: -0.18 (0.51), residues: 96 loop : -1.01 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 343 TYR 0.013 0.001 TYR A 128 PHE 0.013 0.001 PHE C 386 TRP 0.007 0.001 TRP B 18 HIS 0.002 0.000 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (13276) covalent geometry : angle 0.72191 / 0.32 (17948) hydrogen bonds : bond 0.03832 / 2.50 ( 796) hydrogen bonds : angle 4.27770 / 2.97 ( 2304) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 38 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8481 (mm) REVERT: B 114 LYS cc_start: 0.9010 (tppp) cc_final: 0.8705 (tptp) REVERT: B 215 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8282 (pp) REVERT: B 386 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.8848 (t80) REVERT: C 52 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9210 (mm) REVERT: C 255 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8670 (ptm160) REVERT: C 303 LYS cc_start: 0.9094 (tppt) cc_final: 0.8852 (tppp) REVERT: C 392 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7561 (tm) REVERT: D 52 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9294 (pp) REVERT: D 392 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8017 (tm) outliers start: 39 outliers final: 5 residues processed: 67 average time/residue: 0.4821 time to fit residues: 36.1002 Evaluate side-chains 46 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 386 PHE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 392 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [91, 103, 149, 143, 58, 24, 151, 64, 80, 116, 12] chunk 91 optimal weight: 0.0060 chunk 103 optimal weight: 4.9990 chunk 149 optimal weight: 0.1980 chunk 143 optimal weight: 0.0670 chunk 58 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.084412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.059147 restraints weight = 52547.105| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.09 r_work: 0.3168 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13276 Z= 0.119 Angle : 0.719 10.160 17948 Z= 0.320 Chirality : 0.039 0.147 2092 Planarity : 0.004 0.034 2176 Dihedral : 16.877 176.817 2208 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.53 % Allowed : 13.62 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.22), residues: 1548 helix: 1.95 (0.17), residues: 972 sheet: -0.14 (0.52), residues: 96 loop : -1.00 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 330 TYR 0.013 0.001 TYR A 128 PHE 0.013 0.001 PHE C 397 TRP 0.005 0.001 TRP B 18 HIS 0.002 0.000 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (13276) covalent geometry : angle 0.71900 / 0.32 (17948) hydrogen bonds : bond 0.03537 / 2.31 ( 796) hydrogen bonds : angle 4.16300 / 2.89 ( 2304) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 43 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.8027 (p) REVERT: A 334 MET cc_start: 0.9208 (mmp) cc_final: 0.8359 (tmt) REVERT: B 114 LYS cc_start: 0.9032 (tppp) cc_final: 0.8639 (tptp) REVERT: B 215 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8167 (pp) REVERT: B 386 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8925 (t80) REVERT: C 52 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9214 (mm) REVERT: C 215 ILE cc_start: 0.8307 (mm) cc_final: 0.7943 (pp) REVERT: C 255 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8621 (ptm160) REVERT: C 303 LYS cc_start: 0.9116 (tppt) cc_final: 0.8904 (tppp) REVERT: C 392 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7626 (tm) REVERT: D 52 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9314 (pp) REVERT: D 215 ILE cc_start: 0.8334 (mm) cc_final: 0.7963 (pp) REVERT: D 392 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7655 (tm) outliers start: 34 outliers final: 5 residues processed: 73 average time/residue: 0.5104 time to fit residues: 41.4122 Evaluate side-chains 48 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 386 PHE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 392 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [64, 110, 115, 101, 68, 84, 150, 14, 45, 120, 55] chunk 64 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 68 optimal weight: 0.0570 chunk 84 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 55 optimal weight: 0.0770 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.084520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.059137 restraints weight = 52535.673| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.11 r_work: 0.3167 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13276 Z= 0.118 Angle : 0.720 10.899 17948 Z= 0.320 Chirality : 0.039 0.145 2092 Planarity : 0.004 0.030 2176 Dihedral : 16.125 178.996 2208 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.23 % Allowed : 14.88 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.22), residues: 1548 helix: 2.01 (0.17), residues: 972 sheet: -0.10 (0.52), residues: 96 loop : -0.96 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 377 TYR 0.029 0.001 TYR A 26 PHE 0.014 0.001 PHE C 397 TRP 0.004 0.000 TRP B 18 HIS 0.002 0.000 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (13276) covalent geometry : angle 0.72004 / 0.32 (17948) hydrogen bonds : bond 0.03480 / 2.29 ( 796) hydrogen bonds : angle 4.12079 / 2.87 ( 2304) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 35 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8310 (OUTLIER) cc_final: 0.8057 (p) REVERT: A 334 MET cc_start: 0.9214 (mmp) cc_final: 0.8372 (tmt) REVERT: A 386 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7447 (t80) REVERT: B 114 LYS cc_start: 0.8835 (tppp) cc_final: 0.8440 (tptp) REVERT: B 215 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8162 (pp) REVERT: B 334 MET cc_start: 0.9030 (mmp) cc_final: 0.8462 (ppp) REVERT: C 52 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9224 (mm) REVERT: C 215 ILE cc_start: 0.8297 (mm) cc_final: 0.7937 (pp) REVERT: C 255 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8653 (ptm160) REVERT: C 303 LYS cc_start: 0.9104 (tppt) cc_final: 0.8903 (tppp) REVERT: C 392 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7606 (tm) REVERT: D 52 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9300 (pp) REVERT: D 215 ILE cc_start: 0.8332 (mm) cc_final: 0.7960 (pp) REVERT: D 386 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7926 (t80) REVERT: D 392 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7605 (tm) outliers start: 30 outliers final: 5 residues processed: 62 average time/residue: 0.5425 time to fit residues: 37.4438 Evaluate side-chains 47 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 392 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [37, 65, 105, 69, 54, 126, 115, 133, 42, 117, 96] chunk 37 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 105 optimal weight: 0.0980 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.083941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.058431 restraints weight = 52127.009| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.07 r_work: 0.3147 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13276 Z= 0.127 Angle : 0.728 13.508 17948 Z= 0.322 Chirality : 0.039 0.180 2092 Planarity : 0.004 0.030 2176 Dihedral : 15.695 179.748 2208 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.93 % Allowed : 15.10 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.22), residues: 1548 helix: 2.00 (0.17), residues: 972 sheet: -0.10 (0.52), residues: 96 loop : -0.97 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 255 TYR 0.011 0.001 TYR A 128 PHE 0.023 0.001 PHE B 386 TRP 0.005 0.001 TRP B 18 HIS 0.001 0.000 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (13276) covalent geometry : angle 0.72807 / 0.32 (17948) hydrogen bonds : bond 0.03550 / 2.33 ( 796) hydrogen bonds : angle 4.08785 / 2.85 ( 2304) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 36 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8327 (OUTLIER) cc_final: 0.8042 (p) REVERT: A 334 MET cc_start: 0.9193 (mmp) cc_final: 0.8397 (tmt) REVERT: B 215 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8215 (pp) REVERT: B 334 MET cc_start: 0.8971 (mmp) cc_final: 0.8417 (tmt) REVERT: C 52 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9225 (mm) REVERT: C 215 ILE cc_start: 0.8313 (mm) cc_final: 0.7926 (pp) REVERT: C 255 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8673 (ptm160) REVERT: C 303 LYS cc_start: 0.9013 (tppt) cc_final: 0.8800 (tppp) REVERT: C 392 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7485 (tm) REVERT: D 215 ILE cc_start: 0.8349 (mm) cc_final: 0.7950 (pp) outliers start: 26 outliers final: 4 residues processed: 60 average time/residue: 0.4940 time to fit residues: 33.1815 Evaluate side-chains 42 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 285 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [42, 140, 137, 103, 68, 1, 138, 57, 24, 47, 134] chunk 42 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 138 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 134 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 342 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.084019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.058470 restraints weight = 52463.667| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.10 r_work: 0.3151 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13276 Z= 0.122 Angle : 0.750 15.469 17948 Z= 0.327 Chirality : 0.039 0.195 2092 Planarity : 0.004 0.029 2176 Dihedral : 15.296 178.308 2208 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.26 % Allowed : 15.85 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.22), residues: 1548 helix: 2.01 (0.17), residues: 972 sheet: -0.06 (0.52), residues: 96 loop : -0.97 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 255 TYR 0.010 0.001 TYR A 128 PHE 0.018 0.001 PHE B 386 TRP 0.005 0.001 TRP B 18 HIS 0.002 0.000 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (13276) covalent geometry : angle 0.74970 / 0.33 (17948) hydrogen bonds : bond 0.03477 / 2.28 ( 796) hydrogen bonds : angle 4.06656 / 2.84 ( 2304) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.8047 (p) REVERT: A 114 LYS cc_start: 0.8767 (tptp) cc_final: 0.8446 (tptp) REVERT: A 334 MET cc_start: 0.9197 (mmp) cc_final: 0.8420 (tmt) REVERT: B 22 VAL cc_start: 0.8315 (OUTLIER) cc_final: 0.8029 (p) REVERT: B 114 LYS cc_start: 0.8846 (tppp) cc_final: 0.8402 (tptp) REVERT: B 215 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8205 (pp) REVERT: B 334 MET cc_start: 0.9069 (mmp) cc_final: 0.8511 (tmt) REVERT: C 52 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9245 (mm) REVERT: C 215 ILE cc_start: 0.8288 (mm) cc_final: 0.7911 (pp) REVERT: C 255 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8674 (ptm160) REVERT: C 303 LYS cc_start: 0.9047 (tppt) cc_final: 0.8839 (tppp) REVERT: C 392 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7602 (tm) REVERT: D 215 ILE cc_start: 0.8329 (mm) cc_final: 0.7932 (pp) outliers start: 17 outliers final: 3 residues processed: 57 average time/residue: 0.5915 time to fit residues: 37.0503 Evaluate side-chains 43 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [124, 110, 31, 96, 94, 50, 69, 7, 53, 73, 61] chunk 124 optimal weight: 0.0980 chunk 110 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 69 optimal weight: 0.0470 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.084440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.059041 restraints weight = 52757.465| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.10 r_work: 0.3166 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13276 Z= 0.118 Angle : 0.765 12.623 17948 Z= 0.334 Chirality : 0.040 0.238 2092 Planarity : 0.004 0.028 2176 Dihedral : 15.041 176.265 2208 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.19 % Allowed : 16.07 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.22), residues: 1548 helix: 2.06 (0.17), residues: 972 sheet: -0.02 (0.52), residues: 96 loop : -0.92 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 255 TYR 0.011 0.001 TYR A 128 PHE 0.017 0.001 PHE A 386 TRP 0.003 0.000 TRP D 18 HIS 0.001 0.000 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (13276) covalent geometry : angle 0.76492 / 0.33 (17948) hydrogen bonds : bond 0.03360 / 2.19 ( 796) hydrogen bonds : angle 4.06113 / 2.83 ( 2304) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8384 (OUTLIER) cc_final: 0.8095 (p) REVERT: A 114 LYS cc_start: 0.8756 (tptp) cc_final: 0.8436 (tptp) REVERT: A 334 MET cc_start: 0.9097 (mmp) cc_final: 0.8422 (tmt) REVERT: A 386 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.7501 (t80) REVERT: B 22 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.8019 (p) REVERT: B 114 LYS cc_start: 0.8821 (tppp) cc_final: 0.8382 (tptp) REVERT: B 215 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8142 (pp) REVERT: B 334 MET cc_start: 0.9046 (mmp) cc_final: 0.8499 (tmt) REVERT: C 52 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9244 (mm) REVERT: C 215 ILE cc_start: 0.8249 (mm) cc_final: 0.7931 (pp) REVERT: C 255 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8652 (ptm160) REVERT: C 392 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7644 (tm) REVERT: D 215 ILE cc_start: 0.8305 (mm) cc_final: 0.7912 (pp) outliers start: 16 outliers final: 3 residues processed: 51 average time/residue: 0.6218 time to fit residues: 34.6238 Evaluate side-chains 45 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [47, 146, 69, 83, 44, 9, 129, 98, 6, 120, 12] chunk 47 optimal weight: 0.2980 chunk 146 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 83 optimal weight: 0.3980 chunk 44 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.083581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.057856 restraints weight = 52502.307| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.08 r_work: 0.3136 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13276 Z= 0.137 Angle : 0.766 12.404 17948 Z= 0.338 Chirality : 0.040 0.246 2092 Planarity : 0.004 0.031 2176 Dihedral : 15.084 173.533 2208 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.12 % Allowed : 16.15 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.22), residues: 1548 helix: 1.97 (0.17), residues: 996 sheet: -0.08 (0.52), residues: 96 loop : -1.11 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 255 TYR 0.011 0.001 TYR D 262 PHE 0.016 0.001 PHE A 386 TRP 0.007 0.001 TRP B 18 HIS 0.002 0.000 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (13276) covalent geometry : angle 0.76590 / 0.34 (17948) hydrogen bonds : bond 0.03549 / 2.32 ( 796) hydrogen bonds : angle 4.08636 / 2.86 ( 2304) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4247.01 seconds wall clock time: 73 minutes 5.07 seconds (4385.07 seconds total)