Starting phenix.real_space_refine on Mon Jan 20 14:26:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cbz_45429/01_2025/9cbz_45429.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cbz_45429/01_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_45429/01_2025/9cbz_45429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cbz_45429/01_2025/9cbz_45429.map" model { file = "/net/cci-nas-00/data/ceres_data/9cbz_45429/01_2025/9cbz_45429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cbz_45429/01_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-5571/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: 8.92, per 1000 atoms: 0.58 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: 3.97 Conformation dependent library (CDL) restraints added in 1.7 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: 1.69 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: 5.27 Time building geometry restraints manager: 4.54 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: 0.11 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: 0.010 Normalize map: mean=0, sd=1: 2.730 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: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.250 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5848 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15808 Z= 0.318 Angle : 0.643 12.003 21448 Z= 0.357 Chirality : 0.045 0.280 2476 Planarity : 0.004 0.041 2636 Dihedral : 13.202 85.926 5772 Min Nonbonded Distance : 1.462 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.19), residues: 1876 helix: 1.50 (0.15), residues: 1128 sheet: 0.03 (0.29), residues: 252 loop : -0.54 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 404 HIS 0.003 0.001 HIS A 103 PHE 0.016 0.002 PHE B 235 TYR 0.015 0.002 TYR A 149 ARG 0.004 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 1.758 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: 1.0553 time to fit residues: 428.3282 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 : 1.573 ------------------------------------------------------------------------------- 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 = 48)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.093086 restraints weight = 23940.946| |-----------------------------------------------------------------------------| 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 15808 Z= 0.419 Angle : 0.851 11.792 21448 Z= 0.451 Chirality : 0.050 0.242 2476 Planarity : 0.007 0.083 2636 Dihedral : 6.373 57.748 2252 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.66 % Allowed : 11.82 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.19), residues: 1876 helix: 0.89 (0.15), residues: 1128 sheet: 0.80 (0.35), residues: 216 loop : -0.69 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP A 404 HIS 0.011 0.002 HIS D 174 PHE 0.029 0.003 PHE D 182 TYR 0.031 0.003 TYR C 149 ARG 0.015 0.001 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 201 time to evaluate : 1.828 Fit side-chains REVERT: B 142 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7744 (tt) REVERT: B 150 VAL cc_start: 0.7769 (t) cc_final: 0.7546 (m) REVERT: B 176 ASP cc_start: 0.6953 (t0) cc_final: 0.6543 (m-30) REVERT: B 187 ARG cc_start: 0.7228 (ttp-110) cc_final: 0.6732 (ttp-110) REVERT: B 220 ASN cc_start: 0.6539 (m110) cc_final: 0.5727 (t0) REVERT: B 313 PHE cc_start: 0.7830 (t80) cc_final: 0.7514 (t80) REVERT: B 358 LEU cc_start: 0.7947 (mt) cc_final: 0.7503 (mt) REVERT: B 426 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7233 (mtt) REVERT: B 457 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8809 (tp) REVERT: C 176 ASP cc_start: 0.7221 (t70) cc_final: 0.6788 (m-30) REVERT: C 278 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8306 (mtpt) REVERT: C 345 TRP cc_start: 0.5655 (t-100) cc_final: 0.5060 (t60) REVERT: C 508 MET cc_start: 0.8457 (mpp) cc_final: 0.8096 (mmm) REVERT: D 67 MET cc_start: 0.6538 (ppp) cc_final: 0.6141 (ptt) REVERT: A 95 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7756 (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: 1.1151 time to fit residues: 299.7271 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 : 1.718 ------------------------------------------------------------------------------- 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: 0.8980 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: 5.9990 chunk 13 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.113403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.086513 restraints weight = 23620.037| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.74 r_work: 0.2983 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.7799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15808 Z= 0.193 Angle : 0.516 6.892 21448 Z= 0.277 Chirality : 0.039 0.152 2476 Planarity : 0.004 0.045 2636 Dihedral : 5.621 58.643 2252 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.54 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: 1.27 (0.19), residues: 1876 helix: 1.51 (0.15), residues: 1136 sheet: 0.33 (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 0.020 0.002 PHE A 301 TYR 0.015 0.001 TYR D 497 ARG 0.007 0.001 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 1.912 Fit side-chains REVERT: B 107 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8981 (tp) REVERT: B 135 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8647 (mm-40) REVERT: B 176 ASP cc_start: 0.7210 (t0) cc_final: 0.6715 (m-30) REVERT: B 187 ARG cc_start: 0.7342 (ttp-110) cc_final: 0.6724 (tmm160) REVERT: B 299 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7590 (tm) REVERT: B 426 MET cc_start: 0.8037 (mpm) cc_final: 0.7385 (mtp) REVERT: C 176 ASP cc_start: 0.7423 (t70) cc_final: 0.7089 (m-30) REVERT: C 345 TRP cc_start: 0.5536 (t-100) cc_final: 0.4812 (t60) REVERT: D 67 MET cc_start: 0.6581 (ppp) cc_final: 0.6264 (ptt) REVERT: D 376 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7338 (mt-10) REVERT: A 95 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7978 (mt-10) REVERT: A 334 MET cc_start: 0.5408 (tpp) cc_final: 0.5157 (tpt) REVERT: A 508 MET cc_start: 0.8726 (mmt) cc_final: 0.8333 (mmm) outliers start: 44 outliers final: 13 residues processed: 159 average time/residue: 0.9055 time to fit residues: 166.8750 Evaluate side-chains 125 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 1.671 ------------------------------------------------------------------------------- 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: 1.9990 chunk 171 optimal weight: 6.9990 chunk 179 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 469 ASN C 179 ASN D 409 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.104806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.076945 restraints weight = 23598.250| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.74 r_work: 0.2806 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 1.0001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 15808 Z= 0.506 Angle : 0.720 11.371 21448 Z= 0.381 Chirality : 0.047 0.191 2476 Planarity : 0.005 0.046 2636 Dihedral : 6.299 58.308 2252 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.13 % Allowed : 13.59 % Favored : 83.27 % 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: 0.80 (0.19), residues: 1876 helix: 1.19 (0.15), residues: 1132 sheet: 0.02 (0.33), residues: 228 loop : -0.56 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 398 HIS 0.008 0.001 HIS A 103 PHE 0.023 0.003 PHE B 333 TYR 0.022 0.002 TYR C 149 ARG 0.005 0.001 ARG B 168 *********************** 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 179 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 126 time to evaluate : 1.816 Fit side-chains REVERT: B 176 ASP cc_start: 0.8645 (t0) cc_final: 0.8091 (m-30) REVERT: B 187 ARG cc_start: 0.8089 (ttp-110) cc_final: 0.7488 (tmm160) REVERT: B 249 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8012 (mt-10) REVERT: B 426 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7876 (mtp) REVERT: B 508 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.7887 (mmt) REVERT: C 176 ASP cc_start: 0.8394 (t70) cc_final: 0.7773 (m-30) REVERT: C 278 LYS cc_start: 0.8793 (tppt) cc_final: 0.8447 (mtmt) REVERT: C 313 PHE cc_start: 0.8943 (t80) cc_final: 0.8522 (t80) REVERT: D 67 MET cc_start: 0.7629 (ppp) cc_final: 0.7314 (ptt) REVERT: D 174 HIS cc_start: 0.7698 (t-90) cc_final: 0.7336 (t-90) REVERT: D 247 ASN cc_start: 0.8919 (OUTLIER) cc_final: 0.8321 (t0) REVERT: D 312 SER cc_start: 0.8438 (OUTLIER) cc_final: 0.7845 (m) REVERT: D 426 MET cc_start: 0.8479 (mmp) cc_final: 0.8047 (mtm) REVERT: A 249 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8092 (mt-10) REVERT: A 297 PHE cc_start: 0.7721 (t80) cc_final: 0.7459 (t80) REVERT: A 362 ASP cc_start: 0.7371 (p0) cc_final: 0.7155 (p0) REVERT: A 472 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8083 (t0) REVERT: A 508 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8201 (mmm) outliers start: 53 outliers final: 13 residues processed: 164 average time/residue: 1.2120 time to fit residues: 222.4898 Evaluate side-chains 115 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 1.898 ------------------------------------------------------------------------------- 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 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 331 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain A residue 92 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 50 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.106794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.079432 restraints weight = 23782.033| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.75 r_work: 0.2850 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 1.0021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15808 Z= 0.182 Angle : 0.514 7.902 21448 Z= 0.272 Chirality : 0.039 0.191 2476 Planarity : 0.004 0.043 2636 Dihedral : 5.724 57.565 2252 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.77 % Allowed : 15.48 % 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: 1.23 (0.19), residues: 1876 helix: 1.59 (0.15), residues: 1132 sheet: -0.08 (0.30), residues: 252 loop : -0.38 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 404 HIS 0.003 0.001 HIS C 451 PHE 0.024 0.001 PHE B 333 TYR 0.014 0.001 TYR B 497 ARG 0.008 0.000 ARG D 338 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 1.878 Fit side-chains REVERT: B 176 ASP cc_start: 0.8637 (t0) cc_final: 0.8103 (m-30) REVERT: B 187 ARG cc_start: 0.8078 (ttp-110) cc_final: 0.7427 (tmm160) REVERT: B 249 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7992 (mt-10) REVERT: B 299 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7991 (tm) REVERT: B 426 MET cc_start: 0.8165 (mpm) cc_final: 0.7722 (mtp) REVERT: C 176 ASP cc_start: 0.8439 (t70) cc_final: 0.7808 (m-30) REVERT: C 278 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8382 (mtmt) REVERT: C 426 MET cc_start: 0.8403 (mmm) cc_final: 0.7739 (mtp) REVERT: D 67 MET cc_start: 0.7614 (ppp) cc_final: 0.7226 (ptp) REVERT: D 174 HIS cc_start: 0.7507 (t-90) cc_final: 0.7077 (m-70) REVERT: D 176 ASP cc_start: 0.8171 (p0) cc_final: 0.7825 (p0) REVERT: D 312 SER cc_start: 0.8476 (t) cc_final: 0.7937 (m) REVERT: D 326 LEU cc_start: 0.7743 (mm) cc_final: 0.7523 (mt) REVERT: D 371 MET cc_start: 0.9012 (ttm) cc_final: 0.8716 (ttm) REVERT: D 426 MET cc_start: 0.8476 (mmp) cc_final: 0.8029 (mtm) REVERT: A 57 ARG cc_start: 0.7111 (mtt180) cc_final: 0.6669 (mpt-90) REVERT: A 249 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8057 (mt-10) REVERT: A 297 PHE cc_start: 0.7656 (t80) cc_final: 0.7372 (t80) REVERT: A 379 ASN cc_start: 0.8057 (m-40) cc_final: 0.7847 (m-40) REVERT: A 472 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8288 (t70) REVERT: A 508 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8164 (mmm) outliers start: 30 outliers final: 8 residues processed: 134 average time/residue: 1.0269 time to fit residues: 156.6772 Evaluate side-chains 111 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 181 THR 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 D residue 344 LEU 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: 8.9990 chunk 45 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 chunk 164 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3365 r_free = 0.3365 target = 0.104022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.076835 restraints weight = 23830.751| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.72 r_work: 0.2803 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 1.0186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15808 Z= 0.342 Angle : 0.591 8.506 21448 Z= 0.310 Chirality : 0.043 0.242 2476 Planarity : 0.004 0.053 2636 Dihedral : 5.858 59.980 2252 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.07 % Allowed : 15.07 % 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: 1.22 (0.19), residues: 1876 helix: 1.58 (0.15), residues: 1132 sheet: -0.14 (0.30), residues: 252 loop : -0.34 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 404 HIS 0.005 0.001 HIS A 103 PHE 0.027 0.002 PHE B 333 TYR 0.015 0.002 TYR C 497 ARG 0.009 0.001 ARG D 338 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 1.903 Fit side-chains REVERT: B 57 ARG cc_start: 0.7665 (ttm170) cc_final: 0.7459 (mtm-85) REVERT: B 67 MET cc_start: 0.7925 (mtt) cc_final: 0.7694 (mtp) REVERT: B 176 ASP cc_start: 0.8613 (t0) cc_final: 0.8055 (m-30) REVERT: B 187 ARG cc_start: 0.8123 (ttp-110) cc_final: 0.7529 (ttt180) REVERT: B 249 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8091 (mt-10) REVERT: B 426 MET cc_start: 0.8234 (mpm) cc_final: 0.7765 (mtp) REVERT: C 46 LYS cc_start: 0.7806 (ttpt) cc_final: 0.7455 (ttmm) REVERT: C 176 ASP cc_start: 0.8495 (t70) cc_final: 0.7818 (m-30) REVERT: C 278 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8420 (mtmt) REVERT: C 334 MET cc_start: 0.5533 (OUTLIER) cc_final: 0.5209 (mmm) REVERT: C 426 MET cc_start: 0.8578 (mmm) cc_final: 0.7906 (mtp) REVERT: D 67 MET cc_start: 0.7713 (ppp) cc_final: 0.7367 (ptp) REVERT: D 176 ASP cc_start: 0.8247 (p0) cc_final: 0.7984 (p0) REVERT: D 222 THR cc_start: 0.9048 (t) cc_final: 0.8812 (m) REVERT: D 247 ASN cc_start: 0.8877 (OUTLIER) cc_final: 0.8321 (t0) REVERT: D 312 SER cc_start: 0.8522 (t) cc_final: 0.8056 (m) REVERT: D 378 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8185 (mttm) REVERT: D 426 MET cc_start: 0.8595 (mmp) cc_final: 0.8126 (mtm) REVERT: A 57 ARG cc_start: 0.7311 (mtt180) cc_final: 0.7000 (mpt-90) REVERT: A 249 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8201 (mt-10) REVERT: A 312 SER cc_start: 0.8694 (t) cc_final: 0.8489 (m) REVERT: A 379 ASN cc_start: 0.8318 (m-40) cc_final: 0.8010 (m-40) REVERT: A 472 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8256 (t0) REVERT: A 508 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8174 (mmm) outliers start: 35 outliers final: 11 residues processed: 123 average time/residue: 1.1423 time to fit residues: 158.5689 Evaluate side-chains 109 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 1.863 ------------------------------------------------------------------------------- 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 181 THR 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 334 MET Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 378 LYS 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: 10.0000 chunk 155 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 HIS B 280 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.103317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.076203 restraints weight = 23885.086| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 1.71 r_work: 0.2781 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 1.0436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15808 Z= 0.388 Angle : 0.610 10.068 21448 Z= 0.318 Chirality : 0.044 0.226 2476 Planarity : 0.005 0.042 2636 Dihedral : 6.016 59.138 2252 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.19 % Allowed : 14.72 % 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: 1.14 (0.19), residues: 1876 helix: 1.49 (0.15), residues: 1132 sheet: -0.08 (0.31), residues: 228 loop : -0.36 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 404 HIS 0.007 0.001 HIS A 103 PHE 0.027 0.002 PHE B 333 TYR 0.015 0.002 TYR B 497 ARG 0.007 0.001 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 96 time to evaluate : 1.788 Fit side-chains REVERT: B 57 ARG cc_start: 0.7744 (ttm170) cc_final: 0.7326 (mpt-90) REVERT: B 67 MET cc_start: 0.7893 (mtt) cc_final: 0.7662 (mtp) REVERT: B 176 ASP cc_start: 0.8629 (t0) cc_final: 0.8048 (m-30) REVERT: B 187 ARG cc_start: 0.8115 (ttp-110) cc_final: 0.7526 (ttt180) REVERT: B 249 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8112 (mt-10) REVERT: B 297 PHE cc_start: 0.7614 (t80) cc_final: 0.7191 (t80) REVERT: B 328 ASN cc_start: 0.6695 (m-40) cc_final: 0.6465 (m-40) REVERT: B 426 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7773 (mtp) REVERT: C 46 LYS cc_start: 0.7902 (ttpt) cc_final: 0.7533 (ttmm) REVERT: C 176 ASP cc_start: 0.8538 (t70) cc_final: 0.7910 (m-30) REVERT: C 278 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8398 (mtmt) REVERT: D 67 MET cc_start: 0.7793 (ppp) cc_final: 0.7467 (ptp) REVERT: D 176 ASP cc_start: 0.8178 (p0) cc_final: 0.7908 (p0) REVERT: D 222 THR cc_start: 0.9010 (t) cc_final: 0.8790 (m) REVERT: D 312 SER cc_start: 0.8542 (OUTLIER) cc_final: 0.8098 (m) REVERT: D 378 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8029 (mttm) REVERT: D 426 MET cc_start: 0.8616 (mmp) cc_final: 0.8123 (mtm) REVERT: A 57 ARG cc_start: 0.7451 (mtt180) cc_final: 0.7170 (mpt-90) REVERT: A 508 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8182 (mmm) outliers start: 37 outliers final: 13 residues processed: 122 average time/residue: 1.0751 time to fit residues: 149.2048 Evaluate side-chains 106 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 1.565 ------------------------------------------------------------------------------- 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 426 MET Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 452 VAL 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: 7.9990 chunk 153 optimal weight: 7.9990 chunk 186 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 chunk 176 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3365 r_free = 0.3365 target = 0.104016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.077044 restraints weight = 23517.796| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.70 r_work: 0.2807 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 1.0512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15808 Z= 0.275 Angle : 0.557 8.677 21448 Z= 0.290 Chirality : 0.041 0.267 2476 Planarity : 0.004 0.058 2636 Dihedral : 5.849 59.853 2252 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.77 % Allowed : 15.25 % 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: 1.30 (0.19), residues: 1876 helix: 1.63 (0.15), residues: 1132 sheet: -0.09 (0.31), residues: 228 loop : -0.29 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 404 HIS 0.005 0.001 HIS A 103 PHE 0.026 0.002 PHE B 333 TYR 0.014 0.001 TYR B 497 ARG 0.013 0.000 ARG D 338 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 1.898 Fit side-chains REVERT: B 57 ARG cc_start: 0.7738 (ttm170) cc_final: 0.7340 (mpt-90) REVERT: B 67 MET cc_start: 0.7937 (mtt) cc_final: 0.7679 (mtp) REVERT: B 176 ASP cc_start: 0.8622 (t0) cc_final: 0.8051 (m-30) REVERT: B 249 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8105 (mt-10) REVERT: B 297 PHE cc_start: 0.7579 (t80) cc_final: 0.7131 (t80) REVERT: B 345 TRP cc_start: 0.5999 (OUTLIER) cc_final: 0.5292 (t-100) REVERT: B 426 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7746 (mtp) REVERT: C 46 LYS cc_start: 0.7869 (ttpt) cc_final: 0.7436 (ttmm) REVERT: C 176 ASP cc_start: 0.8543 (t70) cc_final: 0.7955 (m-30) REVERT: C 278 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8349 (mtmt) REVERT: C 426 MET cc_start: 0.8567 (mmm) cc_final: 0.7949 (mtp) REVERT: D 67 MET cc_start: 0.7789 (ppp) cc_final: 0.7431 (ptp) REVERT: D 176 ASP cc_start: 0.8177 (p0) cc_final: 0.7879 (p0) REVERT: D 222 THR cc_start: 0.8975 (t) cc_final: 0.8758 (m) REVERT: D 247 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8304 (t0) REVERT: D 312 SER cc_start: 0.8525 (t) cc_final: 0.8091 (m) REVERT: D 378 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8017 (mttm) REVERT: D 426 MET cc_start: 0.8555 (mmp) cc_final: 0.8102 (mtm) REVERT: A 57 ARG cc_start: 0.7514 (mtt180) cc_final: 0.7232 (mpt-90) REVERT: A 508 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8145 (mmm) outliers start: 30 outliers final: 17 residues processed: 112 average time/residue: 1.1203 time to fit residues: 143.8869 Evaluate side-chains 106 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 MET 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 345 TRP Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 181 THR 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 C residue 363 VAL Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 452 VAL 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: 0.5980 chunk 169 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 HIS B 328 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.104731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.077561 restraints weight = 23666.784| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.73 r_work: 0.2812 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 1.0564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15808 Z= 0.225 Angle : 0.534 9.879 21448 Z= 0.277 Chirality : 0.040 0.269 2476 Planarity : 0.004 0.047 2636 Dihedral : 5.658 57.667 2252 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.77 % Allowed : 15.37 % 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: 1.51 (0.19), residues: 1876 helix: 1.79 (0.15), residues: 1132 sheet: -0.02 (0.31), residues: 228 loop : -0.18 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 404 HIS 0.004 0.001 HIS A 103 PHE 0.024 0.001 PHE B 333 TYR 0.014 0.001 TYR B 497 ARG 0.013 0.000 ARG D 338 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 1.808 Fit side-chains REVERT: B 57 ARG cc_start: 0.7757 (ttm170) cc_final: 0.7348 (mpt-90) REVERT: B 67 MET cc_start: 0.7924 (mtt) cc_final: 0.7716 (mtp) REVERT: B 249 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8079 (mt-10) REVERT: B 297 PHE cc_start: 0.7607 (t80) cc_final: 0.7113 (t80) REVERT: B 345 TRP cc_start: 0.6109 (OUTLIER) cc_final: 0.5414 (t-100) REVERT: B 426 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7732 (mtp) REVERT: C 46 LYS cc_start: 0.7824 (ttpt) cc_final: 0.7409 (ttmm) REVERT: C 50 MET cc_start: 0.8305 (ptp) cc_final: 0.7790 (ptm) REVERT: C 176 ASP cc_start: 0.8514 (t70) cc_final: 0.7954 (m-30) REVERT: C 278 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8328 (mtmt) REVERT: C 334 MET cc_start: 0.5492 (mmt) cc_final: 0.5197 (mpp) REVERT: C 426 MET cc_start: 0.8481 (mmm) cc_final: 0.7848 (mtp) REVERT: D 67 MET cc_start: 0.7758 (ppp) cc_final: 0.7409 (ptp) REVERT: D 176 ASP cc_start: 0.8154 (p0) cc_final: 0.7826 (p0) REVERT: D 247 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8309 (t0) REVERT: D 312 SER cc_start: 0.8531 (OUTLIER) cc_final: 0.8089 (m) REVERT: D 338 ARG cc_start: 0.6345 (mtp-110) cc_final: 0.5917 (ptp-110) REVERT: D 371 MET cc_start: 0.8953 (ttm) cc_final: 0.8715 (ttm) REVERT: D 426 MET cc_start: 0.8566 (mmp) cc_final: 0.8052 (mtm) REVERT: A 57 ARG cc_start: 0.7501 (mtt180) cc_final: 0.7211 (mpt-90) REVERT: A 472 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8295 (t0) REVERT: A 508 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8132 (mmm) outliers start: 30 outliers final: 13 residues processed: 111 average time/residue: 1.0579 time to fit residues: 133.9748 Evaluate side-chains 107 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 426 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 92 THR Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 406 THR 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: 4.9990 chunk 92 optimal weight: 4.9990 chunk 86 optimal weight: 0.0570 chunk 114 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 177 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.106901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.080387 restraints weight = 23757.249| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.67 r_work: 0.2857 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 1.0584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15808 Z= 0.153 Angle : 0.501 8.671 21448 Z= 0.259 Chirality : 0.039 0.278 2476 Planarity : 0.004 0.059 2636 Dihedral : 5.359 54.691 2252 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.06 % Allowed : 16.25 % Favored : 82.68 % 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: 1.76 (0.19), residues: 1876 helix: 1.95 (0.15), residues: 1136 sheet: 0.06 (0.31), residues: 228 loop : 0.04 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 404 HIS 0.003 0.001 HIS D 234 PHE 0.026 0.001 PHE B 333 TYR 0.013 0.001 TYR B 497 ARG 0.013 0.000 ARG D 338 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 1.947 Fit side-chains REVERT: B 57 ARG cc_start: 0.7719 (ttm170) cc_final: 0.7345 (mpt-90) REVERT: B 176 ASP cc_start: 0.8642 (t0) cc_final: 0.8132 (m-30) REVERT: B 187 ARG cc_start: 0.8138 (ttp-110) cc_final: 0.7570 (ttt180) REVERT: B 249 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8065 (mt-10) REVERT: B 297 PHE cc_start: 0.7579 (t80) cc_final: 0.7074 (t80) REVERT: B 301 PHE cc_start: 0.7873 (m-80) cc_final: 0.7608 (m-80) REVERT: B 345 TRP cc_start: 0.6021 (OUTLIER) cc_final: 0.5339 (t-100) REVERT: B 426 MET cc_start: 0.8156 (mpm) cc_final: 0.7801 (mtp) REVERT: C 46 LYS cc_start: 0.7821 (ttpt) cc_final: 0.7460 (ttmm) REVERT: C 50 MET cc_start: 0.8146 (ptp) cc_final: 0.7673 (ptm) REVERT: C 176 ASP cc_start: 0.8465 (t70) cc_final: 0.7914 (m-30) REVERT: C 278 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8297 (mtmt) REVERT: C 362 ASP cc_start: 0.7004 (p0) cc_final: 0.6801 (p0) REVERT: C 426 MET cc_start: 0.8498 (mmm) cc_final: 0.7915 (mtp) REVERT: D 67 MET cc_start: 0.7698 (ppp) cc_final: 0.7391 (ptp) REVERT: D 176 ASP cc_start: 0.8096 (p0) cc_final: 0.7759 (p0) REVERT: D 312 SER cc_start: 0.8553 (OUTLIER) cc_final: 0.8130 (m) REVERT: D 338 ARG cc_start: 0.6169 (mtp-110) cc_final: 0.5772 (ptp-110) REVERT: D 371 MET cc_start: 0.8932 (ttm) cc_final: 0.8688 (ttm) REVERT: D 426 MET cc_start: 0.8486 (mmp) cc_final: 0.7793 (mtp) REVERT: A 57 ARG cc_start: 0.7527 (mtt180) cc_final: 0.7239 (mpt-90) REVERT: A 249 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8134 (mt-10) REVERT: A 327 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7335 (tm-30) REVERT: A 472 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8239 (t0) REVERT: A 508 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8148 (mmm) outliers start: 18 outliers final: 6 residues processed: 112 average time/residue: 1.1006 time to fit residues: 140.1687 Evaluate side-chains 103 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 1.961 ------------------------------------------------------------------------------- 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 345 TRP Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 327 GLN 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 111 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 19 optimal weight: 0.0980 chunk 49 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.106154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.079159 restraints weight = 23666.581| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.72 r_work: 0.2847 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 1.0620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15808 Z= 0.169 Angle : 0.505 9.030 21448 Z= 0.260 Chirality : 0.039 0.295 2476 Planarity : 0.004 0.050 2636 Dihedral : 5.304 55.501 2252 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.00 % Allowed : 16.67 % 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: 1.85 (0.19), residues: 1876 helix: 2.05 (0.15), residues: 1128 sheet: 0.16 (0.31), residues: 228 loop : -0.02 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 404 HIS 0.003 0.001 HIS A 103 PHE 0.024 0.001 PHE B 333 TYR 0.013 0.001 TYR B 497 ARG 0.011 0.000 ARG D 338 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9042.15 seconds wall clock time: 161 minutes 40.13 seconds (9700.13 seconds total)