Starting phenix.real_space_refine on Sat Aug 23 23:14:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cbz_45429/08_2025/9cbz_45429.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cbz_45429/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9cbz_45429/08_2025/9cbz_45429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cbz_45429/08_2025/9cbz_45429.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cbz_45429/08_2025/9cbz_45429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cbz_45429/08_2025/9cbz_45429.map" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.03, per 1000 atoms: 0.20 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: 0.83 Conformation dependent library (CDL) restraints added in 586.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.45 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: 2.20 Time building geometry restraints manager: 1.18 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: 0.03 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'A' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.230 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5848 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15816 Z= 0.244 Angle : 0.649 12.003 21472 Z= 0.358 Chirality : 0.045 0.280 2476 Planarity : 0.004 0.041 2636 Dihedral : 13.202 85.926 5772 Min Nonbonded Distance : 1.462 Molprobity Statistics. All-atom Clashscore : 6.05 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG B 44 TYR 0.015 0.002 TYR A 149 PHE 0.016 0.002 PHE B 235 TRP 0.008 0.002 TRP D 404 HIS 0.003 0.001 HIS A 103 Details of bonding type rmsd covalent geometry : bond 0.00492 (15808) covalent geometry : angle 0.64315 (21448) hydrogen bonds : bond 0.10972 ( 1023) hydrogen bonds : angle 5.82806 ( 2970) link_BETA1-4 : bond 0.00069 ( 4) link_BETA1-4 : angle 2.32170 ( 12) link_NAG-ASN : bond 0.00121 ( 4) link_NAG-ASN : angle 2.79767 ( 12) *********************** 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 : 0.365 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: 0.5260 time to fit residues: 212.4874 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 : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.0670 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN B 135 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN C 352 ASN C 483 GLN D 124 GLN D 127 GLN D 135 GLN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN A 483 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.114621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.088737 restraints weight = 23856.344| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.75 r_work: 0.3021 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 15816 Z= 0.196 Angle : 0.641 9.426 21472 Z= 0.341 Chirality : 0.044 0.199 2476 Planarity : 0.005 0.050 2636 Dihedral : 5.497 57.148 2252 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.48 % Allowed : 11.70 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.19), residues: 1876 helix: 1.61 (0.15), residues: 1132 sheet: 0.74 (0.33), residues: 204 loop : -0.41 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG A 298 TYR 0.022 0.002 TYR D 218 PHE 0.027 0.002 PHE B 262 TRP 0.027 0.002 TRP A 404 HIS 0.031 0.002 HIS D 174 Details of bonding type rmsd covalent geometry : bond 0.00437 (15808) covalent geometry : angle 0.63783 (21448) hydrogen bonds : bond 0.04527 ( 1023) hydrogen bonds : angle 4.73498 ( 2970) link_BETA1-4 : bond 0.00686 ( 4) link_BETA1-4 : angle 2.64683 ( 12) link_NAG-ASN : bond 0.00623 ( 4) link_NAG-ASN : angle 1.16180 ( 12) *********************** 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 281 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 239 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: B 46 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.8094 (ttmm) REVERT: B 61 ARG cc_start: 0.4257 (mtt180) cc_final: 0.3126 (ttp-170) REVERT: B 76 VAL cc_start: 0.6119 (m) cc_final: 0.5843 (p) REVERT: B 176 ASP cc_start: 0.6369 (t0) cc_final: 0.5631 (m-30) REVERT: B 304 VAL cc_start: 0.7944 (t) cc_final: 0.7603 (t) REVERT: B 426 MET cc_start: 0.7184 (mpm) cc_final: 0.6515 (mtt) REVERT: B 457 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7557 (tp) REVERT: C 130 PHE cc_start: 0.7548 (m-10) cc_final: 0.7326 (m-10) REVERT: C 285 LYS cc_start: 0.7564 (tppp) cc_final: 0.7290 (mtpp) REVERT: C 312 SER cc_start: 0.7146 (m) cc_final: 0.6748 (t) REVERT: C 334 MET cc_start: 0.5333 (OUTLIER) cc_final: 0.5076 (mmm) REVERT: C 345 TRP cc_start: 0.5562 (t-100) cc_final: 0.5010 (t60) REVERT: C 484 GLN cc_start: 0.4213 (mm-40) cc_final: 0.3725 (tp40) REVERT: D 57 ARG cc_start: 0.7087 (ptp-170) cc_final: 0.6877 (ptp-170) REVERT: D 67 MET cc_start: 0.5282 (ppp) cc_final: 0.4992 (pp-130) REVERT: D 96 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6644 (mt-10) REVERT: D 247 ASN cc_start: 0.8013 (t0) cc_final: 0.7673 (t0) REVERT: A 47 TYR cc_start: 0.6412 (t80) cc_final: 0.6146 (t80) REVERT: A 196 ASP cc_start: 0.6961 (m-30) cc_final: 0.6634 (m-30) REVERT: A 307 LEU cc_start: 0.7421 (tt) cc_final: 0.7220 (mt) REVERT: A 334 MET cc_start: 0.5602 (tpp) cc_final: 0.5378 (tpp) REVERT: A 508 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.7246 (mmm) outliers start: 42 outliers final: 12 residues processed: 267 average time/residue: 0.5195 time to fit residues: 155.7504 Evaluate side-chains 177 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain C residue 289 VAL 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 492 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 508 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 167 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN B 87 ASN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 135 GLN D 469 ASN A 135 GLN A 327 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.114443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.087629 restraints weight = 23817.351| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.73 r_work: 0.3001 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.8100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 15816 Z= 0.220 Angle : 0.705 12.551 21472 Z= 0.367 Chirality : 0.045 0.295 2476 Planarity : 0.006 0.091 2636 Dihedral : 5.939 57.354 2252 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.25 % Allowed : 14.01 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.19), residues: 1876 helix: 1.31 (0.15), residues: 1120 sheet: 0.43 (0.33), residues: 240 loop : -0.52 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 172 TYR 0.028 0.002 TYR C 218 PHE 0.022 0.002 PHE B 235 TRP 0.020 0.002 TRP D 491 HIS 0.009 0.002 HIS B 486 Details of bonding type rmsd covalent geometry : bond 0.00490 (15808) covalent geometry : angle 0.69913 (21448) hydrogen bonds : bond 0.05378 ( 1023) hydrogen bonds : angle 4.86233 ( 2970) link_BETA1-4 : bond 0.00481 ( 4) link_BETA1-4 : angle 2.79475 ( 12) link_NAG-ASN : bond 0.00361 ( 4) link_NAG-ASN : angle 2.62843 ( 12) *********************** 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 222 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 167 time to evaluate : 0.637 Fit side-chains REVERT: B 176 ASP cc_start: 0.7509 (t0) cc_final: 0.6736 (m-30) REVERT: B 299 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7534 (tm) REVERT: B 301 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.7486 (t80) REVERT: B 313 PHE cc_start: 0.7972 (t80) cc_final: 0.7709 (t80) REVERT: B 426 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7232 (mtt) REVERT: B 484 GLN cc_start: 0.5810 (mm-40) cc_final: 0.5458 (tp40) REVERT: C 176 ASP cc_start: 0.7324 (t70) cc_final: 0.7022 (m-30) REVERT: C 191 ASP cc_start: 0.7454 (t70) cc_final: 0.7252 (t70) REVERT: C 278 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8532 (mtpp) REVERT: C 334 MET cc_start: 0.5633 (OUTLIER) cc_final: 0.5301 (mmm) REVERT: C 345 TRP cc_start: 0.5639 (t-100) cc_final: 0.4848 (t60) REVERT: C 364 LEU cc_start: 0.8406 (mt) cc_final: 0.8174 (tp) REVERT: C 508 MET cc_start: 0.8501 (mpp) cc_final: 0.8127 (mmm) REVERT: D 57 ARG cc_start: 0.7011 (ptp-170) cc_final: 0.6725 (ptp-170) REVERT: D 67 MET cc_start: 0.6589 (ppp) cc_final: 0.6312 (ptt) REVERT: D 301 PHE cc_start: 0.7615 (m-80) cc_final: 0.7277 (m-80) REVERT: D 305 VAL cc_start: 0.7960 (t) cc_final: 0.7581 (t) REVERT: A 95 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7981 (mt-10) REVERT: A 174 HIS cc_start: 0.7816 (m-70) cc_final: 0.6667 (t-90) REVERT: A 355 TYR cc_start: 0.8234 (m-10) cc_final: 0.7887 (m-10) REVERT: A 472 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7892 (t70) REVERT: A 508 MET cc_start: 0.8765 (mmt) cc_final: 0.8410 (mmm) outliers start: 55 outliers final: 11 residues processed: 200 average time/residue: 0.5091 time to fit residues: 115.3116 Evaluate side-chains 142 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 301 PHE Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 426 MET 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 331 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 472 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 55 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 11 optimal weight: 0.4980 chunk 37 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN C 179 ASN D 247 ASN D 409 HIS D 481 GLN A 280 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.080008 restraints weight = 24056.380| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.78 r_work: 0.2870 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.8970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15816 Z= 0.183 Angle : 0.553 7.121 21472 Z= 0.295 Chirality : 0.041 0.172 2476 Planarity : 0.004 0.042 2636 Dihedral : 5.587 59.756 2252 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.78 % Allowed : 13.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.19), residues: 1876 helix: 1.62 (0.15), residues: 1124 sheet: 0.29 (0.33), residues: 228 loop : -0.35 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 338 TYR 0.017 0.002 TYR C 218 PHE 0.023 0.002 PHE B 333 TRP 0.009 0.001 TRP C 404 HIS 0.006 0.001 HIS B 486 Details of bonding type rmsd covalent geometry : bond 0.00416 (15808) covalent geometry : angle 0.55002 (21448) hydrogen bonds : bond 0.04523 ( 1023) hydrogen bonds : angle 4.59480 ( 2970) link_BETA1-4 : bond 0.00167 ( 4) link_BETA1-4 : angle 2.29099 ( 12) link_NAG-ASN : bond 0.00298 ( 4) link_NAG-ASN : angle 1.37824 ( 12) *********************** 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 165 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 118 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: B 171 HIS cc_start: 0.7929 (t-90) cc_final: 0.7707 (t-90) REVERT: B 176 ASP cc_start: 0.8237 (t0) cc_final: 0.7585 (m-30) REVERT: B 299 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7638 (tm) REVERT: B 326 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7411 (tt) REVERT: B 376 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7937 (mm-30) REVERT: B 426 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7670 (mtt) REVERT: C 176 ASP cc_start: 0.7860 (t70) cc_final: 0.7469 (m-30) REVERT: C 279 THR cc_start: 0.9015 (t) cc_final: 0.8630 (m) REVERT: C 313 PHE cc_start: 0.8748 (t80) cc_final: 0.8522 (t80) REVERT: C 334 MET cc_start: 0.5729 (OUTLIER) cc_final: 0.5334 (mmm) REVERT: D 57 ARG cc_start: 0.7041 (ptp-170) cc_final: 0.6747 (ptp-170) REVERT: D 67 MET cc_start: 0.7180 (ppp) cc_final: 0.6863 (ptt) REVERT: D 314 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8152 (mp) REVERT: D 426 MET cc_start: 0.8366 (mmp) cc_final: 0.7939 (mtm) REVERT: A 297 PHE cc_start: 0.7565 (t80) cc_final: 0.7348 (t80) REVERT: A 334 MET cc_start: 0.5451 (OUTLIER) cc_final: 0.5245 (tpp) REVERT: A 379 ASN cc_start: 0.7603 (t0) cc_final: 0.7389 (m-40) REVERT: A 418 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8254 (mt) REVERT: A 508 MET cc_start: 0.8746 (mmt) cc_final: 0.8284 (mmm) outliers start: 47 outliers final: 11 residues processed: 150 average time/residue: 0.4998 time to fit residues: 84.2817 Evaluate side-chains 119 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 426 MET 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 376 GLU Chi-restraints excluded: chain D residue 290 SER Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 452 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 160 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 169 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN B 483 GLN A 280 HIS A 327 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.107082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.079208 restraints weight = 24142.082| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.77 r_work: 0.2853 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.9491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15816 Z= 0.146 Angle : 0.512 7.644 21472 Z= 0.269 Chirality : 0.039 0.132 2476 Planarity : 0.004 0.043 2636 Dihedral : 5.400 55.568 2252 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.30 % Allowed : 14.83 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.19), residues: 1876 helix: 1.75 (0.15), residues: 1128 sheet: 0.20 (0.32), residues: 228 loop : -0.18 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 44 TYR 0.014 0.001 TYR D 497 PHE 0.025 0.002 PHE B 333 TRP 0.010 0.001 TRP C 404 HIS 0.011 0.001 HIS D 409 Details of bonding type rmsd covalent geometry : bond 0.00326 (15808) covalent geometry : angle 0.50820 (21448) hydrogen bonds : bond 0.04282 ( 1023) hydrogen bonds : angle 4.45503 ( 2970) link_BETA1-4 : bond 0.00139 ( 4) link_BETA1-4 : angle 2.25907 ( 12) link_NAG-ASN : bond 0.00166 ( 4) link_NAG-ASN : angle 1.23062 ( 12) *********************** 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 153 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: B 176 ASP cc_start: 0.8523 (t0) cc_final: 0.7944 (m-30) REVERT: B 249 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7987 (mt-10) REVERT: B 299 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7774 (tm) REVERT: B 301 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.7201 (t80) REVERT: B 426 MET cc_start: 0.8395 (mpm) cc_final: 0.7660 (mtt) REVERT: C 176 ASP cc_start: 0.8161 (t70) cc_final: 0.7679 (m-30) REVERT: C 278 LYS cc_start: 0.8754 (tppt) cc_final: 0.8376 (mtmt) REVERT: C 279 THR cc_start: 0.9024 (t) cc_final: 0.8740 (m) REVERT: C 313 PHE cc_start: 0.8857 (t80) cc_final: 0.8489 (t80) REVERT: C 324 PHE cc_start: 0.7689 (t80) cc_final: 0.7403 (t80) REVERT: C 334 MET cc_start: 0.5780 (OUTLIER) cc_final: 0.5374 (mmm) REVERT: D 50 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7647 (mpp) REVERT: D 67 MET cc_start: 0.7406 (ppp) cc_final: 0.7051 (ptt) REVERT: D 247 ASN cc_start: 0.8929 (OUTLIER) cc_final: 0.8341 (t0) REVERT: D 426 MET cc_start: 0.8437 (mmp) cc_final: 0.8012 (mtm) REVERT: A 297 PHE cc_start: 0.7692 (t80) cc_final: 0.7424 (t80) REVERT: A 355 TYR cc_start: 0.8360 (m-10) cc_final: 0.8051 (m-10) REVERT: A 362 ASP cc_start: 0.7200 (p0) cc_final: 0.6987 (p0) REVERT: A 379 ASN cc_start: 0.7874 (m-40) cc_final: 0.7591 (m-40) REVERT: A 472 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8018 (t0) REVERT: A 508 MET cc_start: 0.8696 (mmt) cc_final: 0.8199 (mmm) outliers start: 39 outliers final: 10 residues processed: 143 average time/residue: 0.5164 time to fit residues: 82.9684 Evaluate side-chains 108 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 301 PHE Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 290 SER Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 472 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 99 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 82 optimal weight: 0.3980 chunk 162 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 187 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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** ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 GLN A 280 HIS A 327 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.107383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.079565 restraints weight = 23738.335| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.75 r_work: 0.2857 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.9748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15816 Z= 0.144 Angle : 0.507 8.787 21472 Z= 0.266 Chirality : 0.039 0.187 2476 Planarity : 0.004 0.041 2636 Dihedral : 5.378 56.773 2252 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.01 % Allowed : 15.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.19), residues: 1876 helix: 1.88 (0.15), residues: 1124 sheet: 0.19 (0.32), residues: 228 loop : -0.22 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 44 TYR 0.014 0.001 TYR C 497 PHE 0.024 0.001 PHE B 333 TRP 0.009 0.001 TRP B 404 HIS 0.010 0.001 HIS D 409 Details of bonding type rmsd covalent geometry : bond 0.00320 (15808) covalent geometry : angle 0.50378 (21448) hydrogen bonds : bond 0.04193 ( 1023) hydrogen bonds : angle 4.44474 ( 2970) link_BETA1-4 : bond 0.00154 ( 4) link_BETA1-4 : angle 2.14135 ( 12) link_NAG-ASN : bond 0.00176 ( 4) link_NAG-ASN : angle 1.10532 ( 12) *********************** 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 144 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: B 67 MET cc_start: 0.7853 (mtt) cc_final: 0.7562 (mtt) REVERT: B 176 ASP cc_start: 0.8504 (t0) cc_final: 0.7984 (m-30) REVERT: B 249 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8092 (mt-10) REVERT: B 299 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7909 (tm) REVERT: B 321 LEU cc_start: 0.8240 (tp) cc_final: 0.8014 (tm) REVERT: B 426 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7731 (mtt) REVERT: C 176 ASP cc_start: 0.8297 (t70) cc_final: 0.7754 (m-30) REVERT: C 278 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8395 (mtmt) REVERT: C 279 THR cc_start: 0.9008 (t) cc_final: 0.8766 (m) REVERT: C 313 PHE cc_start: 0.8928 (t80) cc_final: 0.8485 (t80) REVERT: C 334 MET cc_start: 0.5781 (OUTLIER) cc_final: 0.5403 (mmm) REVERT: C 426 MET cc_start: 0.8318 (mmm) cc_final: 0.7768 (mtp) REVERT: D 50 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7545 (mpp) REVERT: D 67 MET cc_start: 0.7486 (ppp) cc_final: 0.7163 (ptp) REVERT: D 222 THR cc_start: 0.9084 (t) cc_final: 0.8765 (m) REVERT: D 247 ASN cc_start: 0.8929 (OUTLIER) cc_final: 0.8339 (t0) REVERT: D 312 SER cc_start: 0.8533 (OUTLIER) cc_final: 0.7973 (m) REVERT: D 426 MET cc_start: 0.8488 (mmp) cc_final: 0.8046 (mtm) REVERT: A 61 ARG cc_start: 0.4831 (OUTLIER) cc_final: 0.4274 (ttp-170) REVERT: A 297 PHE cc_start: 0.7756 (t80) cc_final: 0.7444 (t80) REVERT: A 379 ASN cc_start: 0.7998 (m-40) cc_final: 0.7739 (m-40) REVERT: A 472 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8159 (t0) REVERT: A 508 MET cc_start: 0.8718 (mmt) cc_final: 0.8192 (mmm) outliers start: 34 outliers final: 10 residues processed: 131 average time/residue: 0.4442 time to fit residues: 66.5257 Evaluate side-chains 114 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 301 PHE Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 397 VAL 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 334 MET Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 290 SER Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 472 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 103 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 129 optimal weight: 0.0050 chunk 177 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 110 optimal weight: 0.0980 chunk 58 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN B 103 HIS C 194 GLN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.108120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.080802 restraints weight = 23869.950| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.75 r_work: 0.2891 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.9843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15816 Z= 0.103 Angle : 0.473 8.786 21472 Z= 0.245 Chirality : 0.038 0.148 2476 Planarity : 0.003 0.042 2636 Dihedral : 5.146 54.603 2252 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.01 % Allowed : 15.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.19), residues: 1876 helix: 1.98 (0.15), residues: 1128 sheet: 0.25 (0.32), residues: 228 loop : -0.02 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 44 TYR 0.013 0.001 TYR D 497 PHE 0.025 0.001 PHE B 333 TRP 0.009 0.001 TRP B 404 HIS 0.005 0.001 HIS A 409 Details of bonding type rmsd covalent geometry : bond 0.00211 (15808) covalent geometry : angle 0.47053 (21448) hydrogen bonds : bond 0.03772 ( 1023) hydrogen bonds : angle 4.29823 ( 2970) link_BETA1-4 : bond 0.00240 ( 4) link_BETA1-4 : angle 1.94265 ( 12) link_NAG-ASN : bond 0.00031 ( 4) link_NAG-ASN : angle 0.69827 ( 12) *********************** 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 142 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.667 Fit side-chains REVERT: B 67 MET cc_start: 0.7811 (mtt) cc_final: 0.7555 (mtt) REVERT: B 176 ASP cc_start: 0.8420 (t0) cc_final: 0.7925 (m-30) REVERT: B 249 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8075 (mt-10) REVERT: B 297 PHE cc_start: 0.7250 (t80) cc_final: 0.6972 (t80) REVERT: B 299 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7897 (tm) REVERT: B 301 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7414 (t80) REVERT: B 321 LEU cc_start: 0.8235 (tp) cc_final: 0.8001 (tm) REVERT: B 426 MET cc_start: 0.8356 (mpm) cc_final: 0.7672 (mtt) REVERT: C 176 ASP cc_start: 0.8257 (t70) cc_final: 0.7703 (m-30) REVERT: C 278 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8249 (mtmt) REVERT: C 279 THR cc_start: 0.8955 (t) cc_final: 0.8704 (m) REVERT: C 334 MET cc_start: 0.5767 (OUTLIER) cc_final: 0.5396 (mmm) REVERT: C 371 MET cc_start: 0.8890 (ttm) cc_final: 0.8664 (ttm) REVERT: C 426 MET cc_start: 0.8347 (mmm) cc_final: 0.7755 (mtp) REVERT: D 50 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7313 (mpp) REVERT: D 67 MET cc_start: 0.7499 (ppp) cc_final: 0.7140 (ptp) REVERT: D 312 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.7926 (m) REVERT: D 314 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8347 (mp) REVERT: D 326 LEU cc_start: 0.7790 (mm) cc_final: 0.7542 (mt) REVERT: D 378 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7256 (mtmm) REVERT: D 426 MET cc_start: 0.8428 (mmp) cc_final: 0.7984 (mtm) REVERT: A 61 ARG cc_start: 0.4784 (OUTLIER) cc_final: 0.4216 (ttp-170) REVERT: A 297 PHE cc_start: 0.7665 (t80) cc_final: 0.7406 (t80) REVERT: A 379 ASN cc_start: 0.7900 (m-40) cc_final: 0.7677 (m-40) REVERT: A 472 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8176 (t0) REVERT: A 508 MET cc_start: 0.8660 (mmt) cc_final: 0.8104 (mmm) outliers start: 34 outliers final: 10 residues processed: 129 average time/residue: 0.4814 time to fit residues: 70.5860 Evaluate side-chains 116 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 301 PHE Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 290 SER Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 472 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 137 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 194 GLN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.107215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.079596 restraints weight = 24120.101| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.76 r_work: 0.2861 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 1.0011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15816 Z= 0.127 Angle : 0.480 8.417 21472 Z= 0.252 Chirality : 0.038 0.155 2476 Planarity : 0.003 0.040 2636 Dihedral : 5.190 56.097 2252 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.89 % Allowed : 15.60 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.19), residues: 1876 helix: 2.02 (0.15), residues: 1124 sheet: 0.29 (0.32), residues: 228 loop : -0.07 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 44 TYR 0.015 0.001 TYR D 497 PHE 0.025 0.001 PHE B 333 TRP 0.012 0.001 TRP C 157 HIS 0.005 0.001 HIS A 409 Details of bonding type rmsd covalent geometry : bond 0.00275 (15808) covalent geometry : angle 0.47779 (21448) hydrogen bonds : bond 0.04005 ( 1023) hydrogen bonds : angle 4.33461 ( 2970) link_BETA1-4 : bond 0.00205 ( 4) link_BETA1-4 : angle 2.02822 ( 12) link_NAG-ASN : bond 0.00110 ( 4) link_NAG-ASN : angle 0.94564 ( 12) *********************** 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 132 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.643 Fit side-chains REVERT: B 67 MET cc_start: 0.7806 (mtt) cc_final: 0.7539 (mtp) REVERT: B 176 ASP cc_start: 0.8408 (t0) cc_final: 0.7919 (m-30) REVERT: B 249 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8122 (mt-10) REVERT: B 297 PHE cc_start: 0.7287 (t80) cc_final: 0.6972 (t80) REVERT: B 299 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7937 (tm) REVERT: B 321 LEU cc_start: 0.8249 (tp) cc_final: 0.8010 (tm) REVERT: B 426 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7691 (mtt) REVERT: C 176 ASP cc_start: 0.8288 (t70) cc_final: 0.7719 (m-30) REVERT: C 278 LYS cc_start: 0.8677 (tppt) cc_final: 0.8274 (mtmt) REVERT: C 279 THR cc_start: 0.8938 (t) cc_final: 0.8721 (m) REVERT: C 334 MET cc_start: 0.5756 (OUTLIER) cc_final: 0.5420 (mmm) REVERT: C 426 MET cc_start: 0.8376 (mmm) cc_final: 0.7812 (mtp) REVERT: D 67 MET cc_start: 0.7588 (ppp) cc_final: 0.7260 (ptp) REVERT: D 312 SER cc_start: 0.8505 (OUTLIER) cc_final: 0.7938 (m) REVERT: D 314 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8309 (mp) REVERT: D 378 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7024 (mtmm) REVERT: D 426 MET cc_start: 0.8430 (mmp) cc_final: 0.8005 (mtm) REVERT: D 508 MET cc_start: 0.8329 (mpt) cc_final: 0.7721 (mmm) REVERT: A 61 ARG cc_start: 0.5077 (OUTLIER) cc_final: 0.4427 (ttp-170) REVERT: A 297 PHE cc_start: 0.7750 (t80) cc_final: 0.7268 (t80) REVERT: A 301 PHE cc_start: 0.7660 (OUTLIER) cc_final: 0.6526 (t80) REVERT: A 379 ASN cc_start: 0.8010 (m-40) cc_final: 0.7752 (m-40) REVERT: A 472 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8288 (t0) REVERT: A 508 MET cc_start: 0.8671 (mmt) cc_final: 0.8114 (mmm) outliers start: 32 outliers final: 12 residues processed: 121 average time/residue: 0.4787 time to fit residues: 66.1510 Evaluate side-chains 117 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 301 PHE Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 290 SER Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 472 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 88 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 169 optimal weight: 0.8980 chunk 172 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 194 GLN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.107357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.080466 restraints weight = 23527.316| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.68 r_work: 0.2862 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 1.0191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15816 Z= 0.132 Angle : 0.483 9.125 21472 Z= 0.254 Chirality : 0.038 0.152 2476 Planarity : 0.004 0.041 2636 Dihedral : 5.218 56.262 2252 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.19 % Allowed : 15.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.19), residues: 1876 helix: 1.99 (0.15), residues: 1124 sheet: 0.27 (0.32), residues: 228 loop : -0.02 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 43 TYR 0.014 0.001 TYR B 497 PHE 0.027 0.001 PHE B 333 TRP 0.012 0.001 TRP C 157 HIS 0.005 0.001 HIS A 409 Details of bonding type rmsd covalent geometry : bond 0.00289 (15808) covalent geometry : angle 0.48034 (21448) hydrogen bonds : bond 0.04045 ( 1023) hydrogen bonds : angle 4.35761 ( 2970) link_BETA1-4 : bond 0.00226 ( 4) link_BETA1-4 : angle 2.06093 ( 12) link_NAG-ASN : bond 0.00131 ( 4) link_NAG-ASN : angle 0.93084 ( 12) *********************** 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 137 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 100 time to evaluate : 0.625 Fit side-chains REVERT: B 57 ARG cc_start: 0.7493 (ttm170) cc_final: 0.7160 (mtm-85) REVERT: B 67 MET cc_start: 0.7848 (mtt) cc_final: 0.7598 (mtp) REVERT: B 176 ASP cc_start: 0.8476 (t0) cc_final: 0.7984 (m-30) REVERT: B 184 ILE cc_start: 0.8990 (mt) cc_final: 0.8673 (mm) REVERT: B 249 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8046 (mt-10) REVERT: B 297 PHE cc_start: 0.7375 (t80) cc_final: 0.7014 (t80) REVERT: B 299 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7970 (tm) REVERT: B 321 LEU cc_start: 0.8250 (tp) cc_final: 0.8040 (tm) REVERT: B 426 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7639 (mtp) REVERT: C 46 LYS cc_start: 0.7800 (ttpt) cc_final: 0.7378 (ttmm) REVERT: C 176 ASP cc_start: 0.8388 (t70) cc_final: 0.7791 (m-30) REVERT: C 278 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8302 (mtmt) REVERT: C 334 MET cc_start: 0.5845 (OUTLIER) cc_final: 0.5500 (mmm) REVERT: C 426 MET cc_start: 0.8396 (mmm) cc_final: 0.7853 (mtp) REVERT: D 50 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7397 (mpp) REVERT: D 67 MET cc_start: 0.7698 (ppp) cc_final: 0.7386 (ptp) REVERT: D 312 SER cc_start: 0.8536 (OUTLIER) cc_final: 0.8008 (m) REVERT: D 314 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8302 (mp) REVERT: D 378 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7013 (mtmm) REVERT: D 426 MET cc_start: 0.8541 (mmp) cc_final: 0.7853 (mtp) REVERT: D 508 MET cc_start: 0.8368 (mpt) cc_final: 0.7719 (mmm) REVERT: A 61 ARG cc_start: 0.5156 (OUTLIER) cc_final: 0.4517 (ttp-170) REVERT: A 297 PHE cc_start: 0.7821 (t80) cc_final: 0.7437 (t80) REVERT: A 301 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.6381 (t80) REVERT: A 379 ASN cc_start: 0.8043 (m-40) cc_final: 0.7840 (m-40) REVERT: A 508 MET cc_start: 0.8684 (mmt) cc_final: 0.8155 (mmm) outliers start: 37 outliers final: 12 residues processed: 122 average time/residue: 0.4468 time to fit residues: 62.1517 Evaluate side-chains 119 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 301 PHE Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 397 VAL 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 334 MET Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 290 SER Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 393 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 146 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 180 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 194 GLN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.106856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.080001 restraints weight = 23723.841| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.69 r_work: 0.2853 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 1.0299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15816 Z= 0.137 Angle : 0.495 8.557 21472 Z= 0.258 Chirality : 0.039 0.151 2476 Planarity : 0.004 0.040 2636 Dihedral : 5.244 56.537 2252 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.60 % Allowed : 16.13 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.19), residues: 1876 helix: 2.00 (0.15), residues: 1124 sheet: 0.27 (0.32), residues: 228 loop : 0.01 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 338 TYR 0.015 0.001 TYR B 355 PHE 0.023 0.001 PHE B 333 TRP 0.013 0.001 TRP C 157 HIS 0.005 0.001 HIS A 409 Details of bonding type rmsd covalent geometry : bond 0.00302 (15808) covalent geometry : angle 0.49230 (21448) hydrogen bonds : bond 0.04100 ( 1023) hydrogen bonds : angle 4.37310 ( 2970) link_BETA1-4 : bond 0.00172 ( 4) link_BETA1-4 : angle 2.06749 ( 12) link_NAG-ASN : bond 0.00148 ( 4) link_NAG-ASN : angle 0.98477 ( 12) ********************** 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 131 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.381 Fit side-chains REVERT: B 57 ARG cc_start: 0.7469 (ttm170) cc_final: 0.7147 (mtm-85) REVERT: B 67 MET cc_start: 0.7873 (mtt) cc_final: 0.7639 (mtp) REVERT: B 176 ASP cc_start: 0.8451 (t0) cc_final: 0.7978 (m-30) REVERT: B 184 ILE cc_start: 0.8996 (mt) cc_final: 0.8689 (mm) REVERT: B 249 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8071 (mt-10) REVERT: B 297 PHE cc_start: 0.7381 (t80) cc_final: 0.7025 (t80) REVERT: B 321 LEU cc_start: 0.8328 (tp) cc_final: 0.8106 (tm) REVERT: B 426 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7734 (mtp) REVERT: C 46 LYS cc_start: 0.7779 (ttpt) cc_final: 0.7455 (ttmm) REVERT: C 176 ASP cc_start: 0.8307 (t70) cc_final: 0.7836 (m-30) REVERT: C 278 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8335 (mtmt) REVERT: C 296 SER cc_start: 0.7827 (t) cc_final: 0.7561 (m) REVERT: C 334 MET cc_start: 0.5774 (OUTLIER) cc_final: 0.5445 (mmm) REVERT: C 426 MET cc_start: 0.8432 (mmm) cc_final: 0.7883 (mtp) REVERT: D 67 MET cc_start: 0.7690 (ppp) cc_final: 0.7354 (ptp) REVERT: D 312 SER cc_start: 0.8552 (OUTLIER) cc_final: 0.8065 (m) REVERT: D 314 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8316 (mp) REVERT: D 378 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.7015 (mtmm) REVERT: D 426 MET cc_start: 0.8588 (mmp) cc_final: 0.7853 (mtp) REVERT: A 297 PHE cc_start: 0.7850 (t80) cc_final: 0.7436 (t80) REVERT: A 301 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.6374 (t80) REVERT: A 379 ASN cc_start: 0.8121 (m-40) cc_final: 0.7912 (m-40) REVERT: A 508 MET cc_start: 0.8673 (mmt) cc_final: 0.8155 (mmm) outliers start: 27 outliers final: 13 residues processed: 120 average time/residue: 0.4414 time to fit residues: 60.2950 Evaluate side-chains 118 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain B residue 345 TRP Chi-restraints excluded: chain B residue 397 VAL 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 334 MET Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 290 SER Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 393 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 4 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 chunk 151 optimal weight: 0.3980 chunk 115 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 194 GLN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.108256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.081585 restraints weight = 23439.602| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.68 r_work: 0.2882 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 1.0348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15816 Z= 0.109 Angle : 0.489 10.029 21472 Z= 0.252 Chirality : 0.038 0.148 2476 Planarity : 0.003 0.040 2636 Dihedral : 5.140 55.199 2252 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.42 % Allowed : 16.73 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.19), residues: 1876 helix: 2.02 (0.15), residues: 1140 sheet: 0.30 (0.32), residues: 228 loop : 0.13 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 44 TYR 0.013 0.001 TYR B 497 PHE 0.031 0.001 PHE B 333 TRP 0.012 0.001 TRP B 157 HIS 0.005 0.001 HIS A 409 Details of bonding type rmsd covalent geometry : bond 0.00228 (15808) covalent geometry : angle 0.48735 (21448) hydrogen bonds : bond 0.03820 ( 1023) hydrogen bonds : angle 4.29542 ( 2970) link_BETA1-4 : bond 0.00242 ( 4) link_BETA1-4 : angle 1.90629 ( 12) link_NAG-ASN : bond 0.00054 ( 4) link_NAG-ASN : angle 0.73924 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4714.57 seconds wall clock time: 81 minutes 33.65 seconds (4893.65 seconds total)