Starting phenix.real_space_refine on Mon Aug 25 16:11:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ekk_28205/08_2025/8ekk_28205.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ekk_28205/08_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_28205/08_2025/8ekk_28205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ekk_28205/08_2025/8ekk_28205.map" model { file = "/net/cci-nas-00/data/ceres_data/8ekk_28205/08_2025/8ekk_28205.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ekk_28205/08_2025/8ekk_28205.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.016 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.38, per 1000 atoms: 0.25 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: 1.95 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.41 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: 6.68 Time building geometry restraints manager: 2.59 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: 0.02 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: 1.690 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: 0.040 Extract box with map and model: 0.390 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 27.060 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 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:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.620 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (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 ARG 0.006 0.000 ARG B 458 TYR 0.010 0.001 TYR D 439 PHE 0.013 0.001 PHE C 707 TRP 0.005 0.001 TRP F 375 HIS 0.002 0.001 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00244 (30142) covalent geometry : angle 0.48002 (40803) hydrogen bonds : bond 0.23578 ( 819) hydrogen bonds : angle 8.00258 ( 2028) *********************** 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 : 1.100 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: 0.1667 time to fit residues: 65.0870 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 : 1.065 ------------------------------------------------------------------------------- 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 197 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN A 742 ASN A 834 GLN B 368 GLN B 523 ASN B 583 ASN ** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN C 834 GLN E 368 GLN F 368 GLN F 834 GLN G 773 ASN G 784 ASN G 834 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.131237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.104673 restraints weight = 40318.023| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.51 r_work: 0.3226 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 30142 Z= 0.211 Angle : 0.558 9.592 40803 Z= 0.300 Chirality : 0.046 0.172 4543 Planarity : 0.004 0.038 5285 Dihedral : 4.662 37.852 4041 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.57 % Allowed : 26.15 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.14), residues: 3633 helix: -0.02 (0.22), residues: 546 sheet: -0.97 (0.16), residues: 1015 loop : -0.72 (0.14), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 458 TYR 0.014 0.001 TYR G 669 PHE 0.018 0.002 PHE B 707 TRP 0.008 0.002 TRP C 245 HIS 0.003 0.001 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00521 (30142) covalent geometry : angle 0.55799 (40803) hydrogen bonds : bond 0.03809 ( 819) hydrogen bonds : angle 5.46444 ( 2028) *********************** 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 304 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 219 time to evaluate : 0.893 Fit side-chains REVERT: A 414 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8161 (tp) REVERT: D 414 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8106 (tp) REVERT: D 561 ASP cc_start: 0.7448 (t0) cc_final: 0.7229 (t0) REVERT: E 480 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8402 (t) REVERT: F 489 THR cc_start: 0.8908 (p) cc_final: 0.8670 (p) REVERT: F 707 PHE cc_start: 0.6356 (OUTLIER) cc_final: 0.4503 (p90) outliers start: 85 outliers final: 59 residues processed: 297 average time/residue: 0.1604 time to fit residues: 79.1809 Evaluate side-chains 260 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 197 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 414 LEU Chi-restraints excluded: chain A residue 445 SER 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 B residue 219 LEU 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 791 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 594 THR 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 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 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 381 ILE Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 670 VAL 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 381 ILE Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 421 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 707 PHE Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain F residue 870 LEU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 407 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 229 optimal weight: 4.9990 chunk 358 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 242 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 319 optimal weight: 0.6980 chunk 320 optimal weight: 1.9990 chunk 255 optimal weight: 10.0000 chunk 316 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 336 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.129445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.102221 restraints weight = 40589.244| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.59 r_work: 0.3226 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30142 Z= 0.181 Angle : 0.527 9.705 40803 Z= 0.283 Chirality : 0.045 0.170 4543 Planarity : 0.004 0.039 5285 Dihedral : 4.575 25.070 4039 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.78 % Allowed : 25.45 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.14), residues: 3633 helix: -0.06 (0.21), residues: 553 sheet: -0.71 (0.16), residues: 1050 loop : -0.80 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 458 TYR 0.013 0.001 TYR B 261 PHE 0.016 0.002 PHE B 707 TRP 0.006 0.001 TRP C 245 HIS 0.003 0.001 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00447 (30142) covalent geometry : angle 0.52730 (40803) hydrogen bonds : bond 0.03250 ( 819) hydrogen bonds : angle 5.07013 ( 2028) *********************** 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 337 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 212 time to evaluate : 1.162 Fit side-chains REVERT: B 707 PHE cc_start: 0.6740 (OUTLIER) cc_final: 0.6185 (p90) REVERT: D 239 ASP cc_start: 0.7858 (t0) cc_final: 0.7580 (t0) REVERT: D 414 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8088 (tp) REVERT: D 561 ASP cc_start: 0.7711 (t0) cc_final: 0.7456 (t0) REVERT: E 480 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8436 (t) REVERT: E 561 ASP cc_start: 0.7582 (t0) cc_final: 0.7366 (t0) REVERT: E 707 PHE cc_start: 0.5762 (OUTLIER) cc_final: 0.4938 (p90) REVERT: F 489 THR cc_start: 0.8918 (p) cc_final: 0.8690 (p) REVERT: F 630 SER cc_start: 0.6551 (OUTLIER) cc_final: 0.6167 (m) REVERT: F 707 PHE cc_start: 0.6238 (OUTLIER) cc_final: 0.4181 (p90) outliers start: 125 outliers final: 85 residues processed: 328 average time/residue: 0.1591 time to fit residues: 87.9004 Evaluate side-chains 285 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 194 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 377 THR Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 582 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 B residue 381 ILE Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 480 THR 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 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 407 THR 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 757 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 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 705 THR Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 793 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 377 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 480 THR 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 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 480 THR Chi-restraints excluded: chain F residue 530 VAL 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 377 THR Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 407 THR Chi-restraints excluded: chain G residue 421 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 594 THR 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 260 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 146 optimal weight: 20.0000 chunk 276 optimal weight: 0.0980 chunk 316 optimal weight: 9.9990 chunk 348 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 293 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- 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 431 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.146107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.118927 restraints weight = 38721.939| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.56 r_work: 0.3510 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.0983 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= 0.142 Angle : 0.493 9.497 40803 Z= 0.264 Chirality : 0.044 0.177 4543 Planarity : 0.004 0.038 5285 Dihedral : 4.433 25.876 4039 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.42 % Allowed : 25.91 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.14), residues: 3633 helix: 0.03 (0.21), residues: 560 sheet: -0.57 (0.16), residues: 1050 loop : -0.78 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 458 TYR 0.012 0.001 TYR B 261 PHE 0.012 0.001 PHE B 707 TRP 0.005 0.001 TRP B 503 HIS 0.003 0.001 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00349 (30142) covalent geometry : angle 0.49332 (40803) hydrogen bonds : bond 0.02737 ( 819) hydrogen bonds : angle 4.79358 ( 2028) *********************** 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 332 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 219 time to evaluate : 1.137 Fit side-chains REVERT: A 414 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8145 (tp) REVERT: B 371 ASN cc_start: 0.7674 (p0) cc_final: 0.7414 (p0) REVERT: B 707 PHE cc_start: 0.6675 (OUTLIER) cc_final: 0.6129 (p90) REVERT: C 371 ASN cc_start: 0.8012 (p0) cc_final: 0.7299 (p0) REVERT: D 414 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8112 (tp) REVERT: D 458 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8793 (ttt90) REVERT: D 561 ASP cc_start: 0.7645 (t0) cc_final: 0.7411 (t0) REVERT: E 480 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8366 (t) REVERT: E 707 PHE cc_start: 0.5792 (OUTLIER) cc_final: 0.4752 (p90) REVERT: F 489 THR cc_start: 0.8892 (p) cc_final: 0.8673 (p) REVERT: F 707 PHE cc_start: 0.6206 (OUTLIER) cc_final: 0.4491 (p90) outliers start: 113 outliers final: 89 residues processed: 321 average time/residue: 0.1625 time to fit residues: 85.9874 Evaluate side-chains 292 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 196 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 458 ARG 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 705 THR 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 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 480 THR 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 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 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 707 PHE Chi-restraints excluded: chain F residue 791 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 377 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 480 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 307 optimal weight: 5.9990 chunk 324 optimal weight: 0.9980 chunk 42 optimal weight: 0.0040 chunk 70 optimal weight: 10.0000 chunk 231 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 chunk 269 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 332 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 overall best weight: 2.9998 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.132929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.106628 restraints weight = 40181.357| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.50 r_work: 0.3277 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30142 Z= 0.158 Angle : 0.505 9.504 40803 Z= 0.271 Chirality : 0.045 0.191 4543 Planarity : 0.004 0.039 5285 Dihedral : 4.457 23.293 4039 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.63 % Allowed : 25.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.14), residues: 3633 helix: 0.06 (0.21), residues: 560 sheet: -0.53 (0.16), residues: 1050 loop : -0.79 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 668 TYR 0.012 0.001 TYR B 261 PHE 0.014 0.001 PHE B 707 TRP 0.005 0.001 TRP C 245 HIS 0.003 0.001 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00390 (30142) covalent geometry : angle 0.50529 (40803) hydrogen bonds : bond 0.02779 ( 819) hydrogen bonds : angle 4.72101 ( 2028) *********************** 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 362 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 209 time to evaluate : 1.230 Fit side-chains REVERT: A 373 GLU cc_start: 0.8024 (pt0) cc_final: 0.7636 (pt0) REVERT: A 414 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8067 (tp) REVERT: A 625 TYR cc_start: 0.7621 (OUTLIER) cc_final: 0.5615 (m-80) REVERT: B 371 ASN cc_start: 0.7644 (p0) cc_final: 0.7391 (p0) REVERT: B 707 PHE cc_start: 0.6698 (OUTLIER) cc_final: 0.6150 (p90) REVERT: C 371 ASN cc_start: 0.7943 (p0) cc_final: 0.7252 (p0) REVERT: C 668 ARG cc_start: 0.8268 (ptm-80) cc_final: 0.8040 (ptm-80) REVERT: D 414 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8034 (tp) REVERT: D 458 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8781 (ttt90) REVERT: E 480 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.8387 (t) REVERT: E 707 PHE cc_start: 0.5794 (OUTLIER) cc_final: 0.4803 (p90) REVERT: F 489 THR cc_start: 0.8850 (p) cc_final: 0.8622 (p) REVERT: F 668 ARG cc_start: 0.7737 (tmm-80) cc_final: 0.7532 (tmm-80) REVERT: F 707 PHE cc_start: 0.6269 (OUTLIER) cc_final: 0.4594 (p90) REVERT: G 668 ARG cc_start: 0.8302 (ptm-80) cc_final: 0.8018 (ptm-80) REVERT: G 802 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6713 (mt0) outliers start: 153 outliers final: 120 residues processed: 349 average time/residue: 0.1684 time to fit residues: 98.0482 Evaluate side-chains 328 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 199 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 480 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 625 TYR Chi-restraints excluded: chain A residue 670 VAL 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 833 ASN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 456 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 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 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 458 ARG 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 705 THR 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 310 SER 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 480 THR 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 407 THR Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 452 MET 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 705 THR 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 844 SER 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 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 594 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 233 optimal weight: 0.9990 chunk 365 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 315 optimal weight: 2.9990 chunk 28 optimal weight: 0.0040 chunk 129 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 270 optimal weight: 0.8980 chunk 246 optimal weight: 3.9990 chunk 286 optimal weight: 0.6980 overall best weight: 1.1196 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.132928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107218 restraints weight = 39534.127| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.42 r_work: 0.2988 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30142 Z= 0.090 Angle : 0.449 9.377 40803 Z= 0.240 Chirality : 0.043 0.221 4543 Planarity : 0.003 0.039 5285 Dihedral : 4.070 21.582 4039 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.18 % Allowed : 26.69 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.14), residues: 3633 helix: 0.31 (0.22), residues: 560 sheet: -0.31 (0.16), residues: 1050 loop : -0.66 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 668 TYR 0.009 0.001 TYR B 261 PHE 0.008 0.001 PHE A 487 TRP 0.006 0.001 TRP E 375 HIS 0.002 0.000 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00214 (30142) covalent geometry : angle 0.44859 (40803) hydrogen bonds : bond 0.02088 ( 819) hydrogen bonds : angle 4.40833 ( 2028) *********************** 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: 105 poor density : 236 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: B 371 ASN cc_start: 0.7413 (p0) cc_final: 0.7162 (p0) REVERT: C 371 ASN cc_start: 0.7893 (p0) cc_final: 0.7223 (p0) REVERT: C 668 ARG cc_start: 0.8329 (ptm-80) cc_final: 0.8010 (ptm-80) REVERT: D 239 ASP cc_start: 0.7870 (t0) cc_final: 0.7589 (t0) REVERT: E 414 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8040 (tp) REVERT: E 707 PHE cc_start: 0.5432 (OUTLIER) cc_final: 0.4714 (p90) REVERT: F 371 ASN cc_start: 0.8226 (p0) cc_final: 0.7810 (p0) REVERT: F 489 THR cc_start: 0.8870 (p) cc_final: 0.8641 (p) REVERT: F 668 ARG cc_start: 0.7643 (tmm-80) cc_final: 0.7414 (tmm-80) REVERT: F 707 PHE cc_start: 0.5754 (OUTLIER) cc_final: 0.3924 (p90) REVERT: F 843 ARG cc_start: 0.8533 (mmm-85) cc_final: 0.8176 (mmp-170) REVERT: G 668 ARG cc_start: 0.8355 (ptm-80) cc_final: 0.7964 (ptm-80) outliers start: 105 outliers final: 71 residues processed: 334 average time/residue: 0.1768 time to fit residues: 96.9161 Evaluate side-chains 293 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 219 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 407 THR Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 833 ASN Chi-restraints excluded: chain B residue 259 SER 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 492 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 833 ASN 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 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 569 ILE Chi-restraints excluded: chain C residue 791 THR 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 456 SER Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 791 THR 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 414 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 569 ILE 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 F residue 259 SER Chi-restraints excluded: chain F residue 263 GLU 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 630 SER Chi-restraints excluded: chain F residue 705 THR 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 307 LEU Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 407 THR 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 757 THR Chi-restraints excluded: chain G residue 763 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 199 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 298 optimal weight: 10.0000 chunk 200 optimal weight: 8.9990 chunk 339 optimal weight: 2.9990 chunk 359 optimal weight: 7.9990 chunk 257 optimal weight: 10.0000 chunk 148 optimal weight: 0.8980 chunk 240 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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 F 742 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.129220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.102060 restraints weight = 40546.894| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.59 r_work: 0.3220 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 30142 Z= 0.235 Angle : 0.570 9.719 40803 Z= 0.304 Chirality : 0.047 0.219 4543 Planarity : 0.004 0.045 5285 Dihedral : 4.667 22.923 4039 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.45 % Allowed : 26.00 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.14), residues: 3633 helix: 0.05 (0.21), residues: 560 sheet: -0.52 (0.16), residues: 1050 loop : -0.80 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 668 TYR 0.014 0.002 TYR B 261 PHE 0.021 0.002 PHE B 707 TRP 0.010 0.002 TRP C 245 HIS 0.004 0.001 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00585 (30142) covalent geometry : angle 0.57000 (40803) hydrogen bonds : bond 0.03249 ( 819) hydrogen bonds : angle 4.77955 ( 2028) *********************** 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 353 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 206 time to evaluate : 1.098 Fit side-chains REVERT: A 373 GLU cc_start: 0.8028 (pt0) cc_final: 0.7594 (pt0) REVERT: A 414 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8201 (tp) REVERT: A 625 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.5814 (m-80) REVERT: B 371 ASN cc_start: 0.7533 (p0) cc_final: 0.7256 (p0) REVERT: B 602 ASN cc_start: 0.9286 (OUTLIER) cc_final: 0.8794 (t0) REVERT: B 707 PHE cc_start: 0.6726 (OUTLIER) cc_final: 0.6266 (p90) REVERT: B 791 THR cc_start: 0.7973 (m) cc_final: 0.7737 (m) REVERT: C 299 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8594 (mm) REVERT: C 371 ASN cc_start: 0.7865 (p0) cc_final: 0.7210 (p0) REVERT: C 707 PHE cc_start: 0.7164 (OUTLIER) cc_final: 0.5541 (p90) REVERT: E 458 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.7448 (ttt-90) REVERT: E 707 PHE cc_start: 0.5953 (OUTLIER) cc_final: 0.4931 (p90) REVERT: F 489 THR cc_start: 0.8917 (p) cc_final: 0.8697 (p) REVERT: F 707 PHE cc_start: 0.6364 (OUTLIER) cc_final: 0.4701 (p90) REVERT: G 668 ARG cc_start: 0.8378 (ptm-80) cc_final: 0.7992 (ptm-80) outliers start: 147 outliers final: 124 residues processed: 345 average time/residue: 0.1651 time to fit residues: 94.3450 Evaluate side-chains 330 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 197 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 317 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 420 SER 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 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 317 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 407 THR 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 492 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 582 ASP Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 707 PHE 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 272 THR Chi-restraints excluded: chain C residue 288 GLU 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 542 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 670 VAL 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 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 272 THR 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 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 705 THR 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 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 414 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 456 SER Chi-restraints excluded: chain E residue 458 ARG Chi-restraints excluded: chain E residue 513 ILE 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 F residue 219 LEU Chi-restraints excluded: chain F residue 259 SER 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 310 SER Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 377 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 625 TYR Chi-restraints excluded: chain F residue 630 SER Chi-restraints excluded: chain F residue 705 THR Chi-restraints excluded: chain F residue 707 PHE Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain F residue 874 SER Chi-restraints excluded: chain G residue 248 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 317 THR 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 421 THR Chi-restraints excluded: chain G residue 437 ASP 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 238 optimal weight: 4.9990 chunk 318 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 243 optimal weight: 8.9990 chunk 175 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 chunk 353 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 320 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 G 827 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.133045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.107252 restraints weight = 39674.817| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.43 r_work: 0.3238 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30142 Z= 0.091 Angle : 0.459 9.404 40803 Z= 0.245 Chirality : 0.043 0.222 4543 Planarity : 0.003 0.039 5285 Dihedral : 4.112 20.219 4039 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.33 % Allowed : 27.12 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.14), residues: 3633 helix: 0.34 (0.22), residues: 560 sheet: -0.30 (0.16), residues: 1043 loop : -0.68 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 458 TYR 0.011 0.001 TYR C 439 PHE 0.008 0.001 PHE A 487 TRP 0.007 0.001 TRP E 375 HIS 0.002 0.000 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00212 (30142) covalent geometry : angle 0.45936 (40803) hydrogen bonds : bond 0.02073 ( 819) hydrogen bonds : angle 4.34347 ( 2028) *********************** 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 335 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 225 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 625 TYR cc_start: 0.7826 (OUTLIER) cc_final: 0.5838 (m-80) REVERT: B 371 ASN cc_start: 0.7436 (p0) cc_final: 0.7167 (p0) REVERT: B 707 PHE cc_start: 0.6486 (OUTLIER) cc_final: 0.5951 (p90) REVERT: C 371 ASN cc_start: 0.7938 (p0) cc_final: 0.7316 (p0) REVERT: C 707 PHE cc_start: 0.7043 (OUTLIER) cc_final: 0.4943 (p90) REVERT: D 239 ASP cc_start: 0.7883 (t0) cc_final: 0.7650 (t0) REVERT: E 414 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7985 (tp) REVERT: E 707 PHE cc_start: 0.5595 (OUTLIER) cc_final: 0.4916 (p90) REVERT: F 489 THR cc_start: 0.8850 (p) cc_final: 0.8616 (p) REVERT: F 707 PHE cc_start: 0.5944 (OUTLIER) cc_final: 0.4083 (p90) REVERT: F 843 ARG cc_start: 0.8595 (mmm-85) cc_final: 0.8300 (mmp-170) REVERT: G 668 ARG cc_start: 0.8292 (ptm-80) cc_final: 0.7995 (ptm-80) outliers start: 110 outliers final: 88 residues processed: 328 average time/residue: 0.1562 time to fit residues: 84.6915 Evaluate side-chains 307 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 213 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 407 THR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 625 TYR Chi-restraints excluded: chain A residue 707 PHE 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 B residue 219 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 313 GLU 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 502 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 793 THR Chi-restraints excluded: chain B residue 833 ASN Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 263 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 542 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 874 SER Chi-restraints excluded: chain D residue 229 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 456 SER Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 791 THR 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 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 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 310 SER Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 452 MET 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 705 THR 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 307 LEU Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 377 THR 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 757 THR Chi-restraints excluded: chain G residue 763 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 238 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 151 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 202 optimal weight: 0.0060 chunk 303 optimal weight: 6.9990 chunk 242 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 344 optimal weight: 3.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.133649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.107247 restraints weight = 39845.929| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.50 r_work: 0.3265 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1200 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 : 0.502 9.068 40803 Z= 0.268 Chirality : 0.045 0.223 4543 Planarity : 0.003 0.040 5285 Dihedral : 4.298 20.477 4039 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.57 % Allowed : 26.88 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.14), residues: 3633 helix: 0.32 (0.22), residues: 560 sheet: -0.37 (0.17), residues: 1050 loop : -0.67 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 458 TYR 0.012 0.001 TYR B 261 PHE 0.014 0.001 PHE B 707 TRP 0.005 0.001 TRP C 245 HIS 0.003 0.001 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00374 (30142) covalent geometry : angle 0.50246 (40803) hydrogen bonds : bond 0.02562 ( 819) hydrogen bonds : angle 4.44944 ( 2028) *********************** 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 319 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 201 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 625 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.5773 (m-80) REVERT: B 371 ASN cc_start: 0.7469 (p0) cc_final: 0.7198 (p0) REVERT: B 707 PHE cc_start: 0.6704 (OUTLIER) cc_final: 0.6221 (p90) REVERT: C 371 ASN cc_start: 0.7905 (p0) cc_final: 0.7272 (p0) REVERT: C 707 PHE cc_start: 0.7125 (OUTLIER) cc_final: 0.5132 (p90) REVERT: E 707 PHE cc_start: 0.5824 (OUTLIER) cc_final: 0.5011 (p90) REVERT: F 489 THR cc_start: 0.8875 (p) cc_final: 0.8651 (p) REVERT: F 707 PHE cc_start: 0.6173 (OUTLIER) cc_final: 0.4489 (p90) REVERT: G 668 ARG cc_start: 0.8322 (ptm-80) cc_final: 0.8032 (ptm-80) outliers start: 118 outliers final: 109 residues processed: 312 average time/residue: 0.1601 time to fit residues: 82.7581 Evaluate side-chains 311 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 197 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 325 ARG Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 625 TYR Chi-restraints excluded: chain A residue 670 VAL 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 B residue 272 THR Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 502 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 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 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 407 THR Chi-restraints excluded: chain C residue 420 SER 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 229 SER Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 272 THR 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 456 SER 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 705 THR Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 791 THR 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 414 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 456 SER 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 870 LEU Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 259 SER 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 310 SER Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 377 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 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 625 TYR Chi-restraints excluded: chain F residue 630 SER Chi-restraints excluded: chain F residue 705 THR 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 310 SER Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 377 THR 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 705 THR 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 270 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 chunk 309 optimal weight: 0.9990 chunk 338 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 314 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 219 optimal weight: 10.0000 chunk 313 optimal weight: 6.9990 chunk 317 optimal weight: 3.9990 chunk 169 optimal weight: 10.0000 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.132479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.106090 restraints weight = 39946.737| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.50 r_work: 0.3268 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30142 Z= 0.181 Angle : 0.535 9.626 40803 Z= 0.286 Chirality : 0.046 0.232 4543 Planarity : 0.004 0.042 5285 Dihedral : 4.525 22.252 4039 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.81 % Allowed : 26.88 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.14), residues: 3633 helix: 0.24 (0.22), residues: 560 sheet: -0.45 (0.17), residues: 1050 loop : -0.75 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 458 TYR 0.013 0.001 TYR B 261 PHE 0.017 0.002 PHE B 707 TRP 0.008 0.001 TRP C 245 HIS 0.004 0.001 HIS G 314 Details of bonding type rmsd covalent geometry : bond 0.00448 (30142) covalent geometry : angle 0.53486 (40803) hydrogen bonds : bond 0.02859 ( 819) hydrogen bonds : angle 4.59668 ( 2028) ********************** 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 329 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 203 time to evaluate : 1.203 Fit side-chains revert: symmetry clash REVERT: A 625 TYR cc_start: 0.7934 (OUTLIER) cc_final: 0.5996 (m-80) REVERT: B 371 ASN cc_start: 0.7493 (p0) cc_final: 0.7219 (p0) REVERT: B 707 PHE cc_start: 0.6711 (OUTLIER) cc_final: 0.6175 (p90) REVERT: C 371 ASN cc_start: 0.7872 (p0) cc_final: 0.7226 (p0) REVERT: C 707 PHE cc_start: 0.7179 (OUTLIER) cc_final: 0.5486 (p90) REVERT: D 414 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8072 (tp) REVERT: E 707 PHE cc_start: 0.5821 (OUTLIER) cc_final: 0.4813 (p90) REVERT: F 489 THR cc_start: 0.8882 (p) cc_final: 0.8657 (p) REVERT: F 707 PHE cc_start: 0.6288 (OUTLIER) cc_final: 0.4644 (p90) outliers start: 126 outliers final: 117 residues processed: 323 average time/residue: 0.1603 time to fit residues: 86.3592 Evaluate side-chains 321 residues out of total 3304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 198 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 317 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 420 SER Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 625 TYR Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 707 PHE 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 B residue 272 THR Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 502 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 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 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 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 229 SER Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 272 THR 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 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 670 VAL Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 791 THR 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 456 SER 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 870 LEU Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 259 SER 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 310 SER Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 377 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 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 630 SER Chi-restraints excluded: chain F residue 705 THR 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 310 SER Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 377 THR 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 437 ASP 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 705 THR 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 322 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 323 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 352 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 253 optimal weight: 6.9990 chunk 245 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 188 optimal weight: 8.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN C 523 ASN 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 = 0.3633 r_free = 0.3633 target = 0.129711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.102630 restraints weight = 40421.856| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.58 r_work: 0.3224 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 30142 Z= 0.200 Angle : 0.551 9.723 40803 Z= 0.294 Chirality : 0.046 0.223 4543 Planarity : 0.004 0.044 5285 Dihedral : 4.633 22.770 4039 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.93 % Allowed : 26.76 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.14), residues: 3633 helix: 0.15 (0.21), residues: 560 sheet: -0.54 (0.16), residues: 1050 loop : -0.79 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 458 TYR 0.014 0.001 TYR D 439 PHE 0.018 0.002 PHE B 707 TRP 0.009 0.002 TRP C 245 HIS 0.003 0.001 HIS G 314 Details of bonding type rmsd covalent geometry : bond 0.00497 (30142) covalent geometry : angle 0.55137 (40803) hydrogen bonds : bond 0.02977 ( 819) hydrogen bonds : angle 4.65909 ( 2028) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6016.74 seconds wall clock time: 104 minutes 19.83 seconds (6259.83 seconds total)