Starting phenix.real_space_refine on Fri Jun 13 19:03:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cbz_45429/06_2025/9cbz_45429.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cbz_45429/06_2025/9cbz_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_45429/06_2025/9cbz_45429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cbz_45429/06_2025/9cbz_45429.map" model { file = "/net/cci-nas-00/data/ceres_data/9cbz_45429/06_2025/9cbz_45429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cbz_45429/06_2025/9cbz_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-5710/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: 9.24, per 1000 atoms: 0.60 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: 3.95 Conformation dependent library (CDL) restraints added in 2.0 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: 1.67 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: 5.39 Time building geometry restraints manager: 4.65 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: 0.10 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 36.990 Find NCS groups from input model: 0.290 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: 0.000 Load rotamer database and sin/cos tables:13.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.410 ------------------------------------------------------------------------------- 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 15816 Z= 0.244 Angle : 0.649 12.003 21472 Z= 0.358 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 4) link_NAG-ASN : angle 2.79767 ( 12) link_BETA1-4 : bond 0.00069 ( 4) link_BETA1-4 : angle 2.32170 ( 12) hydrogen bonds : bond 0.10972 ( 1023) hydrogen bonds : angle 5.82806 ( 2970) covalent geometry : bond 0.00492 (15808) covalent geometry : angle 0.64315 (21448) *********************** 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 : 1.533 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: 1.0015 time to fit residues: 406.9994 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 : 1.764 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.119119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.093089 restraints weight = 23941.001| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.78 r_work: 0.3105 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 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 15816 Z= 0.286 Angle : 0.856 11.792 21472 Z= 0.452 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00929 ( 4) link_NAG-ASN : angle 2.69771 ( 12) link_BETA1-4 : bond 0.01074 ( 4) link_BETA1-4 : angle 3.24147 ( 12) hydrogen bonds : bond 0.05525 ( 1023) hydrogen bonds : angle 5.21546 ( 2970) covalent geometry : bond 0.00636 (15808) covalent geometry : angle 0.85068 (21448) *********************** 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 : 1.962 Fit side-chains REVERT: B 142 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7742 (tt) REVERT: B 150 VAL cc_start: 0.7768 (t) cc_final: 0.7546 (m) REVERT: B 176 ASP cc_start: 0.6952 (t0) cc_final: 0.6542 (m-30) REVERT: B 187 ARG cc_start: 0.7229 (ttp-110) cc_final: 0.6732 (ttp-110) REVERT: B 220 ASN cc_start: 0.6540 (m110) cc_final: 0.5726 (t0) REVERT: B 313 PHE cc_start: 0.7829 (t80) cc_final: 0.7515 (t80) REVERT: B 358 LEU cc_start: 0.7946 (mt) cc_final: 0.7503 (mt) REVERT: B 426 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7234 (mtt) REVERT: B 457 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8809 (tp) REVERT: C 176 ASP cc_start: 0.7220 (t70) cc_final: 0.6786 (m-30) REVERT: C 278 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8305 (mtpt) REVERT: C 345 TRP cc_start: 0.5653 (t-100) cc_final: 0.5058 (t60) REVERT: C 508 MET cc_start: 0.8457 (mpp) cc_final: 0.8096 (mmm) REVERT: D 67 MET cc_start: 0.6540 (ppp) cc_final: 0.6142 (ptt) REVERT: A 95 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7757 (mt-10) REVERT: A 508 MET cc_start: 0.8578 (mmt) cc_final: 0.8179 (mmm) outliers start: 62 outliers final: 16 residues processed: 239 average time/residue: 1.4040 time to fit residues: 376.9033 Evaluate side-chains 142 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.884 ------------------------------------------------------------------------------- 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 142 ILE 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 B residue 457 LEU 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 9 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN B 280 HIS C 194 GLN D 127 GLN D 135 GLN D 247 ASN D 481 GLN A 286 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.113214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.086264 restraints weight = 23618.755| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.75 r_work: 0.2978 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.7821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15816 Z= 0.139 Angle : 0.521 6.855 21472 Z= 0.278 Chirality : 0.039 0.176 2476 Planarity : 0.004 0.045 2636 Dihedral : 5.609 58.490 2252 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.60 % Allowed : 13.95 % Favored : 83.45 % 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: 1.28 (0.19), residues: 1876 helix: 1.52 (0.15), residues: 1136 sheet: 0.34 (0.32), residues: 264 loop : -0.33 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 404 HIS 0.008 0.001 HIS B 486 PHE 0.027 0.002 PHE A 301 TYR 0.015 0.001 TYR D 497 ARG 0.005 0.000 ARG B 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00181 ( 4) link_NAG-ASN : angle 1.12294 ( 12) link_BETA1-4 : bond 0.00325 ( 4) link_BETA1-4 : angle 2.13804 ( 12) hydrogen bonds : bond 0.04414 ( 1023) hydrogen bonds : angle 4.61938 ( 2970) covalent geometry : bond 0.00297 (15808) covalent geometry : angle 0.51781 (21448) *********************** 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 172 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 128 time to evaluate : 1.837 Fit side-chains REVERT: B 107 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8990 (tp) REVERT: B 135 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8663 (mm-40) REVERT: B 176 ASP cc_start: 0.7222 (t0) cc_final: 0.6717 (m-30) REVERT: B 187 ARG cc_start: 0.7353 (ttp-110) cc_final: 0.6732 (tmm160) REVERT: B 299 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7600 (tm) REVERT: B 426 MET cc_start: 0.8044 (mpm) cc_final: 0.7394 (mtp) REVERT: C 176 ASP cc_start: 0.7386 (t70) cc_final: 0.7054 (m-30) REVERT: C 345 TRP cc_start: 0.5492 (t-100) cc_final: 0.4763 (t60) REVERT: D 67 MET cc_start: 0.6597 (ppp) cc_final: 0.6280 (ptt) REVERT: D 376 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7343 (mt-10) REVERT: A 95 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7991 (mt-10) REVERT: A 334 MET cc_start: 0.5408 (tpp) cc_final: 0.5148 (tpt) REVERT: A 508 MET cc_start: 0.8683 (mmt) cc_final: 0.8304 (mmm) outliers start: 44 outliers final: 13 residues processed: 160 average time/residue: 0.9827 time to fit residues: 182.8632 Evaluate side-chains 126 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 135 GLN 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 113 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 152 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 chunk 129 optimal weight: 0.0050 chunk 133 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 overall best weight: 2.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.107479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.079555 restraints weight = 24023.763| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.79 r_work: 0.2856 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.9010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 15816 Z= 0.185 Angle : 0.573 13.052 21472 Z= 0.304 Chirality : 0.041 0.165 2476 Planarity : 0.004 0.044 2636 Dihedral : 5.659 59.228 2252 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.60 % Allowed : 14.30 % Favored : 83.10 % 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: 1.30 (0.19), residues: 1876 helix: 1.58 (0.15), residues: 1136 sheet: 0.16 (0.31), residues: 264 loop : -0.35 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 491 HIS 0.006 0.001 HIS B 486 PHE 0.022 0.002 PHE B 333 TYR 0.015 0.002 TYR C 218 ARG 0.006 0.000 ARG A 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 4) link_NAG-ASN : angle 1.70817 ( 12) link_BETA1-4 : bond 0.00283 ( 4) link_BETA1-4 : angle 2.39583 ( 12) hydrogen bonds : bond 0.04646 ( 1023) hydrogen bonds : angle 4.61951 ( 2970) covalent geometry : bond 0.00422 (15808) covalent geometry : angle 0.56893 (21448) *********************** 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 167 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 1.467 Fit side-chains revert: symmetry clash REVERT: B 176 ASP cc_start: 0.8236 (t0) cc_final: 0.7721 (m-30) REVERT: B 187 ARG cc_start: 0.7904 (ttp-110) cc_final: 0.7246 (tmm160) REVERT: B 299 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7687 (tm) REVERT: B 376 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7945 (mm-30) REVERT: B 426 MET cc_start: 0.8302 (mpm) cc_final: 0.7634 (mtp) REVERT: B 508 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.7843 (mmt) REVERT: C 176 ASP cc_start: 0.7974 (t70) cc_final: 0.7617 (m-30) REVERT: C 279 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8685 (m) REVERT: C 313 PHE cc_start: 0.8816 (t80) cc_final: 0.8564 (t80) REVERT: D 67 MET cc_start: 0.7241 (ppp) cc_final: 0.6901 (ptt) REVERT: D 247 ASN cc_start: 0.8905 (OUTLIER) cc_final: 0.8342 (t0) REVERT: D 314 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8152 (mp) REVERT: D 376 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7585 (mt-10) REVERT: D 426 MET cc_start: 0.8344 (mmp) cc_final: 0.7923 (mtm) REVERT: A 379 ASN cc_start: 0.7643 (m-40) cc_final: 0.7396 (m-40) REVERT: A 472 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8316 (t70) REVERT: A 508 MET cc_start: 0.8702 (mmt) cc_final: 0.8179 (mmm) outliers start: 44 outliers final: 12 residues processed: 155 average time/residue: 1.0426 time to fit residues: 182.6049 Evaluate side-chains 128 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 1.627 ------------------------------------------------------------------------------- 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 300 LEU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain C residue 279 THR 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 376 GLU Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 279 THR 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 92 THR Chi-restraints excluded: chain A residue 452 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 50 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 178 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 162 optimal weight: 8.9990 chunk 170 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.105326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.077661 restraints weight = 24392.066| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.75 r_work: 0.2822 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.9699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15816 Z= 0.191 Angle : 0.553 8.186 21472 Z= 0.292 Chirality : 0.041 0.249 2476 Planarity : 0.004 0.044 2636 Dihedral : 5.639 57.641 2252 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.42 % Allowed : 14.78 % Favored : 82.80 % 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: 1.32 (0.19), residues: 1876 helix: 1.65 (0.15), residues: 1136 sheet: -0.03 (0.30), residues: 252 loop : -0.34 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 404 HIS 0.003 0.001 HIS D 103 PHE 0.026 0.002 PHE A 301 TYR 0.015 0.001 TYR C 497 ARG 0.007 0.001 ARG D 338 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 4) link_NAG-ASN : angle 1.46641 ( 12) link_BETA1-4 : bond 0.00242 ( 4) link_BETA1-4 : angle 2.42786 ( 12) hydrogen bonds : bond 0.04638 ( 1023) hydrogen bonds : angle 4.63070 ( 2970) covalent geometry : bond 0.00436 (15808) covalent geometry : angle 0.54920 (21448) *********************** 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 154 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 113 time to evaluate : 1.841 Fit side-chains REVERT: B 176 ASP cc_start: 0.8526 (t0) cc_final: 0.8022 (m-30) REVERT: B 187 ARG cc_start: 0.8062 (ttp-110) cc_final: 0.7410 (tmm160) REVERT: B 249 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8039 (mt-10) REVERT: B 299 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7875 (tm) REVERT: B 426 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7643 (mtp) REVERT: B 508 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.7852 (mmt) REVERT: C 176 ASP cc_start: 0.8344 (t70) cc_final: 0.7807 (m-30) REVERT: C 278 LYS cc_start: 0.8715 (tppt) cc_final: 0.8316 (mtmt) REVERT: C 279 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8813 (m) REVERT: C 426 MET cc_start: 0.8402 (mmm) cc_final: 0.7819 (mtp) REVERT: D 67 MET cc_start: 0.7538 (ppp) cc_final: 0.7207 (ptp) REVERT: D 247 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8340 (t0) REVERT: D 312 SER cc_start: 0.8460 (OUTLIER) cc_final: 0.7875 (m) REVERT: D 338 ARG cc_start: 0.6114 (mtp-110) cc_final: 0.5375 (mtp180) REVERT: D 376 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7574 (mt-10) REVERT: D 426 MET cc_start: 0.8457 (mmp) cc_final: 0.8030 (mtm) REVERT: A 50 MET cc_start: 0.8299 (mtm) cc_final: 0.7919 (mtm) REVERT: A 57 ARG cc_start: 0.7114 (mtt180) cc_final: 0.6689 (mpt-90) REVERT: A 297 PHE cc_start: 0.7660 (t80) cc_final: 0.7433 (t80) REVERT: A 379 ASN cc_start: 0.8025 (m-40) cc_final: 0.7687 (m-40) REVERT: A 472 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8324 (t70) REVERT: A 508 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8136 (mmm) outliers start: 41 outliers final: 12 residues processed: 144 average time/residue: 1.1055 time to fit residues: 179.8859 Evaluate side-chains 119 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 1.658 ------------------------------------------------------------------------------- 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 300 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 279 THR 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 247 ASN Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 508 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 88 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 164 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN A 286 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.104352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.077037 restraints weight = 23842.741| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.72 r_work: 0.2806 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 1.0176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15816 Z= 0.233 Angle : 0.600 8.817 21472 Z= 0.313 Chirality : 0.043 0.258 2476 Planarity : 0.005 0.070 2636 Dihedral : 5.861 59.889 2252 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.30 % Allowed : 14.83 % Favored : 82.86 % 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: 1.23 (0.19), residues: 1876 helix: 1.60 (0.15), residues: 1132 sheet: -0.15 (0.30), residues: 252 loop : -0.36 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 335 HIS 0.005 0.001 HIS A 103 PHE 0.028 0.002 PHE B 333 TYR 0.015 0.002 TYR D 497 ARG 0.008 0.001 ARG D 338 Details of bonding type rmsd link_NAG-ASN : bond 0.00500 ( 4) link_NAG-ASN : angle 1.82624 ( 12) link_BETA1-4 : bond 0.00186 ( 4) link_BETA1-4 : angle 2.51538 ( 12) hydrogen bonds : bond 0.04915 ( 1023) hydrogen bonds : angle 4.75032 ( 2970) covalent geometry : bond 0.00538 (15808) covalent geometry : angle 0.59606 (21448) *********************** 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 136 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 97 time to evaluate : 1.802 Fit side-chains revert: symmetry clash REVERT: B 57 ARG cc_start: 0.7659 (ttm170) cc_final: 0.7433 (mtm-85) REVERT: B 176 ASP cc_start: 0.8614 (t0) cc_final: 0.8061 (m-30) REVERT: B 187 ARG cc_start: 0.8175 (ttp-110) cc_final: 0.7476 (ttp80) REVERT: B 249 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8096 (mt-10) REVERT: B 297 PHE cc_start: 0.7468 (t80) cc_final: 0.7148 (t80) REVERT: B 426 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7741 (mtp) REVERT: B 508 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.7925 (mmt) REVERT: C 176 ASP cc_start: 0.8528 (t70) cc_final: 0.7862 (m-30) REVERT: C 278 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8355 (mtmt) REVERT: C 296 SER cc_start: 0.7729 (t) cc_final: 0.7483 (m) REVERT: D 67 MET cc_start: 0.7698 (ppp) cc_final: 0.7352 (ptp) REVERT: D 176 ASP cc_start: 0.8230 (p0) cc_final: 0.7966 (p0) REVERT: D 222 THR cc_start: 0.9111 (t) cc_final: 0.8872 (m) REVERT: D 247 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8311 (t0) REVERT: D 312 SER cc_start: 0.8536 (OUTLIER) cc_final: 0.8054 (m) REVERT: D 426 MET cc_start: 0.8586 (mmp) cc_final: 0.8107 (mtm) REVERT: A 57 ARG cc_start: 0.7264 (mtt180) cc_final: 0.6848 (mpt-90) REVERT: A 312 SER cc_start: 0.8714 (t) cc_final: 0.8452 (m) REVERT: A 338 ARG cc_start: 0.6512 (OUTLIER) cc_final: 0.6225 (tmm-80) REVERT: A 379 ASN cc_start: 0.8251 (m-40) cc_final: 0.7953 (m-40) REVERT: A 472 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8274 (t70) REVERT: A 508 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8177 (mmm) outliers start: 39 outliers final: 12 residues processed: 127 average time/residue: 1.1263 time to fit residues: 163.6198 Evaluate side-chains 108 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 1.711 ------------------------------------------------------------------------------- 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 300 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain C residue 278 LYS 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 325 LEU Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 508 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 70 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN B 280 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.105956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.078795 restraints weight = 23894.400| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.73 r_work: 0.2842 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 1.0224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15816 Z= 0.143 Angle : 0.525 8.467 21472 Z= 0.272 Chirality : 0.040 0.248 2476 Planarity : 0.004 0.041 2636 Dihedral : 5.564 56.761 2252 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.65 % Allowed : 15.54 % Favored : 82.80 % 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: 1.40 (0.19), residues: 1876 helix: 1.75 (0.15), residues: 1132 sheet: -0.10 (0.30), residues: 252 loop : -0.30 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 404 HIS 0.003 0.001 HIS A 103 PHE 0.026 0.001 PHE B 333 TYR 0.013 0.001 TYR B 497 ARG 0.010 0.000 ARG D 338 Details of bonding type rmsd link_NAG-ASN : bond 0.00217 ( 4) link_NAG-ASN : angle 1.13103 ( 12) link_BETA1-4 : bond 0.00171 ( 4) link_BETA1-4 : angle 2.20397 ( 12) hydrogen bonds : bond 0.04287 ( 1023) hydrogen bonds : angle 4.57152 ( 2970) covalent geometry : bond 0.00317 (15808) covalent geometry : angle 0.52203 (21448) *********************** 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 125 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 1.882 Fit side-chains REVERT: B 57 ARG cc_start: 0.7655 (ttm170) cc_final: 0.7450 (mtm-85) REVERT: B 67 MET cc_start: 0.7870 (mtt) cc_final: 0.7637 (mtp) REVERT: B 176 ASP cc_start: 0.8617 (t0) cc_final: 0.8103 (m-30) REVERT: B 187 ARG cc_start: 0.8105 (ttp-110) cc_final: 0.7471 (ttt180) REVERT: B 249 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8108 (mt-10) REVERT: B 297 PHE cc_start: 0.7398 (t80) cc_final: 0.7032 (t80) REVERT: B 426 MET cc_start: 0.8132 (mpm) cc_final: 0.7672 (mtp) REVERT: C 176 ASP cc_start: 0.8402 (t70) cc_final: 0.7880 (m-30) REVERT: C 278 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8302 (mtmt) REVERT: C 296 SER cc_start: 0.7778 (t) cc_final: 0.7553 (m) REVERT: C 426 MET cc_start: 0.8499 (mmm) cc_final: 0.7952 (mtp) REVERT: D 67 MET cc_start: 0.7718 (ppp) cc_final: 0.7338 (ptp) REVERT: D 176 ASP cc_start: 0.8167 (p0) cc_final: 0.7881 (p0) REVERT: D 222 THR cc_start: 0.9050 (t) cc_final: 0.8814 (m) REVERT: D 312 SER cc_start: 0.8519 (t) cc_final: 0.8028 (m) REVERT: D 338 ARG cc_start: 0.6332 (mtp-110) cc_final: 0.5981 (ptp-110) REVERT: D 376 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7529 (mt-10) REVERT: D 426 MET cc_start: 0.8497 (mmp) cc_final: 0.8062 (mtm) REVERT: A 57 ARG cc_start: 0.7321 (mtt180) cc_final: 0.6918 (mpt-90) REVERT: A 312 SER cc_start: 0.8677 (t) cc_final: 0.8456 (m) REVERT: A 379 ASN cc_start: 0.8258 (m-40) cc_final: 0.7980 (m-40) REVERT: A 472 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8288 (t70) REVERT: A 508 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8150 (mmm) outliers start: 28 outliers final: 10 residues processed: 114 average time/residue: 1.0223 time to fit residues: 133.4672 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 : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 278 LYS 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 376 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 508 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 156 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 186 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.105266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.078165 restraints weight = 23527.576| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.71 r_work: 0.2827 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 1.0342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15816 Z= 0.170 Angle : 0.544 8.334 21472 Z= 0.282 Chirality : 0.040 0.267 2476 Planarity : 0.004 0.059 2636 Dihedral : 5.578 57.763 2252 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.65 % Allowed : 15.37 % 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: 1.46 (0.19), residues: 1876 helix: 1.79 (0.15), residues: 1132 sheet: -0.09 (0.30), residues: 252 loop : -0.27 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 404 HIS 0.004 0.001 HIS A 103 PHE 0.027 0.002 PHE B 333 TYR 0.015 0.001 TYR B 497 ARG 0.010 0.000 ARG D 338 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 4) link_NAG-ASN : angle 1.30915 ( 12) link_BETA1-4 : bond 0.00174 ( 4) link_BETA1-4 : angle 2.23849 ( 12) hydrogen bonds : bond 0.04438 ( 1023) hydrogen bonds : angle 4.58172 ( 2970) covalent geometry : bond 0.00384 (15808) covalent geometry : angle 0.54124 (21448) *********************** 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 124 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 1.633 Fit side-chains revert: symmetry clash REVERT: B 67 MET cc_start: 0.7896 (mtt) cc_final: 0.7655 (mtp) REVERT: B 176 ASP cc_start: 0.8613 (t0) cc_final: 0.8087 (m-30) REVERT: B 187 ARG cc_start: 0.8121 (ttp-110) cc_final: 0.7505 (ttt180) REVERT: B 249 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8128 (mt-10) REVERT: B 297 PHE cc_start: 0.7519 (t80) cc_final: 0.7103 (t80) REVERT: B 426 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7767 (mtp) REVERT: C 46 LYS cc_start: 0.7805 (ttpt) cc_final: 0.7405 (ttmm) REVERT: C 176 ASP cc_start: 0.8448 (t70) cc_final: 0.7872 (m-30) REVERT: C 278 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8334 (mtmt) REVERT: C 296 SER cc_start: 0.7762 (t) cc_final: 0.7543 (m) REVERT: C 426 MET cc_start: 0.8517 (mmm) cc_final: 0.7970 (mtp) REVERT: D 67 MET cc_start: 0.7726 (ppp) cc_final: 0.7384 (ptp) REVERT: D 176 ASP cc_start: 0.8151 (p0) cc_final: 0.7873 (p0) REVERT: D 222 THR cc_start: 0.9015 (t) cc_final: 0.8810 (m) REVERT: D 312 SER cc_start: 0.8535 (OUTLIER) cc_final: 0.8056 (m) REVERT: D 426 MET cc_start: 0.8515 (mmp) cc_final: 0.8069 (mtm) REVERT: A 57 ARG cc_start: 0.7382 (mtt180) cc_final: 0.7078 (mpt-90) REVERT: A 312 SER cc_start: 0.8660 (t) cc_final: 0.8453 (m) REVERT: A 379 ASN cc_start: 0.8256 (m-40) cc_final: 0.7995 (m-40) REVERT: A 472 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8187 (t0) REVERT: A 508 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8130 (mmm) outliers start: 28 outliers final: 13 residues processed: 114 average time/residue: 1.0052 time to fit residues: 130.9353 Evaluate side-chains 109 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain C residue 278 LYS 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 344 LEU Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 508 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 38 optimal weight: 0.9990 chunk 169 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 24 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.105562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.078491 restraints weight = 23651.065| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.72 r_work: 0.2835 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 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 0.048 15816 Z= 0.155 Angle : 0.528 8.134 21472 Z= 0.274 Chirality : 0.040 0.265 2476 Planarity : 0.004 0.054 2636 Dihedral : 5.517 57.497 2252 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.60 % Allowed : 15.48 % Favored : 82.92 % 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: 1.52 (0.19), residues: 1876 helix: 1.81 (0.15), residues: 1136 sheet: -0.06 (0.30), residues: 252 loop : -0.18 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 157 HIS 0.004 0.001 HIS A 103 PHE 0.029 0.002 PHE B 333 TYR 0.014 0.001 TYR B 497 ARG 0.012 0.000 ARG D 338 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 4) link_NAG-ASN : angle 1.14100 ( 12) link_BETA1-4 : bond 0.00178 ( 4) link_BETA1-4 : angle 2.17539 ( 12) hydrogen bonds : bond 0.04297 ( 1023) hydrogen bonds : angle 4.54127 ( 2970) covalent geometry : bond 0.00349 (15808) covalent geometry : angle 0.52529 (21448) *********************** 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 122 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 1.663 Fit side-chains revert: symmetry clash REVERT: B 57 ARG cc_start: 0.7742 (ttm170) cc_final: 0.7302 (mpt-90) REVERT: B 67 MET cc_start: 0.7881 (mtt) cc_final: 0.7662 (mtp) REVERT: B 187 ARG cc_start: 0.8132 (ttp-110) cc_final: 0.7515 (ttt180) REVERT: B 249 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8090 (mt-10) REVERT: B 297 PHE cc_start: 0.7474 (t80) cc_final: 0.7045 (t80) REVERT: B 426 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7751 (mtp) REVERT: C 42 ARG cc_start: 0.4291 (OUTLIER) cc_final: 0.3732 (ttm-80) REVERT: C 46 LYS cc_start: 0.7815 (ttpt) cc_final: 0.7428 (ttmm) REVERT: C 176 ASP cc_start: 0.8472 (t70) cc_final: 0.7887 (m-30) REVERT: C 278 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8313 (mtmt) REVERT: C 296 SER cc_start: 0.7737 (t) cc_final: 0.7513 (m) REVERT: C 426 MET cc_start: 0.8501 (mmm) cc_final: 0.7942 (mtp) REVERT: D 67 MET cc_start: 0.7727 (ppp) cc_final: 0.7368 (ptp) REVERT: D 176 ASP cc_start: 0.8152 (p0) cc_final: 0.7878 (p0) REVERT: D 312 SER cc_start: 0.8521 (OUTLIER) cc_final: 0.8057 (m) REVERT: D 338 ARG cc_start: 0.6367 (mtp-110) cc_final: 0.5975 (ptp-110) REVERT: D 426 MET cc_start: 0.8589 (mmp) cc_final: 0.8117 (mtm) REVERT: D 508 MET cc_start: 0.8336 (mpt) cc_final: 0.7768 (mmm) REVERT: A 57 ARG cc_start: 0.7409 (mtt180) cc_final: 0.7120 (mpt-90) REVERT: A 379 ASN cc_start: 0.8225 (m-40) cc_final: 0.7972 (m-40) REVERT: A 472 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8229 (t0) REVERT: A 508 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8120 (mmm) outliers start: 27 outliers final: 13 residues processed: 111 average time/residue: 0.9910 time to fit residues: 125.9867 Evaluate side-chains 106 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 278 LYS 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 344 LEU Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 508 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 127 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.106681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.079859 restraints weight = 23695.964| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.68 r_work: 0.2847 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 1.0468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15816 Z= 0.131 Angle : 0.520 9.738 21472 Z= 0.267 Chirality : 0.039 0.290 2476 Planarity : 0.004 0.063 2636 Dihedral : 5.380 56.194 2252 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.36 % Allowed : 15.90 % 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 (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: 1.65 (0.19), residues: 1876 helix: 1.90 (0.15), residues: 1136 sheet: -0.05 (0.30), residues: 252 loop : -0.08 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 157 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 0.012 0.000 ARG D 338 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 4) link_NAG-ASN : angle 0.94443 ( 12) link_BETA1-4 : bond 0.00183 ( 4) link_BETA1-4 : angle 2.03846 ( 12) hydrogen bonds : bond 0.04110 ( 1023) hydrogen bonds : angle 4.47395 ( 2970) covalent geometry : bond 0.00287 (15808) covalent geometry : angle 0.51797 (21448) ********************** 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 117 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 2.353 Fit side-chains revert: symmetry clash REVERT: B 57 ARG cc_start: 0.7759 (ttm170) cc_final: 0.7320 (mpt-90) REVERT: B 187 ARG cc_start: 0.8125 (ttp-110) cc_final: 0.7548 (ttt180) REVERT: B 249 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8059 (mt-10) REVERT: B 297 PHE cc_start: 0.7540 (t80) cc_final: 0.7135 (t80) REVERT: B 426 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7766 (mtp) REVERT: C 42 ARG cc_start: 0.4400 (OUTLIER) cc_final: 0.3881 (ttm-80) REVERT: C 46 LYS cc_start: 0.7818 (ttpt) cc_final: 0.7499 (ttmm) REVERT: C 50 MET cc_start: 0.8347 (ptp) cc_final: 0.7917 (ptm) REVERT: C 176 ASP cc_start: 0.8467 (t70) cc_final: 0.7896 (m-30) REVERT: C 278 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8278 (mtmt) REVERT: C 296 SER cc_start: 0.7779 (t) cc_final: 0.7563 (m) REVERT: C 426 MET cc_start: 0.8483 (mmm) cc_final: 0.7927 (mtp) REVERT: D 67 MET cc_start: 0.7694 (ppp) cc_final: 0.7371 (ptp) REVERT: D 176 ASP cc_start: 0.8145 (p0) cc_final: 0.7834 (p0) REVERT: D 312 SER cc_start: 0.8539 (OUTLIER) cc_final: 0.8101 (m) REVERT: D 426 MET cc_start: 0.8555 (mmp) cc_final: 0.7835 (mtp) REVERT: D 508 MET cc_start: 0.8359 (mpt) cc_final: 0.7751 (mmm) REVERT: A 57 ARG cc_start: 0.7431 (mtt180) cc_final: 0.7142 (mpt-90) REVERT: A 379 ASN cc_start: 0.8188 (m-40) cc_final: 0.7978 (m-40) REVERT: A 508 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8161 (mmm) outliers start: 23 outliers final: 10 residues processed: 108 average time/residue: 1.2734 time to fit residues: 158.3165 Evaluate side-chains 104 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 278 LYS 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 376 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 508 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 111 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 136 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.104789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.078152 restraints weight = 23641.424| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.70 r_work: 0.2817 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 1.0518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15816 Z= 0.179 Angle : 0.553 11.607 21472 Z= 0.284 Chirality : 0.041 0.291 2476 Planarity : 0.004 0.052 2636 Dihedral : 5.520 58.200 2252 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.24 % Allowed : 16.43 % Favored : 82.33 % 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: 1.59 (0.19), residues: 1876 helix: 1.86 (0.15), residues: 1132 sheet: -0.05 (0.31), residues: 228 loop : -0.12 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 157 HIS 0.005 0.001 HIS A 103 PHE 0.025 0.002 PHE B 333 TYR 0.015 0.001 TYR B 497 ARG 0.013 0.000 ARG D 338 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 4) link_NAG-ASN : angle 1.23941 ( 12) link_BETA1-4 : bond 0.00167 ( 4) link_BETA1-4 : angle 2.22738 ( 12) hydrogen bonds : bond 0.04419 ( 1023) hydrogen bonds : angle 4.55820 ( 2970) covalent geometry : bond 0.00409 (15808) covalent geometry : angle 0.54994 (21448) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9852.93 seconds wall clock time: 175 minutes 45.06 seconds (10545.06 seconds total)