Starting phenix.real_space_refine on Tue Dec 31 09:29:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cbz_45429/12_2024/9cbz_45429.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cbz_45429/12_2024/9cbz_45429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cbz_45429/12_2024/9cbz_45429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cbz_45429/12_2024/9cbz_45429.map" model { file = "/net/cci-nas-00/data/ceres_data/9cbz_45429/12_2024/9cbz_45429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cbz_45429/12_2024/9cbz_45429.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 10088 2.51 5 N 2576 2.21 5 O 2664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15424 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3828 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 14, 'TRANS': 458} Chain breaks: 1 Chain: "C" Number of atoms: 3828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3828 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 14, 'TRANS': 458} Chain breaks: 1 Chain: "D" Number of atoms: 3828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3828 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 14, 'TRANS': 458} Chain breaks: 1 Chain: "A" Number of atoms: 3828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3828 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 14, 'TRANS': 458} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.81, per 1000 atoms: 0.64 Number of scatterers: 15424 At special positions: 0 Unit cell: (109.032, 109.032, 109.032, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 2664 8.00 N 2576 7.00 C 10088 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN B 230 " " NAG F 1 " - " ASN C 230 " " NAG G 1 " - " ASN D 230 " " NAG H 1 " - " ASN A 230 " Time building additional restraints: 4.17 Conformation dependent library (CDL) restraints added in 2.2 seconds 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3576 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 8 sheets defined 67.0% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'B' and resid 41 through 49 Processing helix chain 'B' and resid 51 through 60 Processing helix chain 'B' and resid 63 through 106 removed outlier: 3.943A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 138 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 176 through 179 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 295 through 338 removed outlier: 3.517A pdb=" N PHE B 301 " --> pdb=" O PHE B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 351 Processing helix chain 'B' and resid 352 through 377 Processing helix chain 'B' and resid 382 through 401 removed outlier: 3.725A pdb=" N VAL B 401 " --> pdb=" O VAL B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 406 Processing helix chain 'B' and resid 408 through 411 Processing helix chain 'B' and resid 412 through 447 Proline residue: B 423 - end of helix removed outlier: 3.800A pdb=" N CYS B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL B 434 " --> pdb=" O CYS B 430 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE B 435 " --> pdb=" O CYS B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 455 removed outlier: 4.104A pdb=" N ARG B 455 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 469 removed outlier: 3.564A pdb=" N ASN B 469 " --> pdb=" O PHE B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 482 removed outlier: 3.792A pdb=" N MET B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 486 Processing helix chain 'B' and resid 487 through 507 Processing helix chain 'B' and resid 508 through 524 Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 51 through 60 Processing helix chain 'C' and resid 63 through 106 removed outlier: 3.942A pdb=" N SER C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 138 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 176 through 179 Processing helix chain 'C' and resid 217 through 221 Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 295 through 338 removed outlier: 3.518A pdb=" N PHE C 301 " --> pdb=" O PHE C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 352 through 377 Processing helix chain 'C' and resid 382 through 401 removed outlier: 3.726A pdb=" N VAL C 401 " --> pdb=" O VAL C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 406 Processing helix chain 'C' and resid 408 through 411 Processing helix chain 'C' and resid 412 through 447 Proline residue: C 423 - end of helix removed outlier: 3.800A pdb=" N CYS C 431 " --> pdb=" O ARG C 427 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL C 434 " --> pdb=" O CYS C 430 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE C 435 " --> pdb=" O CYS C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 455 removed outlier: 4.104A pdb=" N ARG C 455 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 469 removed outlier: 3.564A pdb=" N ASN C 469 " --> pdb=" O PHE C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 482 removed outlier: 3.792A pdb=" N MET C 480 " --> pdb=" O THR C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 486 Processing helix chain 'C' and resid 487 through 507 Processing helix chain 'C' and resid 508 through 524 Processing helix chain 'D' and resid 41 through 49 Processing helix chain 'D' and resid 51 through 60 Processing helix chain 'D' and resid 63 through 106 removed outlier: 3.942A pdb=" N SER D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 138 Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 176 through 179 Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 242 through 248 Processing helix chain 'D' and resid 295 through 338 removed outlier: 3.518A pdb=" N PHE D 301 " --> pdb=" O PHE D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 351 Processing helix chain 'D' and resid 352 through 377 Processing helix chain 'D' and resid 382 through 401 removed outlier: 3.725A pdb=" N VAL D 401 " --> pdb=" O VAL D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 408 through 411 Processing helix chain 'D' and resid 412 through 447 Proline residue: D 423 - end of helix removed outlier: 3.800A pdb=" N CYS D 431 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL D 434 " --> pdb=" O CYS D 430 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE D 435 " --> pdb=" O CYS D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 455 removed outlier: 4.104A pdb=" N ARG D 455 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 469 removed outlier: 3.563A pdb=" N ASN D 469 " --> pdb=" O PHE D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 482 removed outlier: 3.792A pdb=" N MET D 480 " --> pdb=" O THR D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 486 Processing helix chain 'D' and resid 487 through 507 Processing helix chain 'D' and resid 508 through 524 Processing helix chain 'A' and resid 41 through 49 Processing helix chain 'A' and resid 51 through 60 Processing helix chain 'A' and resid 63 through 106 removed outlier: 3.942A pdb=" N SER A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 138 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 176 through 179 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 295 through 338 removed outlier: 3.518A pdb=" N PHE A 301 " --> pdb=" O PHE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 352 through 377 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.725A pdb=" N VAL A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 406 Processing helix chain 'A' and resid 408 through 411 Processing helix chain 'A' and resid 412 through 447 Proline residue: A 423 - end of helix removed outlier: 3.800A pdb=" N CYS A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A 434 " --> pdb=" O CYS A 430 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 removed outlier: 4.104A pdb=" N ARG A 455 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 469 removed outlier: 3.564A pdb=" N ASN A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 482 removed outlier: 3.792A pdb=" N MET A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 486 Processing helix chain 'A' and resid 487 through 507 Processing helix chain 'A' and resid 508 through 524 Processing sheet with id=AA1, first strand: chain 'B' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'B' and resid 118 through 119 removed outlier: 6.702A pdb=" N ARG B 168 " --> pdb=" O ILE B 229 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL B 231 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N CYS B 166 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE B 233 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA B 164 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA B 164 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE B 193 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N CYS B 166 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP B 191 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG B 168 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL B 189 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TYR B 170 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ARG B 187 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG B 172 " --> pdb=" O ASP B 185 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 286 through 289 removed outlier: 6.589A pdb=" N HIS B 286 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE C 184 " --> pdb=" O HIS B 286 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER B 288 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG C 172 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG C 187 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR C 170 " --> pdb=" O ARG C 187 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL C 189 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG C 168 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP C 191 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS C 166 " --> pdb=" O ASP C 191 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE C 193 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA C 164 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA C 164 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE C 233 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N CYS C 166 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL C 231 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG C 168 " --> pdb=" O ILE C 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 286 through 289 removed outlier: 6.589A pdb=" N HIS B 286 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE C 184 " --> pdb=" O HIS B 286 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER B 288 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG C 172 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG C 187 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR C 170 " --> pdb=" O ARG C 187 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL C 189 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG C 168 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP C 191 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS C 166 " --> pdb=" O ASP C 191 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE C 193 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA C 164 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA C 164 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE C 233 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N CYS C 166 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL C 231 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG C 168 " --> pdb=" O ILE C 229 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 286 through 289 removed outlier: 6.591A pdb=" N HIS C 286 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE D 184 " --> pdb=" O HIS C 286 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER C 288 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG D 172 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG D 187 " --> pdb=" O TYR D 170 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR D 170 " --> pdb=" O ARG D 187 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL D 189 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG D 168 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASP D 191 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS D 166 " --> pdb=" O ASP D 191 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE D 193 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA D 164 " --> pdb=" O ILE D 193 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA D 164 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE D 233 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N CYS D 166 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL D 231 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG D 168 " --> pdb=" O ILE D 229 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 286 through 289 removed outlier: 6.591A pdb=" N HIS C 286 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE D 184 " --> pdb=" O HIS C 286 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER C 288 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG D 172 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG D 187 " --> pdb=" O TYR D 170 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR D 170 " --> pdb=" O ARG D 187 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL D 189 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG D 168 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASP D 191 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS D 166 " --> pdb=" O ASP D 191 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE D 193 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA D 164 " --> pdb=" O ILE D 193 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA D 164 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE D 233 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N CYS D 166 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL D 231 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG D 168 " --> pdb=" O ILE D 229 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 286 through 289 removed outlier: 6.585A pdb=" N HIS D 286 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE A 184 " --> pdb=" O HIS D 286 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER D 288 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG A 172 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ARG A 187 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR A 170 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL A 189 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG A 168 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASP A 191 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS A 166 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE A 193 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA A 164 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA A 164 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE A 233 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N CYS A 166 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL A 231 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG A 168 " --> pdb=" O ILE A 229 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 286 through 289 removed outlier: 6.585A pdb=" N HIS D 286 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE A 184 " --> pdb=" O HIS D 286 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER D 288 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG A 172 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ARG A 187 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR A 170 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL A 189 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG A 168 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASP A 191 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS A 166 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE A 193 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA A 164 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA A 164 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE A 233 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N CYS A 166 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL A 231 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG A 168 " --> pdb=" O ILE A 229 " (cutoff:3.500A) 1052 hydrogen bonds defined for protein. 2970 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: 5.89 Time building geometry restraints manager: 4.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3516 1.33 - 1.45: 3518 1.45 - 1.57: 8642 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 15808 Sorted by residual: bond pdb=" C VAL D 175 " pdb=" O VAL D 175 " ideal model delta sigma weight residual 1.234 1.210 0.024 9.50e-03 1.11e+04 6.22e+00 bond pdb=" C VAL C 175 " pdb=" O VAL C 175 " ideal model delta sigma weight residual 1.234 1.210 0.024 9.50e-03 1.11e+04 6.22e+00 bond pdb=" C VAL A 175 " pdb=" O VAL A 175 " ideal model delta sigma weight residual 1.234 1.210 0.024 9.50e-03 1.11e+04 6.12e+00 bond pdb=" C VAL B 175 " pdb=" O VAL B 175 " ideal model delta sigma weight residual 1.234 1.210 0.024 9.50e-03 1.11e+04 6.12e+00 bond pdb=" C HIS D 526 " pdb=" N PRO D 527 " ideal model delta sigma weight residual 1.341 1.377 -0.036 1.60e-02 3.91e+03 4.93e+00 ... (remaining 15803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 21229 2.40 - 4.80: 191 4.80 - 7.20: 20 7.20 - 9.60: 4 9.60 - 12.00: 4 Bond angle restraints: 21448 Sorted by residual: angle pdb=" N THR C 417 " pdb=" CA THR C 417 " pdb=" CB THR C 417 " ideal model delta sigma weight residual 110.01 114.97 -4.96 1.45e+00 4.76e-01 1.17e+01 angle pdb=" N THR A 417 " pdb=" CA THR A 417 " pdb=" CB THR A 417 " ideal model delta sigma weight residual 110.01 114.95 -4.94 1.45e+00 4.76e-01 1.16e+01 angle pdb=" N THR D 417 " pdb=" CA THR D 417 " pdb=" CB THR D 417 " ideal model delta sigma weight residual 110.01 114.95 -4.94 1.45e+00 4.76e-01 1.16e+01 angle pdb=" N SER A 343 " pdb=" CA SER A 343 " pdb=" C SER A 343 " ideal model delta sigma weight residual 109.96 115.06 -5.10 1.50e+00 4.44e-01 1.16e+01 angle pdb=" N THR B 417 " pdb=" CA THR B 417 " pdb=" CB THR B 417 " ideal model delta sigma weight residual 110.01 114.94 -4.93 1.45e+00 4.76e-01 1.15e+01 ... (remaining 21443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 8471 17.19 - 34.37: 741 34.37 - 51.56: 92 51.56 - 68.74: 24 68.74 - 85.93: 20 Dihedral angle restraints: 9348 sinusoidal: 3800 harmonic: 5548 Sorted by residual: dihedral pdb=" CG ARG D 151 " pdb=" CD ARG D 151 " pdb=" NE ARG D 151 " pdb=" CZ ARG D 151 " ideal model delta sinusoidal sigma weight residual 90.00 133.93 -43.93 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CG ARG C 151 " pdb=" CD ARG C 151 " pdb=" NE ARG C 151 " pdb=" CZ ARG C 151 " ideal model delta sinusoidal sigma weight residual 90.00 133.92 -43.92 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CG ARG A 151 " pdb=" CD ARG A 151 " pdb=" NE ARG A 151 " pdb=" CZ ARG A 151 " ideal model delta sinusoidal sigma weight residual 90.00 133.92 -43.92 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 9345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2068 0.056 - 0.112: 363 0.112 - 0.168: 33 0.168 - 0.224: 8 0.224 - 0.280: 4 Chirality restraints: 2476 Sorted by residual: chirality pdb=" CA VAL C 289 " pdb=" N VAL C 289 " pdb=" C VAL C 289 " pdb=" CB VAL C 289 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA VAL D 289 " pdb=" N VAL D 289 " pdb=" C VAL D 289 " pdb=" CB VAL D 289 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA VAL A 289 " pdb=" N VAL A 289 " pdb=" C VAL A 289 " pdb=" CB VAL A 289 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 2473 not shown) Planarity restraints: 2640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO C 186 " 0.017 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C PRO C 186 " -0.057 2.00e-02 2.50e+03 pdb=" O PRO C 186 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG C 187 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 186 " 0.017 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C PRO A 186 " -0.057 2.00e-02 2.50e+03 pdb=" O PRO A 186 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG A 187 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 186 " 0.017 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C PRO D 186 " -0.056 2.00e-02 2.50e+03 pdb=" O PRO D 186 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG D 187 " 0.019 2.00e-02 2.50e+03 ... (remaining 2637 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 8 2.15 - 2.84: 4929 2.84 - 3.52: 22206 3.52 - 4.21: 38204 4.21 - 4.90: 67216 Nonbonded interactions: 132563 Sorted by model distance: nonbonded pdb=" CE1 HIS B 174 " pdb=" OD2 ASP B 176 " model vdw 1.462 3.260 nonbonded pdb=" CE1 HIS A 174 " pdb=" OD2 ASP A 176 " model vdw 1.462 3.260 nonbonded pdb=" CE1 HIS D 174 " pdb=" OD2 ASP D 176 " model vdw 1.462 3.260 nonbonded pdb=" CE1 HIS C 174 " pdb=" OD2 ASP C 176 " model vdw 1.462 3.260 nonbonded pdb=" NE2 HIS D 174 " pdb=" OD2 ASP D 176 " model vdw 2.021 3.120 ... (remaining 132558 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.240 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: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 37.560 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.080 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:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5848 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 : 0.005 0.053 15808 Z= 0.318 Angle : 0.643 12.003 21448 Z= 0.357 Chirality : 0.045 0.280 2476 Planarity : 0.004 0.041 2636 Dihedral : 13.202 85.926 5772 Min Nonbonded Distance : 1.462 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: 1.11 (0.19), residues: 1876 helix: 1.50 (0.15), residues: 1128 sheet: 0.03 (0.29), residues: 252 loop : -0.54 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 404 HIS 0.003 0.001 HIS A 103 PHE 0.016 0.002 PHE B 235 TYR 0.015 0.002 TYR A 149 ARG 0.004 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 1.724 Fit side-chains revert: symmetry clash REVERT: B 304 VAL cc_start: 0.7516 (t) cc_final: 0.7163 (t) REVERT: B 331 VAL cc_start: 0.6394 (t) cc_final: 0.6012 (p) REVERT: C 312 SER cc_start: 0.6434 (m) cc_final: 0.6231 (t) REVERT: C 345 TRP cc_start: 0.5350 (t-100) cc_final: 0.4898 (t60) REVERT: A 196 ASP cc_start: 0.6009 (m-30) cc_final: 0.5797 (m-30) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 1.0402 time to fit residues: 422.9536 Evaluate side-chains 204 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 57 optimal weight: 0.0020 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 170 optimal weight: 20.0000 overall best weight: 2.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 ASN B 483 GLN C 352 ASN C 483 GLN C 495 GLN D 124 GLN ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN D 495 GLN A 127 GLN A 483 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.7283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 15808 Z= 0.419 Angle : 0.851 11.792 21448 Z= 0.451 Chirality : 0.050 0.242 2476 Planarity : 0.007 0.083 2636 Dihedral : 6.373 57.748 2252 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.66 % Allowed : 11.82 % 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 (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: 0.60 (0.19), residues: 1876 helix: 0.89 (0.15), residues: 1128 sheet: 0.80 (0.35), residues: 216 loop : -0.69 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP A 404 HIS 0.011 0.002 HIS D 174 PHE 0.029 0.003 PHE D 182 TYR 0.031 0.003 TYR C 149 ARG 0.015 0.001 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 201 time to evaluate : 1.990 Fit side-chains REVERT: B 220 ASN cc_start: 0.6107 (m110) cc_final: 0.5574 (t0) REVERT: B 358 LEU cc_start: 0.7861 (mt) cc_final: 0.7317 (mt) REVERT: B 426 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6947 (mtt) REVERT: C 176 ASP cc_start: 0.6318 (t70) cc_final: 0.6043 (m-30) REVERT: C 278 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8206 (mtpt) REVERT: C 345 TRP cc_start: 0.5570 (t-100) cc_final: 0.5126 (t60) outliers start: 62 outliers final: 16 residues processed: 239 average time/residue: 1.1115 time to fit residues: 299.2088 Evaluate side-chains 139 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 116 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 152 optimal weight: 0.0000 chunk 169 optimal weight: 30.0000 chunk 58 optimal weight: 0.0000 chunk 137 optimal weight: 4.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 HIS C 194 GLN D 127 GLN D 135 GLN D 481 GLN A 286 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.7843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15808 Z= 0.200 Angle : 0.522 6.776 21448 Z= 0.279 Chirality : 0.039 0.152 2476 Planarity : 0.004 0.045 2636 Dihedral : 5.613 58.419 2252 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.42 % Allowed : 14.18 % Favored : 83.39 % 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: 1.26 (0.19), residues: 1876 helix: 1.51 (0.15), residues: 1136 sheet: 0.30 (0.32), residues: 264 loop : -0.33 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 404 HIS 0.004 0.001 HIS C 234 PHE 0.019 0.002 PHE B 333 TYR 0.015 0.001 TYR D 497 ARG 0.006 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 2.009 Fit side-chains REVERT: B 299 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7429 (tm) REVERT: B 426 MET cc_start: 0.7374 (mpm) cc_final: 0.7095 (mtp) REVERT: C 279 THR cc_start: 0.8746 (t) cc_final: 0.8276 (m) REVERT: C 345 TRP cc_start: 0.5384 (t-100) cc_final: 0.4839 (t60) REVERT: D 376 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7096 (mt-10) outliers start: 41 outliers final: 13 residues processed: 155 average time/residue: 0.8992 time to fit residues: 161.6736 Evaluate side-chains 124 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain A residue 314 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 181 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 162 optimal weight: 0.4980 chunk 48 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.8394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15808 Z= 0.166 Angle : 0.499 9.823 21448 Z= 0.264 Chirality : 0.039 0.227 2476 Planarity : 0.004 0.043 2636 Dihedral : 5.306 56.725 2252 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.13 % Allowed : 14.72 % Favored : 83.16 % 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: 1.60 (0.20), residues: 1876 helix: 1.79 (0.15), residues: 1136 sheet: 0.38 (0.31), residues: 264 loop : -0.21 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 491 HIS 0.003 0.001 HIS C 451 PHE 0.024 0.001 PHE B 333 TYR 0.014 0.001 TYR C 218 ARG 0.005 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 1.799 Fit side-chains REVERT: B 299 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7451 (tm) REVERT: B 426 MET cc_start: 0.7516 (mpm) cc_final: 0.7260 (mtt) REVERT: B 508 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.6947 (mmt) REVERT: C 279 THR cc_start: 0.8809 (t) cc_final: 0.8461 (m) REVERT: C 313 PHE cc_start: 0.8557 (t80) cc_final: 0.8172 (t80) REVERT: C 492 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8614 (tp) REVERT: D 247 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8204 (t0) REVERT: D 314 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8087 (mp) REVERT: D 376 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7128 (mt-10) REVERT: A 355 TYR cc_start: 0.8144 (m-10) cc_final: 0.7937 (m-10) REVERT: A 472 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7858 (t70) outliers start: 36 outliers final: 6 residues processed: 143 average time/residue: 1.0353 time to fit residues: 168.7936 Evaluate side-chains 117 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain A residue 472 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.9884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 15808 Z= 0.457 Angle : 0.672 7.986 21448 Z= 0.356 Chirality : 0.046 0.274 2476 Planarity : 0.005 0.044 2636 Dihedral : 6.072 59.764 2252 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.36 % Allowed : 14.66 % Favored : 82.98 % 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: 0.99 (0.19), residues: 1876 helix: 1.37 (0.15), residues: 1132 sheet: -0.10 (0.31), residues: 252 loop : -0.45 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 157 HIS 0.012 0.001 HIS D 409 PHE 0.027 0.003 PHE B 333 TYR 0.018 0.002 TYR D 497 ARG 0.010 0.001 ARG D 338 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 1.853 Fit side-chains revert: symmetry clash REVERT: B 249 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7560 (mt-10) REVERT: B 299 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7823 (tm) REVERT: B 313 PHE cc_start: 0.8829 (t80) cc_final: 0.8473 (t80) REVERT: B 508 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7003 (mmt) REVERT: D 247 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8291 (t0) REVERT: D 338 ARG cc_start: 0.5868 (mtp-110) cc_final: 0.5367 (mtp180) REVERT: D 459 MET cc_start: 0.8783 (ttm) cc_final: 0.8481 (ttp) REVERT: A 50 MET cc_start: 0.8260 (mtm) cc_final: 0.7754 (mtm) REVERT: A 312 SER cc_start: 0.8676 (t) cc_final: 0.8432 (m) REVERT: A 472 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7606 (t0) outliers start: 40 outliers final: 14 residues processed: 143 average time/residue: 1.0896 time to fit residues: 177.0913 Evaluate side-chains 113 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 472 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 181 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN B 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.9958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15808 Z= 0.175 Angle : 0.508 8.441 21448 Z= 0.269 Chirality : 0.039 0.237 2476 Planarity : 0.004 0.043 2636 Dihedral : 5.572 57.264 2252 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.54 % Allowed : 15.90 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.19), residues: 1876 helix: 1.72 (0.15), residues: 1132 sheet: -0.07 (0.30), residues: 252 loop : -0.37 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 404 HIS 0.003 0.001 HIS C 451 PHE 0.025 0.001 PHE B 333 TYR 0.014 0.001 TYR B 497 ARG 0.007 0.000 ARG D 338 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 1.815 Fit side-chains REVERT: B 249 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7554 (mt-10) REVERT: B 321 LEU cc_start: 0.8146 (tt) cc_final: 0.7938 (tm) REVERT: B 508 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.6998 (mmt) REVERT: C 371 MET cc_start: 0.8650 (ttm) cc_final: 0.8433 (ttm) REVERT: C 426 MET cc_start: 0.7541 (mmm) cc_final: 0.7070 (mtp) REVERT: D 312 SER cc_start: 0.8374 (OUTLIER) cc_final: 0.7833 (m) REVERT: D 371 MET cc_start: 0.8714 (ttm) cc_final: 0.8417 (ttm) REVERT: A 50 MET cc_start: 0.8064 (mtm) cc_final: 0.7679 (mtm) REVERT: A 57 ARG cc_start: 0.7037 (mtt180) cc_final: 0.6596 (mpt-90) REVERT: A 312 SER cc_start: 0.8719 (t) cc_final: 0.8454 (m) REVERT: A 472 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7972 (t70) outliers start: 26 outliers final: 7 residues processed: 129 average time/residue: 1.0790 time to fit residues: 159.0144 Evaluate side-chains 104 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain A residue 472 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 101 optimal weight: 0.0000 chunk 181 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS A 286 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 1.0047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15808 Z= 0.179 Angle : 0.505 8.702 21448 Z= 0.264 Chirality : 0.039 0.231 2476 Planarity : 0.004 0.045 2636 Dihedral : 5.344 55.439 2252 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.71 % Allowed : 15.84 % Favored : 82.45 % 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: 1.61 (0.19), residues: 1876 helix: 1.93 (0.15), residues: 1128 sheet: 0.04 (0.30), residues: 252 loop : -0.30 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 404 HIS 0.003 0.001 HIS B 234 PHE 0.027 0.001 PHE B 333 TYR 0.014 0.001 TYR B 497 ARG 0.012 0.000 ARG D 338 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 1.953 Fit side-chains REVERT: B 176 ASP cc_start: 0.6922 (m-30) cc_final: 0.6696 (m-30) REVERT: B 249 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7616 (mt-10) REVERT: B 321 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7900 (tm) REVERT: B 364 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8532 (tp) REVERT: C 371 MET cc_start: 0.8645 (ttm) cc_final: 0.8438 (ttm) REVERT: C 426 MET cc_start: 0.7560 (mmm) cc_final: 0.7134 (mtp) REVERT: D 176 ASP cc_start: 0.7495 (p0) cc_final: 0.6933 (m-30) REVERT: D 312 SER cc_start: 0.8422 (OUTLIER) cc_final: 0.7922 (m) REVERT: D 338 ARG cc_start: 0.6063 (mtp-110) cc_final: 0.5393 (mtp180) REVERT: D 371 MET cc_start: 0.8790 (ttm) cc_final: 0.8500 (ttm) REVERT: A 50 MET cc_start: 0.8110 (mtm) cc_final: 0.7751 (mtm) REVERT: A 57 ARG cc_start: 0.7174 (mtt180) cc_final: 0.6715 (mpt-90) REVERT: A 312 SER cc_start: 0.8700 (t) cc_final: 0.8433 (m) REVERT: A 472 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7680 (t0) outliers start: 29 outliers final: 9 residues processed: 124 average time/residue: 0.9762 time to fit residues: 139.1101 Evaluate side-chains 106 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 472 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 1.0159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15808 Z= 0.218 Angle : 0.524 8.326 21448 Z= 0.273 Chirality : 0.040 0.258 2476 Planarity : 0.004 0.052 2636 Dihedral : 5.418 56.956 2252 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.48 % Allowed : 16.13 % Favored : 82.39 % 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: 1.61 (0.19), residues: 1876 helix: 1.92 (0.15), residues: 1128 sheet: 0.10 (0.30), residues: 252 loop : -0.32 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 404 HIS 0.003 0.001 HIS A 103 PHE 0.028 0.002 PHE B 333 TYR 0.015 0.001 TYR B 497 ARG 0.009 0.000 ARG D 338 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 1.717 Fit side-chains REVERT: B 249 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7648 (mt-10) REVERT: B 364 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8576 (tp) REVERT: C 371 MET cc_start: 0.8662 (ttm) cc_final: 0.8458 (ttm) REVERT: C 426 MET cc_start: 0.7553 (mmm) cc_final: 0.7153 (mtp) REVERT: D 176 ASP cc_start: 0.7363 (p0) cc_final: 0.7112 (m-30) REVERT: D 247 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8239 (t0) REVERT: D 312 SER cc_start: 0.8441 (OUTLIER) cc_final: 0.7958 (m) REVERT: D 371 MET cc_start: 0.8754 (ttm) cc_final: 0.8474 (ttm) REVERT: A 50 MET cc_start: 0.8113 (mtm) cc_final: 0.7745 (mtm) REVERT: A 57 ARG cc_start: 0.7238 (mtt180) cc_final: 0.6911 (mpt-90) REVERT: A 312 SER cc_start: 0.8666 (t) cc_final: 0.8447 (m) REVERT: A 472 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7733 (t0) outliers start: 25 outliers final: 9 residues processed: 115 average time/residue: 0.9798 time to fit residues: 130.3358 Evaluate side-chains 105 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 472 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 4.9990 chunk 158 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 152 optimal weight: 9.9990 chunk 159 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 178 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 1.0242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15808 Z= 0.184 Angle : 0.508 9.113 21448 Z= 0.264 Chirality : 0.039 0.288 2476 Planarity : 0.004 0.056 2636 Dihedral : 5.327 56.043 2252 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.00 % Allowed : 16.96 % Favored : 82.03 % 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: 1.70 (0.19), residues: 1876 helix: 1.95 (0.15), residues: 1132 sheet: 0.12 (0.30), residues: 252 loop : -0.19 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 404 HIS 0.003 0.001 HIS A 103 PHE 0.028 0.001 PHE B 333 TYR 0.014 0.001 TYR B 497 ARG 0.014 0.000 ARG D 338 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 1.932 Fit side-chains REVERT: B 249 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7665 (mt-10) REVERT: B 364 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8565 (tp) REVERT: C 46 LYS cc_start: 0.7789 (ttpt) cc_final: 0.7479 (ttmm) REVERT: C 362 ASP cc_start: 0.6707 (p0) cc_final: 0.6482 (p0) REVERT: C 426 MET cc_start: 0.7536 (mmm) cc_final: 0.7171 (mtp) REVERT: D 50 MET cc_start: 0.7054 (mtm) cc_final: 0.6851 (mtm) REVERT: D 247 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8227 (t0) REVERT: D 312 SER cc_start: 0.8436 (OUTLIER) cc_final: 0.7972 (m) REVERT: D 338 ARG cc_start: 0.6103 (mtp-110) cc_final: 0.5707 (ptp-110) REVERT: D 371 MET cc_start: 0.8763 (ttm) cc_final: 0.8476 (ttm) REVERT: A 50 MET cc_start: 0.8120 (mtm) cc_final: 0.7768 (mtm) REVERT: A 57 ARG cc_start: 0.7275 (mtt180) cc_final: 0.6954 (mpt-90) REVERT: A 312 SER cc_start: 0.8654 (t) cc_final: 0.8438 (m) REVERT: A 472 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7764 (t0) outliers start: 17 outliers final: 10 residues processed: 110 average time/residue: 1.0030 time to fit residues: 126.9766 Evaluate side-chains 104 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 472 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 HIS B 280 HIS ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 1.0381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15808 Z= 0.306 Angle : 0.576 11.212 21448 Z= 0.301 Chirality : 0.042 0.289 2476 Planarity : 0.004 0.068 2636 Dihedral : 5.692 59.322 2252 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.06 % Allowed : 17.02 % Favored : 81.91 % 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: 1.45 (0.19), residues: 1876 helix: 1.79 (0.15), residues: 1128 sheet: 0.01 (0.30), residues: 252 loop : -0.33 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 157 HIS 0.006 0.001 HIS D 174 PHE 0.025 0.002 PHE B 333 TYR 0.016 0.002 TYR B 497 ARG 0.011 0.000 ARG D 338 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 1.739 Fit side-chains REVERT: B 249 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7740 (mt-10) REVERT: C 46 LYS cc_start: 0.7808 (ttpt) cc_final: 0.7450 (ttmm) REVERT: C 426 MET cc_start: 0.7614 (mmm) cc_final: 0.7205 (mtp) REVERT: D 247 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8254 (t0) REVERT: D 312 SER cc_start: 0.8436 (OUTLIER) cc_final: 0.7978 (m) REVERT: D 338 ARG cc_start: 0.6195 (mtp-110) cc_final: 0.5757 (ptp-110) REVERT: A 50 MET cc_start: 0.8112 (mtm) cc_final: 0.7723 (mtm) REVERT: A 57 ARG cc_start: 0.7333 (mtt180) cc_final: 0.7041 (mpt-90) REVERT: A 472 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7826 (t0) outliers start: 18 outliers final: 10 residues processed: 103 average time/residue: 1.0142 time to fit residues: 119.8988 Evaluate side-chains 99 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 472 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 149 optimal weight: 0.9980 chunk 62 optimal weight: 0.0040 chunk 153 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 HIS ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.107055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.080249 restraints weight = 23661.478| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.68 r_work: 0.2854 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 1.0433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15808 Z= 0.166 Angle : 0.513 11.652 21448 Z= 0.264 Chirality : 0.039 0.277 2476 Planarity : 0.004 0.053 2636 Dihedral : 5.381 56.034 2252 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.00 % Allowed : 17.14 % Favored : 81.86 % 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: 1.67 (0.19), residues: 1876 helix: 1.92 (0.15), residues: 1132 sheet: 0.10 (0.30), residues: 252 loop : -0.15 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 157 HIS 0.003 0.001 HIS C 451 PHE 0.025 0.001 PHE B 333 TYR 0.014 0.001 TYR B 497 ARG 0.012 0.000 ARG D 338 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4093.58 seconds wall clock time: 75 minutes 24.34 seconds (4524.34 seconds total)