Starting phenix.real_space_refine on Wed Jun 25 06:08:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ekk_28205/06_2025/8ekk_28205.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ekk_28205/06_2025/8ekk_28205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ekk_28205/06_2025/8ekk_28205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ekk_28205/06_2025/8ekk_28205.map" model { file = "/net/cci-nas-00/data/ceres_data/8ekk_28205/06_2025/8ekk_28205.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ekk_28205/06_2025/8ekk_28205.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.016 sd= 0.951 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 14 9.91 5 S 70 5.16 5 C 18655 2.51 5 N 4788 2.21 5 O 6097 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29624 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4230 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 510} Chain breaks: 6 Chain: "B" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4230 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 510} Chain breaks: 6 Chain: "C" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4230 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 510} Chain breaks: 6 Chain: "D" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4230 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 510} Chain breaks: 6 Chain: "E" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4230 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 510} Chain breaks: 6 Chain: "F" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4230 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 510} Chain breaks: 6 Chain: "G" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4230 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 510} Chain breaks: 6 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.11, per 1000 atoms: 0.58 Number of scatterers: 29624 At special positions: 0 Unit cell: (154.686, 156.464, 135.128, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 14 19.99 S 70 16.00 O 6097 8.00 N 4788 7.00 C 18655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.25 Conformation dependent library (CDL) restraints added in 3.9 seconds 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7014 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 78 sheets defined 20.3% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.52 Creating SS restraints... Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 246 through 253 removed outlier: 3.648A pdb=" N ALA A 250 " --> pdb=" O ASP A 247 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 287 through 291 removed outlier: 3.611A pdb=" N ASP A 291 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.923A pdb=" N ILE A 429 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 503 through 513 removed outlier: 4.590A pdb=" N SER A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 513 " --> pdb=" O GLN A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 555 Processing helix chain 'A' and resid 581 through 593 removed outlier: 3.882A pdb=" N LYS A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'A' and resid 757 through 765 removed outlier: 3.731A pdb=" N HIS A 765 " --> pdb=" O ILE A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 801 Processing helix chain 'A' and resid 829 through 831 No H-bonds generated for 'chain 'A' and resid 829 through 831' Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.696A pdb=" N ALA B 250 " --> pdb=" O ASP B 247 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 286 through 291 removed outlier: 3.654A pdb=" N ASP B 291 " --> pdb=" O GLU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 471 Processing helix chain 'B' and resid 503 through 513 removed outlier: 4.616A pdb=" N SER B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLN B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE B 513 " --> pdb=" O GLN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 581 through 595 removed outlier: 3.991A pdb=" N LYS B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 603 Processing helix chain 'B' and resid 757 through 765 removed outlier: 4.008A pdb=" N HIS B 765 " --> pdb=" O ILE B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 801 Processing helix chain 'B' and resid 829 through 831 No H-bonds generated for 'chain 'B' and resid 829 through 831' Processing helix chain 'B' and resid 843 through 845 No H-bonds generated for 'chain 'B' and resid 843 through 845' Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 246 through 253 removed outlier: 3.577A pdb=" N ALA C 250 " --> pdb=" O ASP C 247 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU C 251 " --> pdb=" O SER C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 279 Processing helix chain 'C' and resid 286 through 291 removed outlier: 3.749A pdb=" N ASP C 291 " --> pdb=" O GLU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.921A pdb=" N ILE C 429 " --> pdb=" O GLU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 471 Processing helix chain 'C' and resid 503 through 513 removed outlier: 4.619A pdb=" N SER C 508 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLN C 509 " --> pdb=" O ASP C 505 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C 513 " --> pdb=" O GLN C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 581 through 595 removed outlier: 3.873A pdb=" N LYS C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'C' and resid 757 through 765 removed outlier: 3.837A pdb=" N HIS C 765 " --> pdb=" O ILE C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 801 removed outlier: 3.600A pdb=" N ILE C 801 " --> pdb=" O ALA C 797 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 831 No H-bonds generated for 'chain 'C' and resid 829 through 831' Processing helix chain 'C' and resid 841 through 845 Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'D' and resid 246 through 253 removed outlier: 3.775A pdb=" N GLU D 251 " --> pdb=" O SER D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 279 Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.736A pdb=" N ASP D 291 " --> pdb=" O GLU D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 removed outlier: 4.045A pdb=" N ILE D 429 " --> pdb=" O GLU D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 471 Processing helix chain 'D' and resid 503 through 513 removed outlier: 4.573A pdb=" N SER D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLN D 509 " --> pdb=" O ASP D 505 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE D 513 " --> pdb=" O GLN D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 555 Processing helix chain 'D' and resid 581 through 595 removed outlier: 3.823A pdb=" N LYS D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 603 Processing helix chain 'D' and resid 757 through 765 removed outlier: 3.967A pdb=" N HIS D 765 " --> pdb=" O ILE D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 801 Processing helix chain 'D' and resid 829 through 831 No H-bonds generated for 'chain 'D' and resid 829 through 831' Processing helix chain 'D' and resid 841 through 845 Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'E' and resid 246 through 253 removed outlier: 4.368A pdb=" N GLU E 251 " --> pdb=" O SER E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 279 Processing helix chain 'E' and resid 286 through 291 removed outlier: 3.595A pdb=" N ASP E 291 " --> pdb=" O GLU E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.955A pdb=" N ILE E 429 " --> pdb=" O GLU E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 471 Processing helix chain 'E' and resid 503 through 513 removed outlier: 4.627A pdb=" N SER E 508 " --> pdb=" O SER E 504 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLN E 509 " --> pdb=" O ASP E 505 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE E 513 " --> pdb=" O GLN E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 556 Processing helix chain 'E' and resid 581 through 595 removed outlier: 3.940A pdb=" N LYS E 593 " --> pdb=" O LYS E 589 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR E 594 " --> pdb=" O ASP E 590 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 595 " --> pdb=" O SER E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 603 Processing helix chain 'E' and resid 757 through 765 removed outlier: 3.982A pdb=" N HIS E 765 " --> pdb=" O ILE E 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 794 through 801 Processing helix chain 'E' and resid 829 through 831 No H-bonds generated for 'chain 'E' and resid 829 through 831' Processing helix chain 'E' and resid 843 through 845 No H-bonds generated for 'chain 'E' and resid 843 through 845' Processing helix chain 'F' and resid 227 through 234 Processing helix chain 'F' and resid 246 through 253 removed outlier: 3.506A pdb=" N ALA F 250 " --> pdb=" O ASP F 247 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU F 251 " --> pdb=" O SER F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 279 Processing helix chain 'F' and resid 286 through 291 removed outlier: 3.666A pdb=" N ASP F 291 " --> pdb=" O GLU F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.882A pdb=" N ILE F 429 " --> pdb=" O GLU F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 471 Processing helix chain 'F' and resid 503 through 513 removed outlier: 4.566A pdb=" N SER F 508 " --> pdb=" O SER F 504 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN F 509 " --> pdb=" O ASP F 505 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE F 513 " --> pdb=" O GLN F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 556 Processing helix chain 'F' and resid 581 through 595 removed outlier: 3.880A pdb=" N LYS F 593 " --> pdb=" O LYS F 589 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR F 594 " --> pdb=" O ASP F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 603 Processing helix chain 'F' and resid 757 through 765 removed outlier: 3.836A pdb=" N HIS F 765 " --> pdb=" O ILE F 761 " (cutoff:3.500A) Processing helix chain 'F' and resid 794 through 801 Processing helix chain 'F' and resid 829 through 831 No H-bonds generated for 'chain 'F' and resid 829 through 831' Processing helix chain 'F' and resid 841 through 845 Processing helix chain 'G' and resid 227 through 234 Processing helix chain 'G' and resid 246 through 251 removed outlier: 3.564A pdb=" N ALA G 250 " --> pdb=" O ASP G 247 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU G 251 " --> pdb=" O SER G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 279 Processing helix chain 'G' and resid 286 through 291 removed outlier: 3.693A pdb=" N ASP G 291 " --> pdb=" O GLU G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.931A pdb=" N ILE G 429 " --> pdb=" O GLU G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 471 Processing helix chain 'G' and resid 503 through 513 removed outlier: 4.751A pdb=" N SER G 508 " --> pdb=" O SER G 504 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLN G 509 " --> pdb=" O ASP G 505 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE G 513 " --> pdb=" O GLN G 509 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 556 Processing helix chain 'G' and resid 581 through 595 removed outlier: 3.931A pdb=" N LYS G 593 " --> pdb=" O LYS G 589 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR G 594 " --> pdb=" O ASP G 590 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 603 Processing helix chain 'G' and resid 757 through 765 removed outlier: 3.840A pdb=" N HIS G 765 " --> pdb=" O ILE G 761 " (cutoff:3.500A) Processing helix chain 'G' and resid 794 through 801 removed outlier: 3.511A pdb=" N ILE G 801 " --> pdb=" O ALA G 797 " (cutoff:3.500A) Processing helix chain 'G' and resid 829 through 831 No H-bonds generated for 'chain 'G' and resid 829 through 831' Processing helix chain 'G' and resid 843 through 845 No H-bonds generated for 'chain 'G' and resid 843 through 845' Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 238 Processing sheet with id=AA2, first strand: chain 'A' and resid 294 through 295 removed outlier: 4.824A pdb=" N ARG A 529 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N ILE A 611 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER A 516 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE A 613 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE A 518 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 300 through 311 removed outlier: 5.643A pdb=" N VAL A 302 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N TYR A 396 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N MET A 304 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ARG A 394 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS A 306 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 314 through 327 removed outlier: 3.529A pdb=" N SER A 316 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 369 " --> pdb=" O THR B 327 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER B 374 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER B 370 " --> pdb=" O SER B 324 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 313 through 323 current: chain 'D' and resid 313 through 327 removed outlier: 3.643A pdb=" N SER D 374 " --> pdb=" O GLY D 320 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER D 370 " --> pdb=" O SER D 324 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP D 369 " --> pdb=" O THR E 327 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG E 325 " --> pdb=" O ASN D 371 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER E 374 " --> pdb=" O GLY E 320 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER E 370 " --> pdb=" O SER E 324 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 313 through 323 current: chain 'G' and resid 313 through 323 Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 423 removed outlier: 6.813A pdb=" N LEU A 412 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS A 423 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LYS A 405 " --> pdb=" O ASN A 486 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASN A 486 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN A 482 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASN A 411 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR A 480 " --> pdb=" O ASN A 411 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL A 413 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LEU A 478 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA7, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AA8, first strand: chain 'A' and resid 618 through 620 Processing sheet with id=AA9, first strand: chain 'A' and resid 674 through 675 Processing sheet with id=AB1, first strand: chain 'A' and resid 768 through 771 removed outlier: 3.523A pdb=" N PHE A 769 " --> pdb=" O TYR A 787 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 785 " --> pdb=" O ASP A 771 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 820 through 821 removed outlier: 4.893A pdb=" N LYS A 803 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 863 " --> pdb=" O LYS A 803 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE A 860 " --> pdb=" O VAL A 872 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 826 through 827 Processing sheet with id=AB4, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AB5, first strand: chain 'B' and resid 300 through 311 removed outlier: 5.692A pdb=" N VAL B 302 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N TYR B 396 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N MET B 304 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG B 394 " --> pdb=" O MET B 304 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS B 306 " --> pdb=" O ASN B 392 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 439 " --> pdb=" O TYR B 395 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 418 through 423 removed outlier: 6.804A pdb=" N LEU B 412 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR B 421 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR B 410 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN B 482 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASN B 411 " --> pdb=" O THR B 480 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N THR B 480 " --> pdb=" O ASN B 411 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL B 413 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU B 478 " --> pdb=" O VAL B 413 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB8, first strand: chain 'B' and resid 526 through 531 removed outlier: 9.077A pdb=" N ILE B 611 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N SER B 516 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE B 613 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE B 518 " --> pdb=" O ILE B 613 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 558 through 559 Processing sheet with id=AC1, first strand: chain 'B' and resid 618 through 619 Processing sheet with id=AC2, first strand: chain 'B' and resid 674 through 675 removed outlier: 3.618A pdb=" N SER B 675 " --> pdb=" O THR B 705 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 705 " --> pdb=" O SER B 675 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 768 through 772 removed outlier: 6.316A pdb=" N PHE B 769 " --> pdb=" O MET B 786 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N MET B 786 " --> pdb=" O PHE B 769 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASP B 771 " --> pdb=" O ASN B 784 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 820 through 821 removed outlier: 4.916A pdb=" N LYS B 803 " --> pdb=" O ILE B 863 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 863 " --> pdb=" O LYS B 803 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE B 860 " --> pdb=" O VAL B 872 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 826 through 827 Processing sheet with id=AC6, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=AC7, first strand: chain 'C' and resid 294 through 295 removed outlier: 4.782A pdb=" N ARG C 529 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N ILE C 611 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER C 516 " --> pdb=" O ILE C 611 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ILE C 613 " --> pdb=" O SER C 516 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE C 518 " --> pdb=" O ILE C 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 300 through 302 Processing sheet with id=AC9, first strand: chain 'C' and resid 306 through 311 removed outlier: 3.832A pdb=" N LYS C 306 " --> pdb=" O ASN C 392 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 391 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 418 through 423 removed outlier: 6.777A pdb=" N LEU C 412 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR C 421 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR C 410 " --> pdb=" O THR C 421 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LYS C 423 " --> pdb=" O PRO C 408 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LYS C 405 " --> pdb=" O ASN C 486 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASN C 486 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN C 482 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASN C 411 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N THR C 480 " --> pdb=" O ASN C 411 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL C 413 " --> pdb=" O LEU C 478 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LEU C 478 " --> pdb=" O VAL C 413 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 489 through 490 Processing sheet with id=AD3, first strand: chain 'C' and resid 558 through 559 Processing sheet with id=AD4, first strand: chain 'C' and resid 618 through 620 removed outlier: 3.613A pdb=" N TYR C 618 " --> pdb=" O ILE C 738 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 674 through 675 removed outlier: 3.558A pdb=" N THR C 705 " --> pdb=" O SER C 675 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 768 through 771 removed outlier: 3.557A pdb=" N PHE C 769 " --> pdb=" O TYR C 787 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 820 through 821 removed outlier: 4.888A pdb=" N LYS C 803 " --> pdb=" O ILE C 863 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE C 863 " --> pdb=" O LYS C 803 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE C 860 " --> pdb=" O VAL C 872 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 826 through 827 Processing sheet with id=AD9, first strand: chain 'D' and resid 235 through 237 Processing sheet with id=AE1, first strand: chain 'D' and resid 294 through 295 removed outlier: 4.843A pdb=" N ARG D 529 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 9.143A pdb=" N ILE D 611 " --> pdb=" O SER D 514 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N SER D 516 " --> pdb=" O ILE D 611 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE D 613 " --> pdb=" O SER D 516 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE D 518 " --> pdb=" O ILE D 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 300 through 311 removed outlier: 5.618A pdb=" N VAL D 302 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N TYR D 396 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N MET D 304 " --> pdb=" O ARG D 394 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARG D 394 " --> pdb=" O MET D 304 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS D 306 " --> pdb=" O ASN D 392 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 418 through 423 removed outlier: 6.795A pdb=" N LEU D 412 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR D 421 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR D 410 " --> pdb=" O THR D 421 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS D 423 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL D 406 " --> pdb=" O SER D 484 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER D 484 " --> pdb=" O VAL D 406 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLN D 482 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR D 410 " --> pdb=" O THR D 480 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR D 480 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU D 412 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU D 478 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AE5, first strand: chain 'D' and resid 558 through 559 Processing sheet with id=AE6, first strand: chain 'D' and resid 618 through 619 Processing sheet with id=AE7, first strand: chain 'D' and resid 768 through 772 removed outlier: 6.231A pdb=" N PHE D 769 " --> pdb=" O MET D 786 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N MET D 786 " --> pdb=" O PHE D 769 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASP D 771 " --> pdb=" O ASN D 784 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 820 through 821 removed outlier: 4.867A pdb=" N LYS D 803 " --> pdb=" O ILE D 863 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE D 863 " --> pdb=" O LYS D 803 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE D 860 " --> pdb=" O VAL D 872 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 826 through 827 Processing sheet with id=AF1, first strand: chain 'E' and resid 235 through 238 Processing sheet with id=AF2, first strand: chain 'E' and resid 300 through 311 removed outlier: 5.599A pdb=" N VAL E 302 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N TYR E 396 " --> pdb=" O VAL E 302 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N MET E 304 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG E 394 " --> pdb=" O MET E 304 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS E 306 " --> pdb=" O ASN E 392 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 403 through 413 removed outlier: 4.825A pdb=" N LYS E 423 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR E 410 " --> pdb=" O THR E 421 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR E 421 " --> pdb=" O THR E 410 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU E 412 " --> pdb=" O LEU E 419 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 489 through 490 Processing sheet with id=AF5, first strand: chain 'E' and resid 526 through 531 removed outlier: 9.110A pdb=" N ILE E 611 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N SER E 516 " --> pdb=" O ILE E 611 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ILE E 613 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE E 518 " --> pdb=" O ILE E 613 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 558 through 559 Processing sheet with id=AF7, first strand: chain 'E' and resid 618 through 620 removed outlier: 3.559A pdb=" N TYR E 618 " --> pdb=" O ILE E 738 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 674 through 675 Processing sheet with id=AF9, first strand: chain 'E' and resid 768 through 772 removed outlier: 6.226A pdb=" N PHE E 769 " --> pdb=" O MET E 786 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N MET E 786 " --> pdb=" O PHE E 769 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP E 771 " --> pdb=" O ASN E 784 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 820 through 821 removed outlier: 4.891A pdb=" N LYS E 803 " --> pdb=" O ILE E 863 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE E 863 " --> pdb=" O LYS E 803 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE E 860 " --> pdb=" O VAL E 872 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 826 through 827 Processing sheet with id=AG3, first strand: chain 'F' and resid 235 through 238 Processing sheet with id=AG4, first strand: chain 'F' and resid 294 through 295 removed outlier: 4.812A pdb=" N ARG F 529 " --> pdb=" O ALA F 295 " (cutoff:3.500A) removed outlier: 9.136A pdb=" N ILE F 611 " --> pdb=" O SER F 514 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER F 516 " --> pdb=" O ILE F 611 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE F 613 " --> pdb=" O SER F 516 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE F 518 " --> pdb=" O ILE F 613 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 300 through 302 removed outlier: 3.503A pdb=" N TYR F 439 " --> pdb=" O TYR F 395 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 306 through 311 removed outlier: 3.720A pdb=" N LYS F 306 " --> pdb=" O ASN F 392 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA F 391 " --> pdb=" O LEU F 449 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 418 through 423 removed outlier: 6.764A pdb=" N LEU F 412 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR F 421 " --> pdb=" O THR F 410 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR F 410 " --> pdb=" O THR F 421 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LYS F 423 " --> pdb=" O PRO F 408 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL F 406 " --> pdb=" O SER F 484 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER F 484 " --> pdb=" O VAL F 406 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN F 482 " --> pdb=" O PRO F 408 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR F 410 " --> pdb=" O THR F 480 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR F 480 " --> pdb=" O THR F 410 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU F 412 " --> pdb=" O LEU F 478 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU F 478 " --> pdb=" O LEU F 412 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 489 through 490 Processing sheet with id=AG9, first strand: chain 'F' and resid 558 through 559 Processing sheet with id=AH1, first strand: chain 'F' and resid 618 through 620 removed outlier: 3.563A pdb=" N TYR F 618 " --> pdb=" O ILE F 738 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 674 through 675 removed outlier: 3.505A pdb=" N THR F 705 " --> pdb=" O SER F 675 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 768 through 771 removed outlier: 3.539A pdb=" N PHE F 769 " --> pdb=" O TYR F 787 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 815 through 821 removed outlier: 6.076A pdb=" N VAL F 806 " --> pdb=" O ILE F 818 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N THR F 820 " --> pdb=" O TYR F 804 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TYR F 804 " --> pdb=" O THR F 820 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LYS F 803 " --> pdb=" O ILE F 863 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE F 863 " --> pdb=" O LYS F 803 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE F 860 " --> pdb=" O VAL F 872 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 826 through 827 Processing sheet with id=AH6, first strand: chain 'G' and resid 235 through 238 Processing sheet with id=AH7, first strand: chain 'G' and resid 294 through 295 removed outlier: 4.811A pdb=" N ARG G 529 " --> pdb=" O ALA G 295 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N ILE G 611 " --> pdb=" O SER G 514 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N SER G 516 " --> pdb=" O ILE G 611 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ILE G 613 " --> pdb=" O SER G 516 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE G 518 " --> pdb=" O ILE G 613 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 300 through 311 removed outlier: 5.636A pdb=" N VAL G 302 " --> pdb=" O TYR G 396 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N TYR G 396 " --> pdb=" O VAL G 302 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N MET G 304 " --> pdb=" O ARG G 394 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG G 394 " --> pdb=" O MET G 304 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS G 306 " --> pdb=" O ASN G 392 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 418 through 423 removed outlier: 6.811A pdb=" N LEU G 412 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR G 421 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR G 410 " --> pdb=" O THR G 421 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LYS G 423 " --> pdb=" O PRO G 408 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL G 406 " --> pdb=" O SER G 484 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER G 484 " --> pdb=" O VAL G 406 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLN G 482 " --> pdb=" O PRO G 408 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR G 410 " --> pdb=" O THR G 480 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N THR G 480 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU G 412 " --> pdb=" O LEU G 478 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU G 478 " --> pdb=" O LEU G 412 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 489 through 490 Processing sheet with id=AI2, first strand: chain 'G' and resid 558 through 559 Processing sheet with id=AI3, first strand: chain 'G' and resid 618 through 619 removed outlier: 3.604A pdb=" N TYR G 618 " --> pdb=" O ILE G 738 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 768 through 772 removed outlier: 6.349A pdb=" N PHE G 769 " --> pdb=" O MET G 786 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N MET G 786 " --> pdb=" O PHE G 769 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASP G 771 " --> pdb=" O ASN G 784 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'G' and resid 820 through 821 removed outlier: 4.876A pdb=" N LYS G 803 " --> pdb=" O ILE G 863 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE G 863 " --> pdb=" O LYS G 803 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE G 860 " --> pdb=" O VAL G 872 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'G' and resid 826 through 827 819 hydrogen bonds defined for protein. 2028 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: 10.80 Time building geometry restraints manager: 8.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9600 1.34 - 1.45: 4248 1.45 - 1.57: 16160 1.57 - 1.69: 1 1.69 - 1.81: 133 Bond restraints: 30142 Sorted by residual: bond pdb=" CB GLU E 522 " pdb=" CG GLU E 522 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.30e+00 bond pdb=" CB GLU G 522 " pdb=" CG GLU G 522 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.29e+00 bond pdb=" C TYR D 297 " pdb=" O TYR D 297 " ideal model delta sigma weight residual 1.249 1.237 0.012 8.50e-03 1.38e+04 1.87e+00 bond pdb=" CB ASP C 561 " pdb=" CG ASP C 561 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.80e+00 bond pdb=" CA GLU E 522 " pdb=" CB GLU E 522 " ideal model delta sigma weight residual 1.533 1.550 -0.017 1.37e-02 5.33e+03 1.53e+00 ... (remaining 30137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 40504 2.12 - 4.25: 265 4.25 - 6.37: 23 6.37 - 8.50: 9 8.50 - 10.62: 2 Bond angle restraints: 40803 Sorted by residual: angle pdb=" CA GLU E 522 " pdb=" CB GLU E 522 " pdb=" CG GLU E 522 " ideal model delta sigma weight residual 114.10 124.72 -10.62 2.00e+00 2.50e-01 2.82e+01 angle pdb=" CB GLU E 522 " pdb=" CG GLU E 522 " pdb=" CD GLU E 522 " ideal model delta sigma weight residual 112.60 119.72 -7.12 1.70e+00 3.46e-01 1.75e+01 angle pdb=" CB GLU G 522 " pdb=" CG GLU G 522 " pdb=" CD GLU G 522 " ideal model delta sigma weight residual 112.60 119.11 -6.51 1.70e+00 3.46e-01 1.47e+01 angle pdb=" CA GLU G 522 " pdb=" CB GLU G 522 " pdb=" CG GLU G 522 " ideal model delta sigma weight residual 114.10 120.92 -6.82 2.00e+00 2.50e-01 1.16e+01 angle pdb=" C MET D 762 " pdb=" N ASP D 763 " pdb=" CA ASP D 763 " ideal model delta sigma weight residual 122.06 116.26 5.80 1.86e+00 2.89e-01 9.74e+00 ... (remaining 40798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 15485 17.43 - 34.86: 2099 34.86 - 52.29: 532 52.29 - 69.71: 106 69.71 - 87.14: 55 Dihedral angle restraints: 18277 sinusoidal: 7322 harmonic: 10955 Sorted by residual: dihedral pdb=" CA ASN C 223 " pdb=" C ASN C 223 " pdb=" N ASP C 224 " pdb=" CA ASP C 224 " ideal model delta harmonic sigma weight residual 180.00 161.01 18.99 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA ASN E 223 " pdb=" C ASN E 223 " pdb=" N ASP E 224 " pdb=" CA ASP E 224 " ideal model delta harmonic sigma weight residual 180.00 161.20 18.80 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA PHE A 566 " pdb=" C PHE A 566 " pdb=" N ASN A 567 " pdb=" CA ASN A 567 " ideal model delta harmonic sigma weight residual 180.00 161.36 18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 18274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3687 0.052 - 0.103: 656 0.103 - 0.155: 193 0.155 - 0.207: 5 0.207 - 0.258: 2 Chirality restraints: 4543 Sorted by residual: chirality pdb=" CB THR G 521 " pdb=" CA THR G 521 " pdb=" OG1 THR G 521 " pdb=" CG2 THR G 521 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB THR D 521 " pdb=" CA THR D 521 " pdb=" OG1 THR D 521 " pdb=" CG2 THR D 521 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ASN D 523 " pdb=" N ASN D 523 " pdb=" C ASN D 523 " pdb=" CB ASN D 523 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.21e-01 ... (remaining 4540 not shown) Planarity restraints: 5285 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU E 522 " -0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" CD GLU E 522 " 0.073 2.00e-02 2.50e+03 pdb=" OE1 GLU E 522 " -0.026 2.00e-02 2.50e+03 pdb=" OE2 GLU E 522 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU G 522 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.84e+00 pdb=" CD GLU G 522 " 0.045 2.00e-02 2.50e+03 pdb=" OE1 GLU G 522 " -0.017 2.00e-02 2.50e+03 pdb=" OE2 GLU G 522 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 522 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" C GLU G 522 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU G 522 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN G 523 " 0.014 2.00e-02 2.50e+03 ... (remaining 5282 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2063 2.73 - 3.27: 27355 3.27 - 3.82: 45305 3.82 - 4.36: 55945 4.36 - 4.90: 101081 Nonbonded interactions: 231749 Sorted by model distance: nonbonded pdb=" OG SER C 672 " pdb=" OG SER C 708 " model vdw 2.191 3.040 nonbonded pdb=" OD1 ASP G 222 " pdb="CA CA G 902 " model vdw 2.233 2.510 nonbonded pdb=" OD1 ASP F 581 " pdb=" OG1 THR F 584 " model vdw 2.245 3.040 nonbonded pdb=" OD1 ASP C 581 " pdb=" OG1 THR C 584 " model vdw 2.247 3.040 nonbonded pdb=" OG SER E 672 " pdb=" OG SER E 708 " model vdw 2.249 3.040 ... (remaining 231744 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.220 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 65.190 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 : 0.002 0.055 30142 Z= 0.106 Angle : 0.480 10.623 40803 Z= 0.258 Chirality : 0.043 0.258 4543 Planarity : 0.003 0.042 5285 Dihedral : 17.363 87.144 11263 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.15 % Allowed : 27.27 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.14), residues: 3633 helix: -0.07 (0.22), residues: 539 sheet: -0.90 (0.17), residues: 973 loop : -0.78 (0.13), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 375 HIS 0.002 0.001 HIS F 314 PHE 0.013 0.001 PHE C 707 TYR 0.010 0.001 TYR D 439 ARG 0.006 0.000 ARG B 458 Details of bonding type rmsd hydrogen bonds : bond 0.23578 ( 819) hydrogen bonds : angle 8.00258 ( 2028) covalent geometry : bond 0.00244 (30142) covalent geometry : angle 0.48002 (40803) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 237 time to evaluate : 3.452 Fit side-chains revert: symmetry clash REVERT: G 709 TYR cc_start: 0.8364 (m-80) cc_final: 0.8156 (m-80) outliers start: 5 outliers final: 1 residues processed: 240 average time/residue: 0.3998 time to fit residues: 157.1818 Evaluate side-chains 219 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 3.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 870 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 313 optimal weight: 10.0000 chunk 281 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 96 optimal weight: 0.0670 chunk 189 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 290 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 216 optimal weight: 0.4980 chunk 336 optimal weight: 2.9990 overall best weight: 1.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN A 834 GLN B 368 GLN B 523 ASN B 583 ASN B 773 ASN B 784 ASN C 368 GLN C 834 GLN E 368 GLN F 368 GLN F 501 ASN F 834 GLN G 431 ASN G 773 ASN G 784 ASN G 834 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.135290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.109011 restraints weight = 39488.108| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.47 r_work: 0.3271 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 30142 Z= 0.101 Angle : 0.463 8.980 40803 Z= 0.250 Chirality : 0.043 0.180 4543 Planarity : 0.003 0.033 5285 Dihedral : 4.094 32.823 4041 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.69 % Allowed : 25.73 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3633 helix: 0.22 (0.22), residues: 553 sheet: -0.71 (0.16), residues: 1015 loop : -0.57 (0.14), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 375 HIS 0.002 0.000 HIS F 314 PHE 0.009 0.001 PHE A 619 TYR 0.013 0.001 TYR G 669 ARG 0.004 0.000 ARG C 458 Details of bonding type rmsd hydrogen bonds : bond 0.03221 ( 819) hydrogen bonds : angle 5.33134 ( 2028) covalent geometry : bond 0.00233 (30142) covalent geometry : angle 0.46337 (40803) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 237 time to evaluate : 3.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 825 MET cc_start: 0.8428 (mmt) cc_final: 0.8137 (mmt) REVERT: E 414 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8062 (tp) REVERT: F 707 PHE cc_start: 0.6173 (OUTLIER) cc_final: 0.4398 (p90) REVERT: F 843 ARG cc_start: 0.8530 (mmm-85) cc_final: 0.8284 (mmp-170) outliers start: 56 outliers final: 27 residues processed: 288 average time/residue: 0.3815 time to fit residues: 180.6439 Evaluate side-chains 236 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 3.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain D residue 371 ASN Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 757 THR Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain E residue 802 GLN Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 582 ASP Chi-restraints excluded: chain F residue 625 TYR Chi-restraints excluded: chain F residue 707 PHE Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain G residue 263 GLU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 763 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 205 optimal weight: 8.9990 chunk 183 optimal weight: 0.2980 chunk 36 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 312 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 chunk 129 optimal weight: 5.9990 chunk 352 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 303 optimal weight: 0.3980 chunk 191 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 742 ASN B 368 GLN C 368 GLN D 368 GLN E 368 GLN F 368 GLN F 501 ASN G 368 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.130701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.103807 restraints weight = 40309.835| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.52 r_work: 0.3233 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30142 Z= 0.157 Angle : 0.500 9.181 40803 Z= 0.268 Chirality : 0.044 0.190 4543 Planarity : 0.003 0.036 5285 Dihedral : 4.281 20.498 4039 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.63 % Allowed : 25.79 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3633 helix: 0.24 (0.22), residues: 553 sheet: -0.68 (0.16), residues: 1015 loop : -0.65 (0.14), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 245 HIS 0.002 0.001 HIS F 314 PHE 0.015 0.001 PHE B 707 TYR 0.012 0.001 TYR B 261 ARG 0.003 0.000 ARG B 458 Details of bonding type rmsd hydrogen bonds : bond 0.03119 ( 819) hydrogen bonds : angle 4.96131 ( 2028) covalent geometry : bond 0.00385 (30142) covalent geometry : angle 0.50037 (40803) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 209 time to evaluate : 3.539 Fit side-chains revert: symmetry clash REVERT: A 414 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8056 (tp) REVERT: C 371 ASN cc_start: 0.8031 (p0) cc_final: 0.7246 (p0) REVERT: D 239 ASP cc_start: 0.7746 (t0) cc_final: 0.7500 (t0) REVERT: D 414 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8091 (tp) REVERT: E 707 PHE cc_start: 0.5740 (OUTLIER) cc_final: 0.4862 (p90) REVERT: F 707 PHE cc_start: 0.6226 (OUTLIER) cc_final: 0.4382 (p90) outliers start: 87 outliers final: 62 residues processed: 285 average time/residue: 0.4096 time to fit residues: 193.6084 Evaluate side-chains 264 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 198 time to evaluate : 3.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 874 SER Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 371 ASN Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 874 SER Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain E residue 757 THR Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 582 ASP Chi-restraints excluded: chain F residue 707 PHE Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain F residue 874 SER Chi-restraints excluded: chain G residue 263 GLU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 407 THR Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 582 ASP Chi-restraints excluded: chain G residue 763 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 149 optimal weight: 0.0470 chunk 61 optimal weight: 5.9990 chunk 200 optimal weight: 0.3980 chunk 141 optimal weight: 9.9990 chunk 292 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 276 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 overall best weight: 3.8884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN C 368 GLN D 368 GLN E 368 GLN E 501 ASN F 368 GLN G 368 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.131530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.104873 restraints weight = 40355.577| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.51 r_work: 0.3212 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 30142 Z= 0.195 Angle : 0.533 9.662 40803 Z= 0.285 Chirality : 0.046 0.199 4543 Planarity : 0.004 0.039 5285 Dihedral : 4.551 27.376 4039 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.57 % Allowed : 25.06 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.14), residues: 3633 helix: 0.07 (0.21), residues: 560 sheet: -0.52 (0.16), residues: 1050 loop : -0.77 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 245 HIS 0.003 0.001 HIS F 314 PHE 0.018 0.002 PHE B 707 TYR 0.013 0.001 TYR B 261 ARG 0.003 0.000 ARG B 458 Details of bonding type rmsd hydrogen bonds : bond 0.03150 ( 819) hydrogen bonds : angle 4.89561 ( 2028) covalent geometry : bond 0.00483 (30142) covalent geometry : angle 0.53312 (40803) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 207 time to evaluate : 3.384 Fit side-chains REVERT: A 414 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8124 (tp) REVERT: B 371 ASN cc_start: 0.7670 (p0) cc_final: 0.7404 (p0) REVERT: C 371 ASN cc_start: 0.8022 (p0) cc_final: 0.7297 (p0) REVERT: C 707 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.5959 (p90) REVERT: D 414 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8102 (tp) REVERT: D 561 ASP cc_start: 0.7505 (t0) cc_final: 0.7283 (t0) REVERT: E 707 PHE cc_start: 0.5825 (OUTLIER) cc_final: 0.4849 (p90) REVERT: F 630 SER cc_start: 0.6353 (OUTLIER) cc_final: 0.5935 (m) REVERT: F 707 PHE cc_start: 0.6350 (OUTLIER) cc_final: 0.4519 (p90) outliers start: 118 outliers final: 90 residues processed: 314 average time/residue: 0.3705 time to fit residues: 194.6855 Evaluate side-chains 294 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 198 time to evaluate : 3.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 874 SER Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 371 ASN Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 582 ASP Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 874 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain E residue 757 THR Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain E residue 802 GLN Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 582 ASP Chi-restraints excluded: chain F residue 625 TYR Chi-restraints excluded: chain F residue 630 SER Chi-restraints excluded: chain F residue 707 PHE Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain F residue 874 SER Chi-restraints excluded: chain G residue 263 GLU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 407 THR Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 582 ASP Chi-restraints excluded: chain G residue 757 THR Chi-restraints excluded: chain G residue 763 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 175 optimal weight: 1.9990 chunk 281 optimal weight: 2.9990 chunk 362 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 364 optimal weight: 9.9990 chunk 242 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 344 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN C 368 GLN D 368 GLN E 368 GLN F 368 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.133138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.106873 restraints weight = 39752.827| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.45 r_work: 0.3266 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30142 Z= 0.132 Angle : 0.482 9.637 40803 Z= 0.258 Chirality : 0.044 0.195 4543 Planarity : 0.003 0.038 5285 Dihedral : 4.339 27.471 4039 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.45 % Allowed : 25.45 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3633 helix: 0.18 (0.21), residues: 560 sheet: -0.42 (0.16), residues: 1050 loop : -0.72 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 375 HIS 0.003 0.001 HIS F 314 PHE 0.012 0.001 PHE B 707 TYR 0.011 0.001 TYR B 261 ARG 0.003 0.000 ARG C 668 Details of bonding type rmsd hydrogen bonds : bond 0.02570 ( 819) hydrogen bonds : angle 4.64387 ( 2028) covalent geometry : bond 0.00324 (30142) covalent geometry : angle 0.48171 (40803) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 218 time to evaluate : 3.175 Fit side-chains REVERT: A 373 GLU cc_start: 0.7995 (pt0) cc_final: 0.7648 (pt0) REVERT: B 371 ASN cc_start: 0.7642 (p0) cc_final: 0.7400 (p0) REVERT: B 707 PHE cc_start: 0.6715 (OUTLIER) cc_final: 0.6188 (p90) REVERT: C 371 ASN cc_start: 0.8046 (p0) cc_final: 0.7318 (p0) REVERT: D 414 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8007 (tp) REVERT: E 707 PHE cc_start: 0.5818 (OUTLIER) cc_final: 0.5046 (p90) REVERT: F 371 ASN cc_start: 0.8359 (p0) cc_final: 0.8097 (p0) REVERT: F 707 PHE cc_start: 0.6185 (OUTLIER) cc_final: 0.4371 (p90) REVERT: F 843 ARG cc_start: 0.8607 (mmm-85) cc_final: 0.8355 (mmp-170) REVERT: G 668 ARG cc_start: 0.8238 (ptm-80) cc_final: 0.8004 (ptm-80) outliers start: 114 outliers final: 91 residues processed: 323 average time/residue: 0.4008 time to fit residues: 216.3902 Evaluate side-chains 296 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 201 time to evaluate : 3.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 707 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 833 ASN Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 874 SER Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 371 ASN Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 582 ASP Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 874 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 310 SER Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 542 THR Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain E residue 757 THR Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain E residue 802 GLN Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 625 TYR Chi-restraints excluded: chain F residue 707 PHE Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain F residue 870 LEU Chi-restraints excluded: chain G residue 263 GLU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 407 THR Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 582 ASP Chi-restraints excluded: chain G residue 757 THR Chi-restraints excluded: chain G residue 763 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 93 optimal weight: 20.0000 chunk 41 optimal weight: 0.4980 chunk 249 optimal weight: 20.0000 chunk 329 optimal weight: 0.4980 chunk 202 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 330 optimal weight: 1.9990 chunk 326 optimal weight: 6.9990 chunk 174 optimal weight: 7.9990 chunk 367 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN C 368 GLN D 368 GLN E 368 GLN F 368 GLN G 368 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.132439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.106137 restraints weight = 40191.037| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.49 r_work: 0.3267 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 30142 Z= 0.183 Angle : 0.521 9.603 40803 Z= 0.279 Chirality : 0.045 0.214 4543 Planarity : 0.004 0.041 5285 Dihedral : 4.512 24.672 4039 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.27 % Allowed : 25.24 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3633 helix: 0.10 (0.21), residues: 560 sheet: -0.47 (0.16), residues: 1050 loop : -0.77 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 245 HIS 0.003 0.001 HIS F 314 PHE 0.016 0.002 PHE B 707 TYR 0.013 0.001 TYR B 261 ARG 0.003 0.000 ARG A 668 Details of bonding type rmsd hydrogen bonds : bond 0.02917 ( 819) hydrogen bonds : angle 4.70160 ( 2028) covalent geometry : bond 0.00452 (30142) covalent geometry : angle 0.52073 (40803) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 200 time to evaluate : 3.810 Fit side-chains REVERT: A 373 GLU cc_start: 0.8035 (pt0) cc_final: 0.7651 (pt0) REVERT: A 414 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8112 (tp) REVERT: A 625 TYR cc_start: 0.7692 (OUTLIER) cc_final: 0.5604 (m-80) REVERT: B 371 ASN cc_start: 0.7609 (p0) cc_final: 0.7359 (p0) REVERT: B 707 PHE cc_start: 0.6743 (OUTLIER) cc_final: 0.6224 (p90) REVERT: C 371 ASN cc_start: 0.7977 (p0) cc_final: 0.7269 (p0) REVERT: C 707 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.5715 (p90) REVERT: D 414 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8091 (tp) REVERT: E 707 PHE cc_start: 0.5857 (OUTLIER) cc_final: 0.4938 (p90) REVERT: F 707 PHE cc_start: 0.6334 (OUTLIER) cc_final: 0.4659 (p90) REVERT: G 668 ARG cc_start: 0.8296 (ptm-80) cc_final: 0.7995 (ptm-80) REVERT: G 802 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6739 (mt0) outliers start: 141 outliers final: 113 residues processed: 329 average time/residue: 0.4617 time to fit residues: 257.0538 Evaluate side-chains 318 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 197 time to evaluate : 4.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 625 TYR Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 833 ASN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 707 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 833 ASN Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 874 SER Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 371 ASN Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 582 ASP Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 874 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 310 SER Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 542 THR Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain E residue 757 THR Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain E residue 802 GLN Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 582 ASP Chi-restraints excluded: chain F residue 625 TYR Chi-restraints excluded: chain F residue 630 SER Chi-restraints excluded: chain F residue 707 PHE Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain F residue 874 SER Chi-restraints excluded: chain G residue 263 GLU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 407 THR Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 582 ASP Chi-restraints excluded: chain G residue 757 THR Chi-restraints excluded: chain G residue 763 ASP Chi-restraints excluded: chain G residue 802 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 57 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 300 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 217 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 259 optimal weight: 10.0000 chunk 308 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN C 368 GLN D 368 GLN E 368 GLN F 368 GLN G 368 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.129111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.102054 restraints weight = 40418.167| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.57 r_work: 0.3221 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 30142 Z= 0.227 Angle : 0.564 9.917 40803 Z= 0.302 Chirality : 0.047 0.208 4543 Planarity : 0.004 0.044 5285 Dihedral : 4.769 23.891 4039 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.42 % Allowed : 25.39 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 3633 helix: 0.07 (0.22), residues: 546 sheet: -0.60 (0.16), residues: 1050 loop : -0.82 (0.14), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 245 HIS 0.004 0.001 HIS F 314 PHE 0.020 0.002 PHE B 707 TYR 0.013 0.002 TYR B 261 ARG 0.007 0.000 ARG D 458 Details of bonding type rmsd hydrogen bonds : bond 0.03253 ( 819) hydrogen bonds : angle 4.84215 ( 2028) covalent geometry : bond 0.00565 (30142) covalent geometry : angle 0.56402 (40803) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 199 time to evaluate : 3.780 Fit side-chains REVERT: A 414 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8125 (tp) REVERT: A 625 TYR cc_start: 0.7998 (OUTLIER) cc_final: 0.5920 (m-80) REVERT: A 825 MET cc_start: 0.8202 (tpp) cc_final: 0.7824 (mmt) REVERT: B 371 ASN cc_start: 0.7548 (p0) cc_final: 0.7285 (p0) REVERT: B 707 PHE cc_start: 0.6812 (OUTLIER) cc_final: 0.6318 (p90) REVERT: C 299 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8603 (mm) REVERT: C 371 ASN cc_start: 0.7910 (p0) cc_final: 0.7215 (p0) REVERT: C 707 PHE cc_start: 0.7244 (OUTLIER) cc_final: 0.5998 (p90) REVERT: D 414 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8096 (tp) REVERT: E 707 PHE cc_start: 0.5903 (OUTLIER) cc_final: 0.4825 (p90) REVERT: F 707 PHE cc_start: 0.6374 (OUTLIER) cc_final: 0.4413 (p90) REVERT: G 668 ARG cc_start: 0.8385 (ptm-80) cc_final: 0.8025 (ptm-80) REVERT: G 802 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6597 (mt0) outliers start: 146 outliers final: 124 residues processed: 334 average time/residue: 0.3805 time to fit residues: 211.7536 Evaluate side-chains 324 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 191 time to evaluate : 3.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 625 TYR Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 833 ASN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 582 ASP Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 707 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 833 ASN Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 874 SER Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 371 ASN Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 582 ASP Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 874 SER Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 310 SER Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 542 THR Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 582 ASP Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain E residue 757 THR Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain E residue 802 GLN Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 582 ASP Chi-restraints excluded: chain F residue 625 TYR Chi-restraints excluded: chain F residue 630 SER Chi-restraints excluded: chain F residue 707 PHE Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain F residue 844 SER Chi-restraints excluded: chain F residue 870 LEU Chi-restraints excluded: chain F residue 874 SER Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 407 THR Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 520 ASP Chi-restraints excluded: chain G residue 542 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 582 ASP Chi-restraints excluded: chain G residue 757 THR Chi-restraints excluded: chain G residue 763 ASP Chi-restraints excluded: chain G residue 802 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 76 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 273 optimal weight: 0.2980 chunk 224 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 339 optimal weight: 2.9990 chunk 203 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 333 optimal weight: 2.9990 chunk 276 optimal weight: 7.9990 chunk 298 optimal weight: 10.0000 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN C 368 GLN D 368 GLN E 368 GLN F 368 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.129891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.103357 restraints weight = 40490.015| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.49 r_work: 0.3218 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30142 Z= 0.177 Angle : 0.525 9.860 40803 Z= 0.281 Chirality : 0.045 0.208 4543 Planarity : 0.004 0.040 5285 Dihedral : 4.647 23.190 4039 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.18 % Allowed : 25.61 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3633 helix: 0.02 (0.21), residues: 560 sheet: -0.59 (0.16), residues: 1050 loop : -0.82 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 245 HIS 0.003 0.001 HIS F 314 PHE 0.016 0.002 PHE B 707 TYR 0.013 0.001 TYR B 261 ARG 0.006 0.000 ARG D 458 Details of bonding type rmsd hydrogen bonds : bond 0.02872 ( 819) hydrogen bonds : angle 4.71039 ( 2028) covalent geometry : bond 0.00439 (30142) covalent geometry : angle 0.52510 (40803) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 199 time to evaluate : 4.714 Fit side-chains REVERT: A 373 GLU cc_start: 0.8032 (pt0) cc_final: 0.7658 (pt0) REVERT: A 414 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8140 (tp) REVERT: A 625 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.5955 (m-80) REVERT: A 825 MET cc_start: 0.8116 (tpp) cc_final: 0.7740 (mmt) REVERT: B 371 ASN cc_start: 0.7562 (p0) cc_final: 0.7281 (p0) REVERT: B 707 PHE cc_start: 0.6749 (OUTLIER) cc_final: 0.6230 (p90) REVERT: C 371 ASN cc_start: 0.7941 (p0) cc_final: 0.7247 (p0) REVERT: C 707 PHE cc_start: 0.7224 (OUTLIER) cc_final: 0.5804 (p90) REVERT: D 414 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8061 (tp) REVERT: E 458 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.7410 (ttt-90) REVERT: E 707 PHE cc_start: 0.5804 (OUTLIER) cc_final: 0.4788 (p90) REVERT: F 707 PHE cc_start: 0.6317 (OUTLIER) cc_final: 0.4446 (p90) REVERT: G 668 ARG cc_start: 0.8346 (ptm-80) cc_final: 0.8026 (ptm-80) REVERT: G 802 GLN cc_start: 0.7092 (OUTLIER) cc_final: 0.6670 (mt0) outliers start: 138 outliers final: 125 residues processed: 329 average time/residue: 0.4037 time to fit residues: 222.3558 Evaluate side-chains 328 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 194 time to evaluate : 3.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 625 TYR Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 833 ASN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 707 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 833 ASN Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 874 SER Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 371 ASN Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 582 ASP Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 874 SER Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 310 SER Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 458 ARG Chi-restraints excluded: chain E residue 542 THR Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 582 ASP Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain E residue 757 THR Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain E residue 802 GLN Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 520 ASP Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 582 ASP Chi-restraints excluded: chain F residue 625 TYR Chi-restraints excluded: chain F residue 630 SER Chi-restraints excluded: chain F residue 707 PHE Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain F residue 844 SER Chi-restraints excluded: chain F residue 870 LEU Chi-restraints excluded: chain F residue 874 SER Chi-restraints excluded: chain G residue 263 GLU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 407 THR Chi-restraints excluded: chain G residue 420 SER Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 542 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 582 ASP Chi-restraints excluded: chain G residue 757 THR Chi-restraints excluded: chain G residue 763 ASP Chi-restraints excluded: chain G residue 802 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 49 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 269 optimal weight: 9.9990 chunk 319 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 173 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 265 optimal weight: 9.9990 chunk 273 optimal weight: 0.4980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN C 368 GLN D 368 GLN E 368 GLN F 368 GLN G 827 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.135265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109053 restraints weight = 39556.392| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.49 r_work: 0.3310 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30142 Z= 0.099 Angle : 0.460 9.286 40803 Z= 0.246 Chirality : 0.043 0.219 4543 Planarity : 0.003 0.040 5285 Dihedral : 4.188 22.183 4039 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.36 % Allowed : 26.48 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3633 helix: 0.28 (0.21), residues: 560 sheet: -0.40 (0.17), residues: 1050 loop : -0.68 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 375 HIS 0.003 0.000 HIS F 314 PHE 0.009 0.001 PHE A 487 TYR 0.009 0.001 TYR B 261 ARG 0.006 0.000 ARG D 458 Details of bonding type rmsd hydrogen bonds : bond 0.02150 ( 819) hydrogen bonds : angle 4.38506 ( 2028) covalent geometry : bond 0.00239 (30142) covalent geometry : angle 0.45976 (40803) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 229 time to evaluate : 3.570 Fit side-chains revert: symmetry clash REVERT: A 625 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.5922 (m-80) REVERT: A 705 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.8163 (p) REVERT: A 825 MET cc_start: 0.8023 (tpp) cc_final: 0.7672 (mmt) REVERT: B 371 ASN cc_start: 0.7463 (p0) cc_final: 0.7192 (p0) REVERT: B 707 PHE cc_start: 0.6543 (OUTLIER) cc_final: 0.5989 (p90) REVERT: C 371 ASN cc_start: 0.7959 (p0) cc_final: 0.7291 (p0) REVERT: C 707 PHE cc_start: 0.7070 (OUTLIER) cc_final: 0.5158 (p90) REVERT: D 239 ASP cc_start: 0.7946 (t0) cc_final: 0.7718 (t0) REVERT: E 414 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8095 (tp) REVERT: E 707 PHE cc_start: 0.5681 (OUTLIER) cc_final: 0.4974 (p90) REVERT: F 707 PHE cc_start: 0.5987 (OUTLIER) cc_final: 0.4160 (p90) REVERT: F 843 ARG cc_start: 0.8629 (mmm-85) cc_final: 0.8355 (mmp-170) REVERT: G 668 ARG cc_start: 0.8299 (ptm-80) cc_final: 0.8022 (ptm-80) outliers start: 111 outliers final: 86 residues processed: 328 average time/residue: 0.3913 time to fit residues: 211.1809 Evaluate side-chains 301 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 208 time to evaluate : 3.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 625 TYR Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 707 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 833 ASN Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 874 SER Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 874 SER Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 542 THR Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain E residue 757 THR Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain E residue 802 GLN Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 625 TYR Chi-restraints excluded: chain F residue 630 SER Chi-restraints excluded: chain F residue 707 PHE Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain F residue 870 LEU Chi-restraints excluded: chain F residue 874 SER Chi-restraints excluded: chain G residue 263 GLU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 407 THR Chi-restraints excluded: chain G residue 420 SER Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 520 ASP Chi-restraints excluded: chain G residue 542 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 757 THR Chi-restraints excluded: chain G residue 763 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 173 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 211 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 140 optimal weight: 0.0170 chunk 251 optimal weight: 20.0000 chunk 370 optimal weight: 10.0000 chunk 343 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 overall best weight: 1.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN C 368 GLN E 368 GLN F 368 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.134562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.108294 restraints weight = 39882.904| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.50 r_work: 0.3305 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30142 Z= 0.119 Angle : 0.483 9.001 40803 Z= 0.258 Chirality : 0.044 0.228 4543 Planarity : 0.003 0.039 5285 Dihedral : 4.203 22.141 4039 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.15 % Allowed : 27.15 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.14), residues: 3633 helix: 0.34 (0.21), residues: 560 sheet: -0.33 (0.17), residues: 1050 loop : -0.67 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 375 HIS 0.003 0.001 HIS F 314 PHE 0.011 0.001 PHE B 707 TYR 0.011 0.001 TYR B 261 ARG 0.006 0.000 ARG D 458 Details of bonding type rmsd hydrogen bonds : bond 0.02321 ( 819) hydrogen bonds : angle 4.38065 ( 2028) covalent geometry : bond 0.00291 (30142) covalent geometry : angle 0.48301 (40803) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 211 time to evaluate : 3.334 Fit side-chains REVERT: A 625 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.5857 (m-80) REVERT: A 825 MET cc_start: 0.8054 (tpp) cc_final: 0.7688 (mmt) REVERT: B 371 ASN cc_start: 0.7465 (p0) cc_final: 0.7198 (p0) REVERT: B 707 PHE cc_start: 0.6608 (OUTLIER) cc_final: 0.6074 (p90) REVERT: C 371 ASN cc_start: 0.7956 (p0) cc_final: 0.7281 (p0) REVERT: C 707 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.5189 (p90) REVERT: D 736 LEU cc_start: 0.8543 (mt) cc_final: 0.8303 (mt) REVERT: E 707 PHE cc_start: 0.5743 (OUTLIER) cc_final: 0.5011 (p90) REVERT: F 707 PHE cc_start: 0.6087 (OUTLIER) cc_final: 0.4314 (p90) REVERT: F 843 ARG cc_start: 0.8647 (mmm-85) cc_final: 0.8383 (mmp-170) outliers start: 104 outliers final: 94 residues processed: 306 average time/residue: 0.3849 time to fit residues: 194.9741 Evaluate side-chains 304 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 205 time to evaluate : 3.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 625 TYR Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 707 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 833 ASN Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 874 SER Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 874 SER Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 542 THR Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain E residue 757 THR Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain E residue 802 GLN Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 625 TYR Chi-restraints excluded: chain F residue 630 SER Chi-restraints excluded: chain F residue 707 PHE Chi-restraints excluded: chain F residue 870 LEU Chi-restraints excluded: chain F residue 874 SER Chi-restraints excluded: chain G residue 263 GLU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 407 THR Chi-restraints excluded: chain G residue 420 SER Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 520 ASP Chi-restraints excluded: chain G residue 542 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 757 THR Chi-restraints excluded: chain G residue 763 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 259 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 348 optimal weight: 0.0050 chunk 213 optimal weight: 9.9990 chunk 164 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 201 optimal weight: 7.9990 chunk 172 optimal weight: 10.0000 chunk 300 optimal weight: 4.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN C 368 GLN E 368 GLN F 368 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.133480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.107138 restraints weight = 39971.351| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.50 r_work: 0.3268 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30142 Z= 0.151 Angle : 0.510 9.269 40803 Z= 0.272 Chirality : 0.045 0.229 4543 Planarity : 0.004 0.039 5285 Dihedral : 4.353 22.088 4039 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.27 % Allowed : 27.03 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3633 helix: 0.28 (0.21), residues: 560 sheet: -0.39 (0.17), residues: 1050 loop : -0.70 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 503 HIS 0.003 0.001 HIS F 314 PHE 0.014 0.001 PHE B 707 TYR 0.014 0.001 TYR D 439 ARG 0.006 0.000 ARG D 458 Details of bonding type rmsd hydrogen bonds : bond 0.02593 ( 819) hydrogen bonds : angle 4.47279 ( 2028) covalent geometry : bond 0.00373 (30142) covalent geometry : angle 0.50952 (40803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14245.58 seconds wall clock time: 250 minutes 48.52 seconds (15048.52 seconds total)