Starting phenix.real_space_refine on Sat Mar 7 06:52:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jg5_22311/03_2026/7jg5_22311.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jg5_22311/03_2026/7jg5_22311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jg5_22311/03_2026/7jg5_22311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jg5_22311/03_2026/7jg5_22311.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jg5_22311/03_2026/7jg5_22311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jg5_22311/03_2026/7jg5_22311.map" } resolution = 3.4 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= 0.011 sd= 0.277 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4941 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 4 5.21 5 S 105 5.16 5 C 22570 2.51 5 N 6186 2.21 5 O 6619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 149 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35497 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3910 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 10} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3787 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 483} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3713 Classifications: {'peptide': 503} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 481} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'UNK:plan-1': 11, 'GLU:plan': 9, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 59 Chain: "D" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3495 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3486 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'ASP:plan': 11, 'GLU:plan': 5, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 64 Chain: "F" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3525 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "G" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2121 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 269} Chain breaks: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 33 Chain: "H" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 824 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 10, 'GLU:plan': 10} Unresolved non-hydrogen planarities: 70 Chain: "a" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1602 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "b" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1052 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 141} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "d" Number of atoms: 2841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 2841 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 11, 'TRANS': 415} Chain breaks: 4 Unresolved non-hydrogen bonds: 375 Unresolved non-hydrogen angles: 472 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLU:plan': 24, 'ASP:plan': 18, 'GLN:plan1': 3, 'ARG:plan': 10, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 218 Chain: "1" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 552 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "3" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 548 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 76} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "4" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "5" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 550 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "6" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "7" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "8" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 569 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 78} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "9" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.17, per 1000 atoms: 0.23 Number of scatterers: 35497 At special positions: 0 Unit cell: (123.6, 136.99, 249.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 13 15.00 Mg 4 11.99 O 6619 8.00 N 6186 7.00 C 22570 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: 3.39 Conformation dependent library (CDL) restraints added in 1.6 seconds 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8698 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 23 sheets defined 62.6% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 7 through 22 removed outlier: 3.996A pdb=" N ILE A 11 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 177 through 188 Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 212 through 226 removed outlier: 3.657A pdb=" N GLY A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 230 removed outlier: 3.706A pdb=" N GLU A 230 " --> pdb=" O GLY A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 242 through 263 removed outlier: 3.506A pdb=" N LYS A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Proline residue: A 250 - end of helix removed outlier: 3.852A pdb=" N TRP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 288 removed outlier: 3.663A pdb=" N GLN A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 300 through 310 removed outlier: 3.724A pdb=" N HIS A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG A 307 " --> pdb=" O TYR A 303 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 removed outlier: 3.532A pdb=" N GLY A 320 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 336 removed outlier: 4.017A pdb=" N ASP A 336 " --> pdb=" O LYS A 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 333 through 336' Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.628A pdb=" N GLN A 382 " --> pdb=" O GLY A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 Processing helix chain 'A' and resid 392 through 407 Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 414 through 432 removed outlier: 3.566A pdb=" N ALA A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 453 removed outlier: 4.043A pdb=" N VAL A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 459 removed outlier: 4.210A pdb=" N SER A 458 " --> pdb=" O HIS A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 479 removed outlier: 3.569A pdb=" N GLU A 473 " --> pdb=" O SER A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 490 Processing helix chain 'A' and resid 493 through 509 removed outlier: 3.519A pdb=" N LYS A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 22 removed outlier: 3.760A pdb=" N PHE B 22 " --> pdb=" O TYR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.541A pdb=" N LYS B 84 " --> pdb=" O GLU B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.594A pdb=" N PHE B 106 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 177 through 189 removed outlier: 3.978A pdb=" N GLN B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 194 Processing helix chain 'B' and resid 212 through 225 Processing helix chain 'B' and resid 226 through 230 removed outlier: 5.962A pdb=" N MET B 229 " --> pdb=" O GLY B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 263 Proline residue: B 250 - end of helix removed outlier: 3.692A pdb=" N HIS B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 removed outlier: 3.724A pdb=" N GLN B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 298 through 299 No H-bonds generated for 'chain 'B' and resid 298 through 299' Processing helix chain 'B' and resid 300 through 310 removed outlier: 3.701A pdb=" N LEU B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 333 through 336 Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 356 through 363 Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.876A pdb=" N ALA B 380 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.858A pdb=" N VAL B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 391 " --> pdb=" O LYS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 404 Processing helix chain 'B' and resid 405 through 413 removed outlier: 3.744A pdb=" N ALA B 408 " --> pdb=" O ALA B 405 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N SER B 411 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 432 removed outlier: 4.319A pdb=" N GLN B 420 " --> pdb=" O ALA B 416 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS B 432 " --> pdb=" O VAL B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 453 removed outlier: 4.280A pdb=" N VAL B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 463 through 479 Processing helix chain 'B' and resid 479 through 490 removed outlier: 4.384A pdb=" N PHE B 483 " --> pdb=" O HIS B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 509 Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.648A pdb=" N PHE C 106 " --> pdb=" O GLY C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 177 through 188 Processing helix chain 'C' and resid 189 through 194 Processing helix chain 'C' and resid 212 through 226 Processing helix chain 'C' and resid 227 through 230 removed outlier: 3.513A pdb=" N GLU C 230 " --> pdb=" O GLY C 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 227 through 230' Processing helix chain 'C' and resid 242 through 263 removed outlier: 3.617A pdb=" N LYS C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) Proline residue: C 250 - end of helix removed outlier: 3.563A pdb=" N HIS C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN C 263 " --> pdb=" O HIS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 removed outlier: 4.042A pdb=" N GLN C 277 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 301 through 310 Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'C' and resid 332 through 336 removed outlier: 3.825A pdb=" N ASN C 335 " --> pdb=" O THR C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 347 Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 377 through 382 removed outlier: 4.022A pdb=" N ALA C 380 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA C 381 " --> pdb=" O GLY C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 391 Processing helix chain 'C' and resid 392 through 408 Processing helix chain 'C' and resid 414 through 432 removed outlier: 3.677A pdb=" N LYS C 432 " --> pdb=" O VAL C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 453 removed outlier: 4.222A pdb=" N VAL C 446 " --> pdb=" O GLU C 442 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY C 451 " --> pdb=" O ALA C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 478 removed outlier: 4.528A pdb=" N GLN C 465 " --> pdb=" O VAL C 461 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ARG C 466 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 490 removed outlier: 3.546A pdb=" N THR C 489 " --> pdb=" O GLY C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 511 removed outlier: 4.181A pdb=" N LYS C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 46 Processing helix chain 'D' and resid 91 through 95 removed outlier: 3.601A pdb=" N VAL D 94 " --> pdb=" O GLY D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 115 removed outlier: 4.262A pdb=" N ASP D 114 " --> pdb=" O TYR D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 130 Processing helix chain 'D' and resid 141 through 148 Processing helix chain 'D' and resid 165 through 181 removed outlier: 3.902A pdb=" N ARG D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASN D 180 " --> pdb=" O ARG D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 207 removed outlier: 3.731A pdb=" N GLY D 197 " --> pdb=" O ARG D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 211 Processing helix chain 'D' and resid 223 through 244 removed outlier: 4.809A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 271 removed outlier: 4.388A pdb=" N THR D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LEU D 269 " --> pdb=" O GLU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 292 removed outlier: 3.850A pdb=" N LEU D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 295 No H-bonds generated for 'chain 'D' and resid 293 through 295' Processing helix chain 'D' and resid 311 through 314 Processing helix chain 'D' and resid 317 through 324 Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 334 through 339 Processing helix chain 'D' and resid 357 through 362 Processing helix chain 'D' and resid 362 through 390 removed outlier: 3.567A pdb=" N VAL D 368 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE D 388 " --> pdb=" O ASP D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 394 Processing helix chain 'D' and resid 395 through 412 removed outlier: 3.645A pdb=" N ARG D 407 " --> pdb=" O ASN D 403 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG D 410 " --> pdb=" O ARG D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 419 through 424 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 451 through 456 removed outlier: 3.870A pdb=" N PHE D 455 " --> pdb=" O GLU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 471 Processing helix chain 'E' and resid 42 through 46 Processing helix chain 'E' and resid 91 through 95 Processing helix chain 'E' and resid 126 through 130 removed outlier: 3.567A pdb=" N LEU E 130 " --> pdb=" O PHE E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 148 Processing helix chain 'E' and resid 165 through 181 Processing helix chain 'E' and resid 193 through 207 Processing helix chain 'E' and resid 209 through 211 No H-bonds generated for 'chain 'E' and resid 209 through 211' Processing helix chain 'E' and resid 223 through 244 removed outlier: 3.610A pdb=" N ARG E 227 " --> pdb=" O PRO E 223 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 270 removed outlier: 3.543A pdb=" N PHE E 259 " --> pdb=" O ASN E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 292 removed outlier: 4.022A pdb=" N LEU E 290 " --> pdb=" O GLU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 314 removed outlier: 3.655A pdb=" N ASP E 314 " --> pdb=" O PRO E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 327 removed outlier: 3.721A pdb=" N ALA E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS E 326 " --> pdb=" O THR E 322 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU E 327 " --> pdb=" O THR E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 339 Processing helix chain 'E' and resid 362 through 390 removed outlier: 4.769A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 394 Processing helix chain 'E' and resid 395 through 412 removed outlier: 3.793A pdb=" N LEU E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG E 404 " --> pdb=" O GLN E 400 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG E 407 " --> pdb=" O ASN E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 418 No H-bonds generated for 'chain 'E' and resid 416 through 418' Processing helix chain 'E' and resid 419 through 424 Processing helix chain 'E' and resid 431 through 445 removed outlier: 3.597A pdb=" N GLU E 437 " --> pdb=" O LYS E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 455 Processing helix chain 'E' and resid 460 through 471 removed outlier: 3.584A pdb=" N LYS E 466 " --> pdb=" O ASP E 462 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU E 469 " --> pdb=" O ALA E 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 95 Processing helix chain 'F' and resid 126 through 130 Processing helix chain 'F' and resid 141 through 148 Processing helix chain 'F' and resid 165 through 177 Processing helix chain 'F' and resid 193 through 207 removed outlier: 3.532A pdb=" N GLY F 197 " --> pdb=" O ARG F 193 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA F 205 " --> pdb=" O TRP F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 223 through 244 removed outlier: 3.600A pdb=" N ARG F 229 " --> pdb=" O GLY F 225 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU F 232 " --> pdb=" O MET F 228 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET F 237 " --> pdb=" O SER F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 271 removed outlier: 3.797A pdb=" N THR F 260 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU F 269 " --> pdb=" O GLU F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 292 Processing helix chain 'F' and resid 311 through 314 Processing helix chain 'F' and resid 317 through 324 Processing helix chain 'F' and resid 325 through 327 No H-bonds generated for 'chain 'F' and resid 325 through 327' Processing helix chain 'F' and resid 334 through 340 Processing helix chain 'F' and resid 357 through 362 Processing helix chain 'F' and resid 362 through 390 removed outlier: 3.617A pdb=" N VAL F 368 " --> pdb=" O GLU F 364 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE F 388 " --> pdb=" O ASP F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 394 Processing helix chain 'F' and resid 395 through 412 removed outlier: 3.768A pdb=" N LEU F 401 " --> pdb=" O GLU F 397 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG F 404 " --> pdb=" O GLN F 400 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG F 407 " --> pdb=" O ASN F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 424 Processing helix chain 'F' and resid 431 through 445 Processing helix chain 'F' and resid 451 through 456 removed outlier: 3.657A pdb=" N PHE F 456 " --> pdb=" O GLN F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 471 removed outlier: 3.590A pdb=" N SER F 470 " --> pdb=" O LYS F 466 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU F 471 " --> pdb=" O LYS F 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 59 removed outlier: 3.957A pdb=" N ALA G 34 " --> pdb=" O THR G 30 " (cutoff:3.500A) Proline residue: G 45 - end of helix removed outlier: 3.676A pdb=" N GLU G 49 " --> pdb=" O PRO G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 69 Processing helix chain 'G' and resid 90 through 111 removed outlier: 4.689A pdb=" N ALA G 94 " --> pdb=" O GLY G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 130 Processing helix chain 'G' and resid 146 through 163 removed outlier: 3.647A pdb=" N ALA G 150 " --> pdb=" O THR G 146 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU G 152 " --> pdb=" O GLU G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 303 Proline residue: G 237 - end of helix removed outlier: 3.572A pdb=" N LEU G 303 " --> pdb=" O GLY G 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 91 through 99 removed outlier: 3.550A pdb=" N ALA H 95 " --> pdb=" O ASP H 91 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS H 96 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLU H 97 " --> pdb=" O ASP H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 117 Processing helix chain 'a' and resid 32 through 53 removed outlier: 3.812A pdb=" N THR a 38 " --> pdb=" O ALA a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 62 through 81 removed outlier: 3.657A pdb=" N TRP a 66 " --> pdb=" O VAL a 62 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN a 72 " --> pdb=" O ALA a 68 " (cutoff:3.500A) Processing helix chain 'a' and resid 88 through 106 removed outlier: 4.102A pdb=" N LEU a 92 " --> pdb=" O PHE a 88 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE a 100 " --> pdb=" O ILE a 96 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER a 103 " --> pdb=" O PHE a 99 " (cutoff:3.500A) Processing helix chain 'a' and resid 107 through 109 No H-bonds generated for 'chain 'a' and resid 107 through 109' Processing helix chain 'a' and resid 126 through 129 Processing helix chain 'a' and resid 130 through 154 removed outlier: 3.680A pdb=" N VAL a 134 " --> pdb=" O ASP a 130 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE a 140 " --> pdb=" O ALA a 136 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 165 removed outlier: 3.906A pdb=" N ILE a 160 " --> pdb=" O VAL a 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 170 through 203 removed outlier: 3.965A pdb=" N VAL a 176 " --> pdb=" O PRO a 172 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU a 179 " --> pdb=" O ILE a 175 " (cutoff:3.500A) Proline residue: a 182 - end of helix removed outlier: 4.002A pdb=" N ARG a 188 " --> pdb=" O SER a 184 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY a 196 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA a 201 " --> pdb=" O GLY a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 204 through 206 No H-bonds generated for 'chain 'a' and resid 204 through 206' Processing helix chain 'a' and resid 207 through 246 removed outlier: 4.866A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.840A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU a 246 " --> pdb=" O SER a 242 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 49 removed outlier: 4.295A pdb=" N ALA b 33 " --> pdb=" O GLY b 29 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL b 41 " --> pdb=" O ILE b 37 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 161 removed outlier: 3.846A pdb=" N SER b 142 " --> pdb=" O ASP b 138 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY b 143 " --> pdb=" O GLN b 139 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER b 146 " --> pdb=" O SER b 142 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER b 147 " --> pdb=" O GLY b 143 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP b 149 " --> pdb=" O GLU b 145 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLY b 150 " --> pdb=" O SER b 146 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 22 Processing helix chain 'd' and resid 22 through 137 Processing helix chain 'd' and resid 139 through 157 removed outlier: 3.507A pdb=" N GLN d 143 " --> pdb=" O ASP d 139 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA d 145 " --> pdb=" O GLN d 141 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 194 Processing helix chain 'd' and resid 195 through 216 Processing helix chain 'd' and resid 216 through 224 removed outlier: 3.557A pdb=" N ASN d 220 " --> pdb=" O GLU d 216 " (cutoff:3.500A) Processing helix chain 'd' and resid 230 through 245 removed outlier: 4.043A pdb=" N LEU d 240 " --> pdb=" O LEU d 236 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASP d 243 " --> pdb=" O ARG d 239 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS d 244 " --> pdb=" O LEU d 240 " (cutoff:3.500A) Processing helix chain 'd' and resid 246 through 254 Processing helix chain 'd' and resid 263 through 285 removed outlier: 3.906A pdb=" N VAL d 271 " --> pdb=" O LEU d 267 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU d 272 " --> pdb=" O ILE d 268 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 306 Processing helix chain 'd' and resid 306 through 314 Processing helix chain 'd' and resid 319 through 331 Processing helix chain 'd' and resid 338 through 350 Processing helix chain 'd' and resid 356 through 372 Processing helix chain 'd' and resid 386 through 401 removed outlier: 3.646A pdb=" N ARG d 399 " --> pdb=" O GLU d 395 " (cutoff:3.500A) Processing helix chain 'd' and resid 431 through 442 Processing helix chain '1' and resid 6 through 46 Processing helix chain '1' and resid 49 through 81 removed outlier: 4.273A pdb=" N THR 1 55 " --> pdb=" O GLY 1 51 " (cutoff:3.500A) Proline residue: 1 56 - end of helix Processing helix chain '2' and resid 6 through 46 Processing helix chain '2' and resid 49 through 80 removed outlier: 4.569A pdb=" N THR 2 55 " --> pdb=" O GLY 2 51 " (cutoff:3.500A) Proline residue: 2 56 - end of helix Processing helix chain '3' and resid 6 through 46 Processing helix chain '3' and resid 49 through 81 removed outlier: 4.760A pdb=" N THR 3 55 " --> pdb=" O GLY 3 51 " (cutoff:3.500A) Proline residue: 3 56 - end of helix removed outlier: 3.770A pdb=" N ALA 3 67 " --> pdb=" O LEU 3 63 " (cutoff:3.500A) Processing helix chain '4' and resid 6 through 46 removed outlier: 3.710A pdb=" N ARG 4 45 " --> pdb=" O SER 4 41 " (cutoff:3.500A) Processing helix chain '4' and resid 49 through 80 removed outlier: 5.219A pdb=" N THR 4 55 " --> pdb=" O GLY 4 51 " (cutoff:3.500A) Proline residue: 4 56 - end of helix removed outlier: 3.686A pdb=" N ALA 4 67 " --> pdb=" O LEU 4 63 " (cutoff:3.500A) Processing helix chain '5' and resid 6 through 46 Processing helix chain '5' and resid 49 through 81 Proline residue: 5 56 - end of helix Processing helix chain '6' and resid 6 through 46 removed outlier: 3.550A pdb=" N ALA 6 38 " --> pdb=" O ILE 6 34 " (cutoff:3.500A) Processing helix chain '6' and resid 47 through 53 removed outlier: 4.156A pdb=" N GLY 6 51 " --> pdb=" O PRO 6 47 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 81 removed outlier: 3.962A pdb=" N ALA 6 67 " --> pdb=" O LEU 6 63 " (cutoff:3.500A) Processing helix chain '7' and resid 6 through 46 removed outlier: 3.572A pdb=" N ALA 7 38 " --> pdb=" O ILE 7 34 " (cutoff:3.500A) Processing helix chain '7' and resid 49 through 82 removed outlier: 4.375A pdb=" N THR 7 55 " --> pdb=" O GLY 7 51 " (cutoff:3.500A) Proline residue: 7 56 - end of helix Processing helix chain '8' and resid 4 through 46 removed outlier: 3.569A pdb=" N ILE 8 8 " --> pdb=" O ASP 8 4 " (cutoff:3.500A) Processing helix chain '8' and resid 49 through 82 removed outlier: 4.433A pdb=" N THR 8 55 " --> pdb=" O GLY 8 51 " (cutoff:3.500A) Proline residue: 8 56 - end of helix Processing helix chain '9' and resid 6 through 46 Processing helix chain '9' and resid 49 through 81 removed outlier: 4.067A pdb=" N THR 9 55 " --> pdb=" O GLY 9 51 " (cutoff:3.500A) Proline residue: 9 56 - end of helix removed outlier: 3.617A pdb=" N ALA 9 66 " --> pdb=" O GLY 9 62 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN 9 71 " --> pdb=" O ALA 9 67 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 63 through 64 removed outlier: 4.669A pdb=" N LEU B 55 " --> pdb=" O THR B 94 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N ILE B 35 " --> pdb=" O GLY D 58 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY D 58 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG D 63 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N HIS D 56 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU D 61 " --> pdb=" O HIS D 56 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N GLU D 23 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N VAL D 12 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU A 54 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU A 55 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG A 93 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU A 30 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 29 " --> pdb=" O VAL d 427 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL d 375 " --> pdb=" O SER d 406 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N GLN d 408 " --> pdb=" O VAL d 375 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA d 377 " --> pdb=" O GLN d 408 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 405 through 409 removed outlier: 6.208A pdb=" N VAL d 375 " --> pdb=" O SER d 406 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N GLN d 408 " --> pdb=" O VAL d 375 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA d 377 " --> pdb=" O GLN d 408 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 29 " --> pdb=" O VAL d 427 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N HIS A 43 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA A 37 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY A 75 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU A 63 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 9.776A pdb=" N THR D 80 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N GLU D 39 " --> pdb=" O THR D 80 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N THR D 82 " --> pdb=" O HIS D 37 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N HIS D 37 " --> pdb=" O THR D 82 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ALA D 84 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ASN D 34 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY D 58 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N ILE B 35 " --> pdb=" O GLY D 58 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N HIS B 43 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA B 37 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N THR E 80 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLU E 39 " --> pdb=" O THR E 80 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR E 82 " --> pdb=" O HIS E 37 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N HIS E 37 " --> pdb=" O THR E 82 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ALA E 84 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASN E 34 " --> pdb=" O VAL E 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 47 through 58 removed outlier: 6.650A pdb=" N ARG E 63 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N HIS E 56 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU E 61 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU E 23 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL E 12 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA B 37 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N HIS B 43 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU B 55 " --> pdb=" O THR B 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 99 through 102 Processing sheet with id=AA5, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.668A pdb=" N PHE A 271 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A 169 " --> pdb=" O CYS A 353 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N LEU A 355 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE A 171 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 534 through 540 removed outlier: 6.844A pdb=" N GLU A 534 " --> pdb=" O ARG G 202 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ALA G 204 " --> pdb=" O GLU A 534 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N GLU A 536 " --> pdb=" O ALA G 204 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N MET G 206 " --> pdb=" O GLU A 536 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL A 538 " --> pdb=" O MET G 206 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL G 208 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A 540 " --> pdb=" O VAL G 208 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR G 210 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N SER G 195 " --> pdb=" O ARG G 191 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG G 191 " --> pdb=" O SER G 195 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR G 197 " --> pdb=" O GLU G 189 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU G 183 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU G 182 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N THR G 188 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ALA G 77 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N TYR G 117 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL G 79 " --> pdb=" O TYR G 117 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL G 119 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL G 81 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL G 135 " --> pdb=" O PRO G 114 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU G 116 " --> pdb=" O VAL G 135 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N SER G 137 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL G 118 " --> pdb=" O SER G 137 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 99 through 102 Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.634A pdb=" N PHE B 271 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU B 169 " --> pdb=" O CYS B 353 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU B 355 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE B 171 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 62 through 69 removed outlier: 3.893A pdb=" N VAL C 62 " --> pdb=" O PHE C 58 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU C 54 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU C 55 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N HIS C 43 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ALA C 37 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL C 77 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ALA C 66 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU C 79 " --> pdb=" O GLY C 64 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N GLY C 64 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 9.923A pdb=" N THR F 80 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N GLU F 39 " --> pdb=" O THR F 80 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N THR F 82 " --> pdb=" O HIS F 37 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N HIS F 37 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ALA F 84 " --> pdb=" O ALA F 35 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASN F 34 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG F 63 " --> pdb=" O ALA F 54 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N HIS F 56 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU F 61 " --> pdb=" O HIS F 56 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE F 15 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASP F 21 " --> pdb=" O VAL F 13 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 99 through 102 Processing sheet with id=AB2, first strand: chain 'C' and resid 110 through 111 Processing sheet with id=AB3, first strand: chain 'C' and resid 351 through 352 Processing sheet with id=AB4, first strand: chain 'D' and resid 87 through 90 removed outlier: 3.980A pdb=" N GLU D 116 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 98 through 100 removed outlier: 6.573A pdb=" N PHE D 99 " --> pdb=" O PHE D 217 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER D 185 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL D 216 " --> pdb=" O SER D 185 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N PHE D 187 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N GLY D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLY D 189 " --> pdb=" O GLY D 218 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR D 184 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N PHE D 252 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL D 186 " --> pdb=" O PHE D 252 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ASP D 254 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA D 188 " --> pdb=" O ASP D 254 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL D 249 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N MET D 305 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU D 251 " --> pdb=" O MET D 305 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ALA D 307 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE D 253 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N TYR D 309 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS D 155 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N THR D 331 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ALA D 157 " --> pdb=" O THR D 331 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 136 through 137 removed outlier: 4.143A pdb=" N TYR D 150 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 87 through 90 removed outlier: 4.036A pdb=" N GLU E 116 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 98 through 99 removed outlier: 6.266A pdb=" N PHE E 99 " --> pdb=" O PHE E 217 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N GLN E 219 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER E 185 " --> pdb=" O ALA E 214 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N VAL E 216 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE E 187 " --> pdb=" O VAL E 216 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLY E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLY E 189 " --> pdb=" O GLY E 218 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE E 156 " --> pdb=" O GLN E 306 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS E 155 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N THR E 331 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA E 157 " --> pdb=" O THR E 331 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 136 through 137 removed outlier: 4.592A pdb=" N TYR E 150 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 87 through 90 removed outlier: 3.916A pdb=" N GLU F 116 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 98 through 99 Processing sheet with id=AC3, first strand: chain 'F' and resid 136 through 137 removed outlier: 4.163A pdb=" N TYR F 150 " --> pdb=" O LEU F 137 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 223 through 225 removed outlier: 6.503A pdb=" N SER G 223 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N GLN H 44 " --> pdb=" O SER G 223 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N GLU G 225 " --> pdb=" O GLN H 44 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASN H 5 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE H 79 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU H 7 " --> pdb=" O ILE H 79 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL H 81 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL H 9 " --> pdb=" O VAL H 81 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 223 through 225 removed outlier: 6.503A pdb=" N SER G 223 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N GLN H 44 " --> pdb=" O SER G 223 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N GLU G 225 " --> pdb=" O GLN H 44 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASN H 5 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE H 79 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU H 7 " --> pdb=" O ILE H 79 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL H 81 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL H 9 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE H 22 " --> pdb=" O GLU H 54 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) 2413 hydrogen bonds defined for protein. 6939 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: 8.57 Time building geometry restraints manager: 4.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10772 1.33 - 1.45: 5167 1.45 - 1.57: 19942 1.57 - 1.69: 18 1.69 - 1.82: 191 Bond restraints: 36090 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.50e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.02e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 4.99e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 4.03e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.53e+01 ... (remaining 36085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.69: 48955 4.69 - 9.37: 52 9.37 - 14.06: 0 14.06 - 18.74: 3 18.74 - 23.43: 3 Bond angle restraints: 49013 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 116.44 23.43 1.00e+00 1.00e+00 5.49e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 116.94 22.93 1.00e+00 1.00e+00 5.26e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 117.80 22.07 1.00e+00 1.00e+00 4.87e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 118.50 18.33 1.00e+00 1.00e+00 3.36e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 118.65 18.18 1.00e+00 1.00e+00 3.31e+02 ... (remaining 49008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 19804 18.00 - 36.00: 1305 36.00 - 54.00: 263 54.00 - 72.00: 87 72.00 - 90.00: 72 Dihedral angle restraints: 21531 sinusoidal: 7959 harmonic: 13572 Sorted by residual: dihedral pdb=" CA ALA D 276 " pdb=" C ALA D 276 " pdb=" N VAL D 277 " pdb=" CA VAL D 277 " ideal model delta harmonic sigma weight residual -180.00 -150.32 -29.68 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" O1B ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PB ADP F 600 " pdb=" PA ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 -149.37 89.37 1 2.00e+01 2.50e-03 2.37e+01 dihedral pdb=" CA ALA F 276 " pdb=" C ALA F 276 " pdb=" N VAL F 277 " pdb=" CA VAL F 277 " ideal model delta harmonic sigma weight residual -180.00 -156.12 -23.88 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 21528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4143 0.045 - 0.089: 1353 0.089 - 0.134: 266 0.134 - 0.178: 18 0.178 - 0.223: 1 Chirality restraints: 5781 Sorted by residual: chirality pdb=" CA GLN b 82 " pdb=" N GLN b 82 " pdb=" C GLN b 82 " pdb=" CB GLN b 82 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ASP b 70 " pdb=" N ASP b 70 " pdb=" C ASP b 70 " pdb=" CB ASP b 70 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CB THR b 67 " pdb=" CA THR b 67 " pdb=" OG1 THR b 67 " pdb=" CG2 THR b 67 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.62e-01 ... (remaining 5778 not shown) Planarity restraints: 6366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER F 275 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" C SER F 275 " -0.040 2.00e-02 2.50e+03 pdb=" O SER F 275 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA F 276 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG b 60 " 0.191 9.50e-02 1.11e+02 8.57e-02 4.56e+00 pdb=" NE ARG b 60 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG b 60 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG b 60 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG b 60 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 275 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.38e+00 pdb=" C SER E 275 " 0.036 2.00e-02 2.50e+03 pdb=" O SER E 275 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA E 276 " -0.012 2.00e-02 2.50e+03 ... (remaining 6363 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 28 2.25 - 2.92: 15267 2.92 - 3.58: 52664 3.58 - 4.24: 81471 4.24 - 4.90: 141219 Nonbonded interactions: 290649 Sorted by model distance: nonbonded pdb=" CD1 ILE H 39 " pdb=" CA ARG 3 45 " model vdw 1.593 3.890 nonbonded pdb=" O1B ATP B 600 " pdb="MG MG B 601 " model vdw 1.787 2.170 nonbonded pdb=" O ARG H 37 " pdb=" CG PRO 3 47 " model vdw 1.824 3.440 nonbonded pdb=" O2B ATP C 600 " pdb="MG MG C 601 " model vdw 1.825 2.170 nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.893 2.170 ... (remaining 290644 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: 0.00 Found NCS groups: ncs_group { reference = (chain '1' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '2' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 84)) selection = (chain '3' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '4' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '5' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 84)) selection = (chain '6' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '7' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '8' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '9' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) } ncs_group { reference = (chain 'A' and ((resid 29 and (name N or name CA or name C or name O or name CB \ )) or resid 30 through 44 or (resid 45 and (name N or name CA or name C or name \ O or name CB )) or resid 46 through 132 or (resid 133 and (name N or name CA or \ name C or name O or name CB )) or resid 134 through 294 or (resid 295 through 29 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 297 through \ 355 or (resid 356 and (name N or name CA or name C or name O or name CB )) or re \ sid 357 or (resid 358 and (name N or name CA or name C or name O or name CB )) o \ r resid 359 through 400 or (resid 401 through 402 and (name N or name CA or name \ C or name O or name CB )) or resid 403 through 411 or (resid 412 and (name N or \ name CA or name C or name O or name CB )) or resid 413 or (resid 414 through 41 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 420 through \ 461 or (resid 462 through 463 and (name N or name CA or name C or name O or name \ CB )) or resid 464 through 467 or (resid 468 and (name N or name CA or name C o \ r name O or name CB )) or resid 469 or (resid 470 and (name N or name CA or name \ C or name O or name CB )) or resid 471 through 475 or (resid 476 through 477 an \ d (name N or name CA or name C or name O or name CB )) or resid 478 through 494 \ or (resid 495 through 499 and (name N or name CA or name C or name O or name CB \ )) or resid 500 through 505 or (resid 506 and (name N or name CA or name C or na \ me O or name CB )) or resid 507 through 516 or resid 537 through 538 or resid 54 \ 0 or resid 600 through 601)) selection = (chain 'B' and ((resid 29 and (name N or name CA or name C or name O or name CB \ )) or resid 30 through 38 or (resid 39 and (name N or name CA or name C or name \ O or name CB )) or resid 40 through 44 or (resid 45 and (name N or name CA or na \ me C or name O or name CB )) or resid 46 through 80 or (resid 81 and (name N or \ name CA or name C or name O or name CB )) or resid 82 through 132 or (resid 133 \ and (name N or name CA or name C or name O or name CB )) or resid 134 through 19 \ 0 or (resid 191 through 192 and (name N or name CA or name C or name O or name C \ B )) or resid 193 through 294 or (resid 295 through 296 and (name N or name CA o \ r name C or name O or name CB )) or resid 297 through 316 or (resid 317 through \ 318 and (name N or name CA or name C or name O or name CB )) or resid 319 throug \ h 355 or (resid 356 and (name N or name CA or name C or name O or name CB )) or \ resid 357 or (resid 358 and (name N or name CA or name C or name O or name CB )) \ or resid 359 through 401 or (resid 402 and (name N or name CA or name C or name \ O or name CB )) or resid 403 through 411 or (resid 412 and (name N or name CA o \ r name C or name O or name CB )) or resid 413 through 416 or (resid 417 through \ 419 and (name N or name CA or name C or name O or name CB )) or resid 420 throug \ h 456 or (resid 457 and (name N or name CA or name C or name O or name CB )) or \ resid 458 through 467 or (resid 468 and (name N or name CA or name C or name O o \ r name CB )) or resid 469 through 475 or (resid 476 through 477 and (name N or n \ ame CA or name C or name O or name CB )) or resid 478 through 493 or (resid 494 \ through 499 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 0 through 505 or (resid 506 and (name N or name CA or name C or name O or name C \ B )) or resid 507 through 514 or (resid 515 and (name N or name CA or name C or \ name O or name CB )) or resid 516 or resid 518 through 601)) selection = (chain 'C' and (resid 29 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 80 or (resid 81 and (name N or nam \ e CA or name C or name O or name CB )) or resid 82 through 190 or (resid 191 thr \ ough 192 and (name N or name CA or name C or name O or name CB )) or resid 193 t \ hrough 316 or (resid 317 through 318 and (name N or name CA or name C or name O \ or name CB )) or resid 319 through 400 or (resid 401 through 402 and (name N or \ name CA or name C or name O or name CB )) or resid 403 through 413 or (resid 414 \ through 419 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 20 through 456 or (resid 457 and (name N or name CA or name C or name O or name \ CB )) or resid 458 through 469 or (resid 470 and (name N or name CA or name C or \ name O or name CB )) or resid 471 through 493 or (resid 494 through 499 and (na \ me N or name CA or name C or name O or name CB )) or resid 500 through 516 or re \ sid 518 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 103 or (resid 104 through 105 and (name N or nam \ e CA or name C or name O or name CB )) or resid 106 or (resid 107 through 108 an \ d (name N or name CA or name C or name O or name CB )) or resid 109 through 113 \ or (resid 114 and (name N or name CA or name C or name O or name CB )) or resid \ 115 through 198 or (resid 199 and (name N or name CA or name C or name O or name \ CB )) or resid 200 through 202 or (resid 203 and (name N or name CA or name C o \ r name O or name CB )) or resid 204 through 205 or (resid 206 through 207 and (n \ ame N or name CA or name C or name O or name CB )) or resid 208 through 285 or ( \ resid 286 and (name N or name CA or name C or name O or name CB )) or resid 287 \ through 362 or (resid 363 through 364 and (name N or name CA or name C or name O \ or name CB )) or resid 365 through 369 or (resid 370 through 371 and (name N or \ name CA or name C or name O or name CB )) or resid 372 through 380 or (resid 38 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 382 through \ 391 or (resid 392 through 393 and (name N or name CA or name C or name O or name \ CB )) or resid 394 through 402 or (resid 403 and (name N or name CA or name C o \ r name O or name CB )) or resid 404 through 424 or (resid 425 and (name N or nam \ e CA or name C or name O or name CB )) or resid 426 through 471)) selection = (chain 'E' and (resid 8 through 104 or (resid 105 and (name N or name CA or name \ C or name O or name CB )) or resid 106 through 137 or (resid 138 and (name N or \ name CA or name C or name O or name CB )) or resid 139 through 220 or (resid 22 \ 1 through 222 and (name N or name CA or name C or name O or name CB )) or resid \ 223 through 285 or (resid 286 and (name N or name CA or name C or name O or name \ CB )) or resid 287 through 288 or (resid 289 and (name N or name CA or name C o \ r name O or name CB )) or resid 290 through 291 or (resid 292 and (name N or nam \ e CA or name C or name O or name CB )) or resid 293 through 370 or (resid 371 an \ d (name N or name CA or name C or name O or name CB )) or resid 372 through 395 \ or (resid 396 through 398 and (name N or name CA or name C or name O or name CB \ )) or resid 399 through 461 or (resid 462 through 463 and (name N or name CA or \ name C or name O or name CB )) or resid 464 through 465 or (resid 466 and (name \ N or name CA or name C or name O or name CB )) or resid 467 through 471)) selection = (chain 'F' and (resid 8 through 103 or (resid 104 through 105 and (name N or nam \ e CA or name C or name O or name CB )) or resid 106 through 107 or (resid 108 an \ d (name N or name CA or name C or name O or name CB )) or resid 109 through 113 \ or (resid 114 and (name N or name CA or name C or name O or name CB )) or resid \ 115 through 134 or (resid 135 and (name N or name CA or name C or name O or name \ CB )) or resid 136 through 137 or (resid 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 198 or (resid 199 and (name N or nam \ e CA or name C or name O or name CB )) or resid 200 through 202 or (resid 203 an \ d (name N or name CA or name C or name O or name CB )) or resid 204 through 205 \ or (resid 206 through 207 and (name N or name CA or name C or name O or name CB \ )) or resid 208 through 220 or (resid 221 through 222 and (name N or name CA or \ name C or name O or name CB )) or resid 223 through 291 or (resid 292 and (name \ N or name CA or name C or name O or name CB )) or resid 293 through 369 or (resi \ d 370 through 371 and (name N or name CA or name C or name O or name CB )) or re \ sid 372 through 380 or (resid 381 and (name N or name CA or name C or name O or \ name CB )) or resid 382 through 383 or (resid 384 and (name N or name CA or name \ C or name O or name CB )) or resid 385 through 391 or (resid 392 through 393 an \ d (name N or name CA or name C or name O or name CB )) or resid 394 through 395 \ or (resid 396 through 398 and (name N or name CA or name C or name O or name CB \ )) or resid 399 through 402 or (resid 403 and (name N or name CA or name C or na \ me O or name CB )) or resid 404 through 432 or (resid 433 and (name N or name CA \ or name C or name O or name CB )) or resid 434 through 461 or (resid 462 throug \ h 463 and (name N or name CA or name C or name O or name CB )) or resid 464 thro \ ugh 465 or (resid 466 and (name N or name CA or name C or name O or name CB )) o \ r resid 467 through 471)) } 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: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 34.790 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.100 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 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 : 0.006 0.074 36090 Z= 0.309 Angle : 0.721 23.430 49013 Z= 0.472 Chirality : 0.043 0.223 5781 Planarity : 0.004 0.086 6366 Dihedral : 14.512 89.999 12833 Min Nonbonded Distance : 1.593 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.51 % Favored : 98.36 % Rotamer: Outliers : 0.14 % Allowed : 3.82 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.13 % 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 are not related in a simple way. whole: -0.99 (0.11), residues: 4761 helix: -0.25 (0.09), residues: 2542 sheet: -0.62 (0.21), residues: 551 loop : -1.08 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 423 TYR 0.021 0.002 TYR a 48 PHE 0.025 0.002 PHE a 99 TRP 0.028 0.002 TRP a 208 HIS 0.006 0.001 HIS C 474 Details of bonding type rmsd covalent geometry : bond 0.00648 (36090) covalent geometry : angle 0.72064 (49013) hydrogen bonds : bond 0.12066 ( 2368) hydrogen bonds : angle 6.34438 ( 6939) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 850 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8442 (mm) cc_final: 0.8173 (mm) REVERT: A 78 ILE cc_start: 0.8154 (mt) cc_final: 0.7826 (mm) REVERT: A 153 ILE cc_start: 0.7945 (mt) cc_final: 0.7735 (mt) REVERT: A 272 ASP cc_start: 0.7382 (t0) cc_final: 0.7138 (t0) REVERT: A 444 GLN cc_start: 0.7886 (mt0) cc_final: 0.7449 (mt0) REVERT: B 77 VAL cc_start: 0.8576 (p) cc_final: 0.8213 (m) REVERT: B 83 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6825 (tt0) REVERT: B 159 MET cc_start: 0.7825 (mtp) cc_final: 0.7601 (mtp) REVERT: B 199 LYS cc_start: 0.8065 (mtmm) cc_final: 0.7855 (mmtm) REVERT: B 330 ILE cc_start: 0.7977 (pt) cc_final: 0.7777 (mt) REVERT: B 337 ILE cc_start: 0.8980 (pt) cc_final: 0.8689 (mt) REVERT: B 356 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6616 (mt-10) REVERT: B 488 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7633 (mt-10) REVERT: B 491 LYS cc_start: 0.8319 (mttt) cc_final: 0.8105 (ttmm) REVERT: C 78 ILE cc_start: 0.8584 (mm) cc_final: 0.8340 (mm) REVERT: C 121 GLN cc_start: 0.8508 (tt0) cc_final: 0.8243 (tt0) REVERT: C 153 ILE cc_start: 0.8065 (mm) cc_final: 0.7758 (mt) REVERT: C 336 ASP cc_start: 0.7656 (t0) cc_final: 0.7401 (t0) REVERT: C 404 GLU cc_start: 0.8023 (tp30) cc_final: 0.7526 (tt0) REVERT: C 429 GLU cc_start: 0.7514 (tp30) cc_final: 0.7296 (tp30) REVERT: D 74 VAL cc_start: 0.8527 (t) cc_final: 0.8279 (p) REVERT: D 87 SER cc_start: 0.8501 (m) cc_final: 0.8233 (p) REVERT: D 175 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7935 (t0) REVERT: D 219 GLN cc_start: 0.6512 (mm-40) cc_final: 0.6224 (mm-40) REVERT: D 235 LEU cc_start: 0.7936 (tp) cc_final: 0.7731 (tp) REVERT: E 13 VAL cc_start: 0.8248 (m) cc_final: 0.8047 (t) REVERT: E 34 ASN cc_start: 0.8185 (m-40) cc_final: 0.7946 (m-40) REVERT: E 164 VAL cc_start: 0.8588 (m) cc_final: 0.8255 (t) REVERT: E 173 MET cc_start: 0.7581 (mmm) cc_final: 0.7339 (mmt) REVERT: E 287 MET cc_start: 0.8051 (tpp) cc_final: 0.7530 (tpp) REVERT: E 292 GLU cc_start: 0.7415 (tp30) cc_final: 0.7122 (tp30) REVERT: E 413 SER cc_start: 0.8294 (m) cc_final: 0.7866 (t) REVERT: F 71 ASP cc_start: 0.7745 (t0) cc_final: 0.7512 (t0) REVERT: F 79 VAL cc_start: 0.8642 (t) cc_final: 0.8318 (m) REVERT: F 173 MET cc_start: 0.6724 (mmt) cc_final: 0.6176 (mmt) REVERT: F 196 GLU cc_start: 0.6508 (tm-30) cc_final: 0.6201 (tm-30) REVERT: F 209 VAL cc_start: 0.8427 (t) cc_final: 0.8152 (p) REVERT: F 212 ASP cc_start: 0.7480 (t0) cc_final: 0.7120 (t0) REVERT: F 222 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7336 (mm-30) REVERT: F 391 ILE cc_start: 0.7994 (tt) cc_final: 0.7775 (mp) REVERT: F 414 GLN cc_start: 0.8484 (tt0) cc_final: 0.8140 (tt0) REVERT: F 466 LYS cc_start: 0.8103 (ttmt) cc_final: 0.7748 (tttm) REVERT: G 41 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7525 (mm-30) REVERT: G 162 MET cc_start: 0.7571 (tpp) cc_final: 0.7266 (mmt) REVERT: G 207 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7581 (mt-10) REVERT: G 208 VAL cc_start: 0.8688 (t) cc_final: 0.8364 (p) REVERT: a 228 ILE cc_start: 0.8245 (mt) cc_final: 0.7939 (mt) REVERT: d 89 GLU cc_start: 0.7736 (tt0) cc_final: 0.7281 (mt-10) REVERT: d 295 GLN cc_start: 0.9133 (tp40) cc_final: 0.8893 (tp-100) REVERT: 3 53 LEU cc_start: 0.7575 (tp) cc_final: 0.7341 (tp) REVERT: 7 43 ILE cc_start: 0.8221 (mm) cc_final: 0.7928 (mt) outliers start: 5 outliers final: 1 residues processed: 855 average time/residue: 0.2179 time to fit residues: 299.0587 Evaluate side-chains 614 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 612 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain 7 residue 55 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 470 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 263 ASN B 259 HIS B 305 HIS C 121 GLN C 258 GLN C 455 HIS C 512 GLN D 97 HIS D 326 HIS D 425 GLN E 97 HIS E 121 HIS E 219 GLN E 383 GLN F 219 GLN G 25 GLN a 146 HIS d 116 GLN 4 71 ASN 6 71 ASN 9 50 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.144150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.111562 restraints weight = 53614.981| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.97 r_work: 0.3218 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 36090 Z= 0.195 Angle : 0.627 9.729 49013 Z= 0.331 Chirality : 0.044 0.182 5781 Planarity : 0.005 0.055 6366 Dihedral : 6.700 86.021 5242 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.68 % Favored : 98.19 % Rotamer: Outliers : 2.07 % Allowed : 11.22 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 are not related in a simple way. whole: 0.70 (0.12), residues: 4761 helix: 1.26 (0.10), residues: 2602 sheet: -0.41 (0.21), residues: 573 loop : -0.40 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 151 TYR 0.018 0.002 TYR A 400 PHE 0.035 0.002 PHE C 449 TRP 0.032 0.002 TRP a 66 HIS 0.005 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00459 (36090) covalent geometry : angle 0.62729 (49013) hydrogen bonds : bond 0.04806 ( 2368) hydrogen bonds : angle 4.76427 ( 6939) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 649 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8676 (mm) cc_final: 0.8425 (mm) REVERT: A 78 ILE cc_start: 0.8522 (mt) cc_final: 0.8218 (mm) REVERT: A 308 LEU cc_start: 0.8128 (tp) cc_final: 0.7784 (tt) REVERT: A 421 LEU cc_start: 0.8000 (tp) cc_final: 0.7778 (tt) REVERT: A 490 LYS cc_start: 0.8577 (mmtt) cc_final: 0.8189 (mttm) REVERT: B 67 LEU cc_start: 0.8619 (tp) cc_final: 0.8368 (mt) REVERT: B 77 VAL cc_start: 0.8840 (p) cc_final: 0.8564 (m) REVERT: B 78 ILE cc_start: 0.8667 (mm) cc_final: 0.8333 (mm) REVERT: B 83 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7574 (tt0) REVERT: B 188 ASN cc_start: 0.9028 (t0) cc_final: 0.8764 (t0) REVERT: B 199 LYS cc_start: 0.8460 (mtmm) cc_final: 0.8033 (mmtm) REVERT: B 337 ILE cc_start: 0.8938 (pt) cc_final: 0.8724 (mt) REVERT: B 384 LYS cc_start: 0.8130 (tppt) cc_final: 0.7756 (tptt) REVERT: B 491 LYS cc_start: 0.8803 (mttt) cc_final: 0.8532 (ttmm) REVERT: C 84 LYS cc_start: 0.8945 (mtmt) cc_final: 0.8698 (mttm) REVERT: C 207 VAL cc_start: 0.8561 (t) cc_final: 0.8233 (m) REVERT: C 284 ILE cc_start: 0.8545 (mm) cc_final: 0.8293 (mt) REVERT: C 308 LEU cc_start: 0.8026 (tp) cc_final: 0.7741 (tt) REVERT: C 310 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7809 (mm-30) REVERT: C 318 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8243 (tm-30) REVERT: C 336 ASP cc_start: 0.8084 (t0) cc_final: 0.7806 (t0) REVERT: C 404 GLU cc_start: 0.8070 (tp30) cc_final: 0.7698 (tt0) REVERT: C 429 GLU cc_start: 0.8049 (tp30) cc_final: 0.7794 (tp30) REVERT: D 26 ARG cc_start: 0.8340 (tpp80) cc_final: 0.8130 (mmm-85) REVERT: D 87 SER cc_start: 0.8595 (m) cc_final: 0.8336 (p) REVERT: D 175 ASN cc_start: 0.8589 (OUTLIER) cc_final: 0.8106 (t0) REVERT: D 286 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7946 (mt-10) REVERT: D 443 THR cc_start: 0.8763 (p) cc_final: 0.8539 (t) REVERT: E 120 ILE cc_start: 0.8463 (pt) cc_final: 0.8228 (pt) REVERT: E 173 MET cc_start: 0.8115 (mmm) cc_final: 0.7915 (mmt) REVERT: E 286 GLU cc_start: 0.7854 (tt0) cc_final: 0.7613 (tt0) REVERT: E 292 GLU cc_start: 0.8056 (tp30) cc_final: 0.7827 (tp30) REVERT: E 305 MET cc_start: 0.8305 (mtp) cc_final: 0.8070 (mtp) REVERT: E 378 ARG cc_start: 0.7996 (tpt-90) cc_final: 0.7765 (tpt-90) REVERT: E 413 SER cc_start: 0.8670 (m) cc_final: 0.8317 (t) REVERT: F 71 ASP cc_start: 0.8394 (t0) cc_final: 0.8182 (t0) REVERT: F 173 MET cc_start: 0.7155 (mmt) cc_final: 0.6725 (mmt) REVERT: F 193 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7409 (mtt180) REVERT: F 196 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7302 (tm-30) REVERT: F 212 ASP cc_start: 0.8165 (t0) cc_final: 0.7727 (t0) REVERT: F 277 VAL cc_start: 0.8916 (m) cc_final: 0.8437 (p) REVERT: F 310 VAL cc_start: 0.8513 (t) cc_final: 0.8244 (m) REVERT: F 314 ASP cc_start: 0.8131 (t70) cc_final: 0.7360 (t70) REVERT: F 316 THR cc_start: 0.8833 (m) cc_final: 0.8398 (t) REVERT: F 360 ILE cc_start: 0.8823 (mt) cc_final: 0.8508 (mt) REVERT: F 414 GLN cc_start: 0.8599 (tt0) cc_final: 0.8362 (tt0) REVERT: G 83 SER cc_start: 0.8887 (m) cc_final: 0.8509 (p) REVERT: G 162 MET cc_start: 0.7837 (tpp) cc_final: 0.7518 (mmt) REVERT: H 50 MET cc_start: 0.8280 (tmm) cc_final: 0.8052 (tmm) REVERT: a 62 VAL cc_start: 0.7281 (m) cc_final: 0.6971 (p) REVERT: a 228 ILE cc_start: 0.8238 (mt) cc_final: 0.7911 (mt) REVERT: d 295 GLN cc_start: 0.8963 (tp40) cc_final: 0.8753 (tp-100) REVERT: d 346 SER cc_start: 0.9209 (m) cc_final: 0.8827 (p) REVERT: d 400 ILE cc_start: 0.9076 (mt) cc_final: 0.8849 (mt) REVERT: 4 21 MET cc_start: 0.8665 (tpp) cc_final: 0.8373 (tpp) REVERT: 7 43 ILE cc_start: 0.7909 (mm) cc_final: 0.7674 (mt) outliers start: 72 outliers final: 40 residues processed: 687 average time/residue: 0.1849 time to fit residues: 213.2932 Evaluate side-chains 633 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 590 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 452 GLU Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 274 ILE Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 81 ILE Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 176 VAL Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 80 SER Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 351 LEU Chi-restraints excluded: chain d residue 391 THR Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 6 residue 20 ILE Chi-restraints excluded: chain 7 residue 59 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 90 optimal weight: 0.8980 chunk 365 optimal weight: 6.9990 chunk 440 optimal weight: 20.0000 chunk 196 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 428 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 471 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 GLN E 175 ASN G 93 ASN ** G 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 146 HIS d 410 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.143431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.111077 restraints weight = 53781.171| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.96 r_work: 0.3212 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 36090 Z= 0.174 Angle : 0.574 9.755 49013 Z= 0.301 Chirality : 0.043 0.183 5781 Planarity : 0.004 0.060 6366 Dihedral : 6.455 86.322 5241 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.66 % Favored : 98.21 % Rotamer: Outliers : 2.61 % Allowed : 14.04 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 are not related in a simple way. whole: 1.13 (0.12), residues: 4761 helix: 1.71 (0.10), residues: 2576 sheet: -0.39 (0.21), residues: 573 loop : -0.29 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 26 TYR 0.016 0.001 TYR a 145 PHE 0.029 0.002 PHE D 456 TRP 0.012 0.001 TRP a 212 HIS 0.004 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00407 (36090) covalent geometry : angle 0.57449 (49013) hydrogen bonds : bond 0.04441 ( 2368) hydrogen bonds : angle 4.47959 ( 6939) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 617 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ILE cc_start: 0.8864 (pt) cc_final: 0.8569 (pt) REVERT: A 41 ILE cc_start: 0.8648 (mm) cc_final: 0.8368 (mm) REVERT: A 52 THR cc_start: 0.8959 (m) cc_final: 0.8687 (t) REVERT: A 78 ILE cc_start: 0.8502 (mt) cc_final: 0.8213 (mm) REVERT: A 304 LEU cc_start: 0.7847 (tp) cc_final: 0.7599 (tp) REVERT: A 308 LEU cc_start: 0.8136 (tp) cc_final: 0.7838 (tt) REVERT: A 399 GLN cc_start: 0.8150 (mt0) cc_final: 0.7906 (mt0) REVERT: A 490 LYS cc_start: 0.8544 (mmtt) cc_final: 0.8194 (mttm) REVERT: A 512 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8268 (tm-30) REVERT: B 67 LEU cc_start: 0.8508 (tp) cc_final: 0.8280 (mt) REVERT: B 77 VAL cc_start: 0.8802 (p) cc_final: 0.8536 (m) REVERT: B 78 ILE cc_start: 0.8694 (mm) cc_final: 0.8351 (mm) REVERT: B 83 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7628 (tt0) REVERT: B 188 ASN cc_start: 0.8972 (t0) cc_final: 0.8719 (t0) REVERT: B 199 LYS cc_start: 0.8327 (mtmm) cc_final: 0.8112 (mmtm) REVERT: B 384 LYS cc_start: 0.8162 (tppt) cc_final: 0.7879 (tptt) REVERT: B 491 LYS cc_start: 0.8892 (mttt) cc_final: 0.8628 (ttmm) REVERT: C 84 LYS cc_start: 0.9056 (mtmt) cc_final: 0.8795 (mttp) REVERT: C 102 VAL cc_start: 0.8671 (p) cc_final: 0.8168 (t) REVERT: C 207 VAL cc_start: 0.8556 (t) cc_final: 0.8246 (m) REVERT: C 284 ILE cc_start: 0.8547 (mm) cc_final: 0.8288 (mt) REVERT: C 308 LEU cc_start: 0.7982 (tp) cc_final: 0.7748 (tt) REVERT: C 318 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8286 (tm-30) REVERT: C 336 ASP cc_start: 0.8073 (t0) cc_final: 0.7721 (t0) REVERT: C 404 GLU cc_start: 0.8140 (tp30) cc_final: 0.7653 (tt0) REVERT: C 429 GLU cc_start: 0.8048 (tp30) cc_final: 0.7769 (tp30) REVERT: C 442 GLU cc_start: 0.7741 (pt0) cc_final: 0.7514 (mt-10) REVERT: C 449 PHE cc_start: 0.8513 (t80) cc_final: 0.8280 (t80) REVERT: C 470 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7501 (mt-10) REVERT: D 26 ARG cc_start: 0.8397 (tpp80) cc_final: 0.8184 (mmm-85) REVERT: D 87 SER cc_start: 0.8538 (m) cc_final: 0.8308 (p) REVERT: D 175 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.7957 (t0) REVERT: D 256 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8357 (tp) REVERT: D 453 GLN cc_start: 0.8887 (tp40) cc_final: 0.8671 (tp40) REVERT: E 13 VAL cc_start: 0.8723 (OUTLIER) cc_final: 0.8414 (t) REVERT: E 120 ILE cc_start: 0.8419 (pt) cc_final: 0.8195 (pt) REVERT: E 413 SER cc_start: 0.8580 (m) cc_final: 0.8301 (t) REVERT: F 71 ASP cc_start: 0.8323 (t0) cc_final: 0.8001 (t0) REVERT: F 173 MET cc_start: 0.7306 (mmt) cc_final: 0.6941 (mmt) REVERT: F 193 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7586 (mtt180) REVERT: F 196 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7241 (tm-30) REVERT: F 212 ASP cc_start: 0.8165 (t0) cc_final: 0.7819 (t0) REVERT: F 277 VAL cc_start: 0.8978 (m) cc_final: 0.8613 (p) REVERT: F 310 VAL cc_start: 0.8587 (t) cc_final: 0.8351 (m) REVERT: F 314 ASP cc_start: 0.8074 (t70) cc_final: 0.7360 (t70) REVERT: F 316 THR cc_start: 0.8873 (m) cc_final: 0.8357 (t) REVERT: F 360 ILE cc_start: 0.8821 (mt) cc_final: 0.8494 (mt) REVERT: G 6 ARG cc_start: 0.8307 (mmm160) cc_final: 0.7420 (mtm-85) REVERT: G 79 VAL cc_start: 0.8135 (OUTLIER) cc_final: 0.7881 (m) REVERT: G 83 SER cc_start: 0.8816 (m) cc_final: 0.8473 (p) REVERT: G 162 MET cc_start: 0.7862 (tpp) cc_final: 0.7561 (mmt) REVERT: H 31 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7972 (mt-10) REVERT: a 62 VAL cc_start: 0.7251 (m) cc_final: 0.6952 (p) REVERT: a 206 PHE cc_start: 0.6812 (m-80) cc_final: 0.6319 (m-80) REVERT: a 228 ILE cc_start: 0.8257 (mt) cc_final: 0.7932 (mt) REVERT: d 295 GLN cc_start: 0.8973 (tp40) cc_final: 0.8770 (tp-100) REVERT: d 346 SER cc_start: 0.9179 (m) cc_final: 0.8791 (p) REVERT: d 400 ILE cc_start: 0.8951 (mt) cc_final: 0.8719 (mt) REVERT: 1 21 MET cc_start: 0.7209 (mmm) cc_final: 0.5984 (mpp) REVERT: 2 75 MET cc_start: 0.8445 (ttp) cc_final: 0.8087 (ttp) REVERT: 4 21 MET cc_start: 0.8756 (tpp) cc_final: 0.8429 (tpp) REVERT: 7 43 ILE cc_start: 0.7890 (mm) cc_final: 0.7619 (mt) outliers start: 91 outliers final: 58 residues processed: 665 average time/residue: 0.1840 time to fit residues: 205.9369 Evaluate side-chains 650 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 587 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 452 GLU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 274 ILE Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 81 ILE Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 179 LEU Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 53 ASP Chi-restraints excluded: chain d residue 109 MET Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 351 LEU Chi-restraints excluded: chain d residue 391 THR Chi-restraints excluded: chain 1 residue 14 LEU Chi-restraints excluded: chain 4 residue 54 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 139 optimal weight: 2.9990 chunk 345 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 453 optimal weight: 0.9990 chunk 403 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 304 optimal weight: 0.9990 chunk 330 optimal weight: 8.9990 chunk 333 optimal weight: 0.7980 chunk 291 optimal weight: 0.8980 chunk 233 optimal weight: 0.4980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN B 435 GLN C 382 GLN C 455 HIS E 117 HIS G 184 HIS G 196 GLN a 146 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.143844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.111602 restraints weight = 53719.430| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.95 r_work: 0.3209 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36090 Z= 0.144 Angle : 0.546 9.428 49013 Z= 0.286 Chirality : 0.042 0.244 5781 Planarity : 0.004 0.061 6366 Dihedral : 6.193 85.830 5241 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.87 % Favored : 98.00 % Rotamer: Outliers : 2.55 % Allowed : 15.53 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 are not related in a simple way. whole: 1.38 (0.12), residues: 4761 helix: 1.97 (0.10), residues: 2570 sheet: -0.40 (0.21), residues: 583 loop : -0.23 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 26 TYR 0.016 0.001 TYR a 145 PHE 0.033 0.001 PHE D 456 TRP 0.014 0.001 TRP a 66 HIS 0.004 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00327 (36090) covalent geometry : angle 0.54579 (49013) hydrogen bonds : bond 0.04119 ( 2368) hydrogen bonds : angle 4.33155 ( 6939) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 609 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8648 (mm) cc_final: 0.8368 (mm) REVERT: A 52 THR cc_start: 0.8954 (m) cc_final: 0.8665 (t) REVERT: A 78 ILE cc_start: 0.8466 (mt) cc_final: 0.8159 (mm) REVERT: A 304 LEU cc_start: 0.7896 (tp) cc_final: 0.7635 (tp) REVERT: A 308 LEU cc_start: 0.8137 (tp) cc_final: 0.7861 (tt) REVERT: A 490 LYS cc_start: 0.8526 (mmtt) cc_final: 0.8222 (mttm) REVERT: B 67 LEU cc_start: 0.8494 (tp) cc_final: 0.8281 (mt) REVERT: B 77 VAL cc_start: 0.8807 (p) cc_final: 0.8570 (m) REVERT: B 78 ILE cc_start: 0.8693 (mm) cc_final: 0.8349 (mm) REVERT: B 83 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7637 (tt0) REVERT: B 188 ASN cc_start: 0.8952 (t0) cc_final: 0.8662 (t0) REVERT: B 199 LYS cc_start: 0.8401 (mtmm) cc_final: 0.8095 (mmtm) REVERT: B 277 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7397 (tt0) REVERT: B 384 LYS cc_start: 0.8105 (tppt) cc_final: 0.7807 (tptt) REVERT: B 491 LYS cc_start: 0.8909 (mttt) cc_final: 0.8652 (ttmm) REVERT: C 78 ILE cc_start: 0.8731 (mt) cc_final: 0.8270 (tp) REVERT: C 84 LYS cc_start: 0.9024 (mtmt) cc_final: 0.8798 (mttp) REVERT: C 102 VAL cc_start: 0.8672 (p) cc_final: 0.8178 (t) REVERT: C 207 VAL cc_start: 0.8551 (t) cc_final: 0.8240 (m) REVERT: C 284 ILE cc_start: 0.8531 (mm) cc_final: 0.8271 (mt) REVERT: C 318 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8335 (tm-30) REVERT: C 336 ASP cc_start: 0.8045 (t0) cc_final: 0.7686 (t0) REVERT: C 404 GLU cc_start: 0.8109 (tp30) cc_final: 0.7732 (tt0) REVERT: C 429 GLU cc_start: 0.8008 (tp30) cc_final: 0.7708 (tp30) REVERT: C 442 GLU cc_start: 0.7740 (pt0) cc_final: 0.7519 (mt-10) REVERT: D 175 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8009 (t0) REVERT: D 256 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8335 (tp) REVERT: E 13 VAL cc_start: 0.8777 (OUTLIER) cc_final: 0.8464 (t) REVERT: E 120 ILE cc_start: 0.8387 (pt) cc_final: 0.8185 (pt) REVERT: E 221 ASP cc_start: 0.8650 (t70) cc_final: 0.8372 (t0) REVERT: E 280 GLN cc_start: 0.8077 (pm20) cc_final: 0.7564 (pm20) REVERT: E 413 SER cc_start: 0.8582 (m) cc_final: 0.8307 (t) REVERT: F 70 THR cc_start: 0.8666 (p) cc_final: 0.8411 (p) REVERT: F 71 ASP cc_start: 0.8321 (t0) cc_final: 0.8006 (t0) REVERT: F 196 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7216 (tm-30) REVERT: F 212 ASP cc_start: 0.8168 (t0) cc_final: 0.7818 (t0) REVERT: F 277 VAL cc_start: 0.9015 (m) cc_final: 0.8713 (p) REVERT: F 310 VAL cc_start: 0.8579 (t) cc_final: 0.8358 (m) REVERT: F 314 ASP cc_start: 0.8068 (t70) cc_final: 0.7344 (t70) REVERT: F 316 THR cc_start: 0.8843 (m) cc_final: 0.8327 (t) REVERT: F 343 PHE cc_start: 0.8246 (m-80) cc_final: 0.7824 (m-80) REVERT: F 360 ILE cc_start: 0.8794 (mt) cc_final: 0.8463 (mt) REVERT: G 6 ARG cc_start: 0.8256 (mmm160) cc_final: 0.7354 (mtm-85) REVERT: G 83 SER cc_start: 0.8839 (m) cc_final: 0.8504 (p) REVERT: G 162 MET cc_start: 0.7862 (tpp) cc_final: 0.7578 (mmt) REVERT: a 62 VAL cc_start: 0.7352 (m) cc_final: 0.7077 (p) REVERT: a 206 PHE cc_start: 0.6736 (m-80) cc_final: 0.6279 (m-80) REVERT: a 228 ILE cc_start: 0.8318 (mt) cc_final: 0.8009 (mt) REVERT: d 295 GLN cc_start: 0.9003 (tp40) cc_final: 0.8801 (tp-100) REVERT: d 346 SER cc_start: 0.9146 (m) cc_final: 0.8782 (p) REVERT: d 400 ILE cc_start: 0.8943 (mt) cc_final: 0.8720 (mt) REVERT: 1 21 MET cc_start: 0.7342 (mmm) cc_final: 0.6733 (mmm) REVERT: 4 21 MET cc_start: 0.8732 (tpp) cc_final: 0.8400 (tpp) REVERT: 8 21 MET cc_start: 0.7110 (tpt) cc_final: 0.6668 (tpt) outliers start: 89 outliers final: 67 residues processed: 661 average time/residue: 0.1848 time to fit residues: 206.3457 Evaluate side-chains 649 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 578 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 196 GLN Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 274 ILE Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 81 ILE Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 179 LEU Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 53 ASP Chi-restraints excluded: chain d residue 109 MET Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain d residue 351 LEU Chi-restraints excluded: chain d residue 397 LEU Chi-restraints excluded: chain d residue 423 VAL Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 6 residue 20 ILE Chi-restraints excluded: chain 9 residue 82 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 98 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 337 optimal weight: 4.9990 chunk 343 optimal weight: 3.9990 chunk 203 optimal weight: 0.9980 chunk 188 optimal weight: 0.7980 chunk 94 optimal weight: 0.0270 chunk 101 optimal weight: 0.4980 chunk 176 optimal weight: 0.8980 chunk 316 optimal weight: 5.9990 chunk 294 optimal weight: 0.7980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.144434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.112336 restraints weight = 53692.762| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.91 r_work: 0.3225 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 36090 Z= 0.127 Angle : 0.531 9.481 49013 Z= 0.277 Chirality : 0.041 0.241 5781 Planarity : 0.004 0.058 6366 Dihedral : 5.970 84.487 5241 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.72 % Favored : 98.13 % Rotamer: Outliers : 2.53 % Allowed : 16.45 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 are not related in a simple way. whole: 1.51 (0.12), residues: 4761 helix: 2.10 (0.10), residues: 2572 sheet: -0.35 (0.21), residues: 583 loop : -0.22 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 26 TYR 0.015 0.001 TYR a 145 PHE 0.032 0.001 PHE D 456 TRP 0.019 0.001 TRP a 66 HIS 0.003 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00281 (36090) covalent geometry : angle 0.53086 (49013) hydrogen bonds : bond 0.03943 ( 2368) hydrogen bonds : angle 4.23134 ( 6939) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 615 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 LEU cc_start: 0.7847 (tp) cc_final: 0.7586 (tp) REVERT: A 308 LEU cc_start: 0.8158 (tp) cc_final: 0.7867 (tt) REVERT: A 490 LYS cc_start: 0.8495 (mmtt) cc_final: 0.8245 (mttm) REVERT: A 512 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8210 (tm-30) REVERT: B 77 VAL cc_start: 0.8800 (p) cc_final: 0.8564 (m) REVERT: B 78 ILE cc_start: 0.8679 (mm) cc_final: 0.8303 (mm) REVERT: B 83 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7541 (tt0) REVERT: B 188 ASN cc_start: 0.8933 (t0) cc_final: 0.8648 (t0) REVERT: B 199 LYS cc_start: 0.8252 (mtmm) cc_final: 0.7971 (mmtm) REVERT: B 277 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: B 384 LYS cc_start: 0.8069 (tppt) cc_final: 0.7768 (tptt) REVERT: B 491 LYS cc_start: 0.8920 (mttt) cc_final: 0.8675 (ttmm) REVERT: C 78 ILE cc_start: 0.8776 (mt) cc_final: 0.8332 (tp) REVERT: C 84 LYS cc_start: 0.9002 (mtmt) cc_final: 0.8799 (mttp) REVERT: C 102 VAL cc_start: 0.8656 (p) cc_final: 0.8169 (t) REVERT: C 207 VAL cc_start: 0.8575 (t) cc_final: 0.8259 (m) REVERT: C 336 ASP cc_start: 0.8078 (t0) cc_final: 0.7675 (t0) REVERT: C 404 GLU cc_start: 0.8117 (tp30) cc_final: 0.7746 (tt0) REVERT: C 429 GLU cc_start: 0.7975 (tp30) cc_final: 0.7678 (tp30) REVERT: C 442 GLU cc_start: 0.7678 (pt0) cc_final: 0.7461 (mt-10) REVERT: C 470 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7477 (mt-10) REVERT: D 256 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8261 (tp) REVERT: D 305 MET cc_start: 0.8457 (tpp) cc_final: 0.8014 (ttm) REVERT: E 13 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8454 (t) REVERT: E 67 MET cc_start: 0.8319 (mmt) cc_final: 0.8104 (mmm) REVERT: E 120 ILE cc_start: 0.8389 (pt) cc_final: 0.8183 (pt) REVERT: E 221 ASP cc_start: 0.8604 (t70) cc_final: 0.8363 (t0) REVERT: E 277 VAL cc_start: 0.8946 (OUTLIER) cc_final: 0.8660 (p) REVERT: E 413 SER cc_start: 0.8576 (m) cc_final: 0.8303 (t) REVERT: F 26 ARG cc_start: 0.8476 (tpp80) cc_final: 0.8037 (mmm-85) REVERT: F 70 THR cc_start: 0.8664 (p) cc_final: 0.8419 (p) REVERT: F 71 ASP cc_start: 0.8322 (t0) cc_final: 0.8042 (t0) REVERT: F 196 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7166 (tm-30) REVERT: F 212 ASP cc_start: 0.8171 (t0) cc_final: 0.7851 (t0) REVERT: F 277 VAL cc_start: 0.9018 (m) cc_final: 0.8729 (p) REVERT: F 305 MET cc_start: 0.7817 (tpp) cc_final: 0.7414 (ttt) REVERT: F 310 VAL cc_start: 0.8568 (t) cc_final: 0.8361 (m) REVERT: F 314 ASP cc_start: 0.8028 (t70) cc_final: 0.7571 (t70) REVERT: F 343 PHE cc_start: 0.8237 (m-80) cc_final: 0.7835 (m-80) REVERT: F 360 ILE cc_start: 0.8785 (mt) cc_final: 0.8440 (mt) REVERT: G 6 ARG cc_start: 0.8194 (mmm160) cc_final: 0.7324 (mtm-85) REVERT: G 79 VAL cc_start: 0.8092 (OUTLIER) cc_final: 0.7858 (m) REVERT: G 83 SER cc_start: 0.8814 (m) cc_final: 0.8466 (p) REVERT: G 96 VAL cc_start: 0.8041 (t) cc_final: 0.7772 (p) REVERT: G 162 MET cc_start: 0.7856 (tpp) cc_final: 0.7584 (mmt) REVERT: G 202 ARG cc_start: 0.8349 (ttm170) cc_final: 0.7941 (ttp-170) REVERT: a 146 HIS cc_start: 0.7240 (OUTLIER) cc_final: 0.6962 (m-70) REVERT: a 206 PHE cc_start: 0.6825 (m-80) cc_final: 0.6382 (m-80) REVERT: a 228 ILE cc_start: 0.8278 (mt) cc_final: 0.7967 (mt) REVERT: b 133 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7523 (mt) REVERT: d 1 MET cc_start: 0.6604 (ppp) cc_final: 0.6326 (ppp) REVERT: d 346 SER cc_start: 0.9141 (m) cc_final: 0.8777 (p) REVERT: d 400 ILE cc_start: 0.8929 (mt) cc_final: 0.8712 (mt) REVERT: 1 21 MET cc_start: 0.7401 (mmm) cc_final: 0.6996 (mmm) REVERT: 2 21 MET cc_start: 0.7745 (mmm) cc_final: 0.7006 (tpp) REVERT: 3 21 MET cc_start: 0.6054 (mmp) cc_final: 0.5789 (mmt) REVERT: 3 75 MET cc_start: 0.6362 (tmm) cc_final: 0.5992 (tmm) REVERT: 4 21 MET cc_start: 0.8711 (tpp) cc_final: 0.8321 (tpp) REVERT: 8 21 MET cc_start: 0.6995 (tpt) cc_final: 0.6700 (tpt) outliers start: 88 outliers final: 62 residues processed: 669 average time/residue: 0.1962 time to fit residues: 221.4358 Evaluate side-chains 660 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 591 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 274 ILE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 81 ILE Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 146 HIS Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 133 LEU Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 66 LYS Chi-restraints excluded: chain d residue 109 MET Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain d residue 351 LEU Chi-restraints excluded: chain d residue 397 LEU Chi-restraints excluded: chain d residue 423 VAL Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 9 residue 82 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 338 optimal weight: 10.0000 chunk 467 optimal weight: 7.9990 chunk 450 optimal weight: 9.9990 chunk 306 optimal weight: 5.9990 chunk 201 optimal weight: 0.9990 chunk 256 optimal weight: 0.0040 chunk 392 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 269 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 351 optimal weight: 0.9980 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 453 GLN D 219 GLN d 295 GLN 8 37 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.143181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.111236 restraints weight = 53770.194| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.90 r_work: 0.3211 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36090 Z= 0.156 Angle : 0.541 9.242 49013 Z= 0.282 Chirality : 0.042 0.199 5781 Planarity : 0.004 0.068 6366 Dihedral : 5.874 86.103 5239 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.91 % Favored : 97.96 % Rotamer: Outliers : 3.07 % Allowed : 16.88 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 are not related in a simple way. whole: 1.57 (0.12), residues: 4761 helix: 2.13 (0.10), residues: 2592 sheet: -0.38 (0.21), residues: 585 loop : -0.17 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 335 TYR 0.014 0.001 TYR a 145 PHE 0.037 0.001 PHE D 456 TRP 0.040 0.001 TRP a 66 HIS 0.004 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00361 (36090) covalent geometry : angle 0.54078 (49013) hydrogen bonds : bond 0.03987 ( 2368) hydrogen bonds : angle 4.20318 ( 6939) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 605 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 THR cc_start: 0.8944 (m) cc_final: 0.8634 (t) REVERT: A 308 LEU cc_start: 0.8199 (tp) cc_final: 0.7942 (tt) REVERT: A 490 LYS cc_start: 0.8481 (mmtt) cc_final: 0.8261 (mttm) REVERT: B 77 VAL cc_start: 0.8818 (p) cc_final: 0.8575 (m) REVERT: B 78 ILE cc_start: 0.8702 (mm) cc_final: 0.8314 (mm) REVERT: B 83 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7503 (tt0) REVERT: B 188 ASN cc_start: 0.8922 (t0) cc_final: 0.8613 (t0) REVERT: B 199 LYS cc_start: 0.8209 (mtmm) cc_final: 0.7945 (mmtm) REVERT: B 277 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7442 (tt0) REVERT: B 384 LYS cc_start: 0.8078 (tppt) cc_final: 0.7867 (tptt) REVERT: B 491 LYS cc_start: 0.8919 (mttt) cc_final: 0.8655 (ttmm) REVERT: C 84 LYS cc_start: 0.8992 (mtmt) cc_final: 0.8762 (mttm) REVERT: C 102 VAL cc_start: 0.8676 (p) cc_final: 0.8182 (t) REVERT: C 199 LYS cc_start: 0.8257 (mtmm) cc_final: 0.7991 (mttp) REVERT: C 207 VAL cc_start: 0.8573 (t) cc_final: 0.8246 (m) REVERT: C 284 ILE cc_start: 0.8518 (mm) cc_final: 0.8236 (mt) REVERT: C 336 ASP cc_start: 0.8066 (t0) cc_final: 0.7621 (t0) REVERT: C 404 GLU cc_start: 0.8165 (tp30) cc_final: 0.7755 (tt0) REVERT: C 429 GLU cc_start: 0.8012 (tp30) cc_final: 0.7712 (tp30) REVERT: C 442 GLU cc_start: 0.7737 (pt0) cc_final: 0.7524 (mt-10) REVERT: D 59 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.8019 (p0) REVERT: D 219 GLN cc_start: 0.7154 (mm110) cc_final: 0.6925 (mm110) REVERT: D 256 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8214 (tp) REVERT: E 13 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8455 (t) REVERT: E 120 ILE cc_start: 0.8385 (pt) cc_final: 0.8182 (pt) REVERT: E 221 ASP cc_start: 0.8639 (t70) cc_final: 0.8374 (t0) REVERT: E 277 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8718 (p) REVERT: E 287 MET cc_start: 0.8331 (tpp) cc_final: 0.7929 (tpp) REVERT: E 413 SER cc_start: 0.8590 (m) cc_final: 0.8319 (t) REVERT: F 26 ARG cc_start: 0.8459 (tpp80) cc_final: 0.8038 (mmm-85) REVERT: F 70 THR cc_start: 0.8709 (p) cc_final: 0.8462 (p) REVERT: F 71 ASP cc_start: 0.8318 (t0) cc_final: 0.8054 (t0) REVERT: F 94 VAL cc_start: 0.8529 (t) cc_final: 0.8148 (p) REVERT: F 196 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7174 (tm-30) REVERT: F 212 ASP cc_start: 0.8177 (t0) cc_final: 0.7873 (t0) REVERT: F 247 GLN cc_start: 0.8331 (mm-40) cc_final: 0.8096 (mt0) REVERT: F 277 VAL cc_start: 0.9049 (m) cc_final: 0.8774 (p) REVERT: F 305 MET cc_start: 0.7870 (tpp) cc_final: 0.7449 (ttt) REVERT: F 314 ASP cc_start: 0.8001 (t70) cc_final: 0.7568 (t70) REVERT: F 343 PHE cc_start: 0.8218 (m-80) cc_final: 0.7881 (m-80) REVERT: F 360 ILE cc_start: 0.8791 (mt) cc_final: 0.8447 (mt) REVERT: G 79 VAL cc_start: 0.8104 (OUTLIER) cc_final: 0.7886 (m) REVERT: G 83 SER cc_start: 0.8810 (m) cc_final: 0.8487 (p) REVERT: G 96 VAL cc_start: 0.8048 (t) cc_final: 0.7783 (p) REVERT: G 162 MET cc_start: 0.7890 (tpp) cc_final: 0.7589 (mmt) REVERT: G 202 ARG cc_start: 0.8361 (ttm170) cc_final: 0.7959 (ttp-170) REVERT: a 146 HIS cc_start: 0.7247 (OUTLIER) cc_final: 0.6967 (m-70) REVERT: a 206 PHE cc_start: 0.6756 (m-80) cc_final: 0.6347 (m-80) REVERT: a 228 ILE cc_start: 0.8248 (mt) cc_final: 0.7940 (mt) REVERT: b 133 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7540 (mt) REVERT: d 346 SER cc_start: 0.9139 (m) cc_final: 0.8778 (p) REVERT: d 400 ILE cc_start: 0.8941 (mt) cc_final: 0.8735 (mt) REVERT: 1 21 MET cc_start: 0.7430 (mmm) cc_final: 0.7017 (mmm) REVERT: 2 21 MET cc_start: 0.7712 (mmm) cc_final: 0.6926 (tpp) REVERT: 2 58 PHE cc_start: 0.6883 (OUTLIER) cc_final: 0.6489 (t80) REVERT: 3 75 MET cc_start: 0.6535 (tmm) cc_final: 0.6023 (tmm) REVERT: 4 21 MET cc_start: 0.8711 (tpp) cc_final: 0.8288 (tpp) REVERT: 4 54 PHE cc_start: 0.5063 (OUTLIER) cc_final: 0.4823 (m-80) REVERT: 4 75 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7802 (tmm) REVERT: 8 21 MET cc_start: 0.6990 (tpt) cc_final: 0.6749 (tpt) REVERT: 9 75 MET cc_start: 0.8317 (ttp) cc_final: 0.7806 (ttp) outliers start: 107 outliers final: 78 residues processed: 672 average time/residue: 0.1925 time to fit residues: 220.7277 Evaluate side-chains 665 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 576 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 274 ILE Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 81 ILE Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 146 HIS Chi-restraints excluded: chain a residue 179 LEU Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain b residue 133 LEU Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 53 ASP Chi-restraints excluded: chain d residue 66 LYS Chi-restraints excluded: chain d residue 72 VAL Chi-restraints excluded: chain d residue 109 MET Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain d residue 351 LEU Chi-restraints excluded: chain d residue 397 LEU Chi-restraints excluded: chain d residue 423 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 2 residue 58 PHE Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 5 residue 75 MET Chi-restraints excluded: chain 6 residue 20 ILE Chi-restraints excluded: chain 9 residue 82 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 331 optimal weight: 0.8980 chunk 209 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 349 optimal weight: 1.9990 chunk 257 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 150 optimal weight: 0.6980 chunk 370 optimal weight: 0.8980 chunk 235 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 GLN A 420 GLN 6 71 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.143676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.111660 restraints weight = 53835.300| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.95 r_work: 0.3212 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 36090 Z= 0.141 Angle : 0.546 9.273 49013 Z= 0.283 Chirality : 0.041 0.181 5781 Planarity : 0.004 0.059 6366 Dihedral : 5.745 85.566 5239 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.72 % Favored : 98.17 % Rotamer: Outliers : 2.84 % Allowed : 17.94 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 are not related in a simple way. whole: 1.62 (0.12), residues: 4761 helix: 2.19 (0.10), residues: 2591 sheet: -0.39 (0.21), residues: 590 loop : -0.15 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 122 TYR 0.014 0.001 TYR F 279 PHE 0.032 0.001 PHE D 456 TRP 0.057 0.002 TRP a 66 HIS 0.003 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00329 (36090) covalent geometry : angle 0.54566 (49013) hydrogen bonds : bond 0.03916 ( 2368) hydrogen bonds : angle 4.17068 ( 6939) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 590 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 LEU cc_start: 0.8705 (tm) cc_final: 0.8431 (tt) REVERT: A 308 LEU cc_start: 0.8174 (tp) cc_final: 0.7938 (tt) REVERT: A 490 LYS cc_start: 0.8523 (mmtt) cc_final: 0.8259 (mttm) REVERT: A 512 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8217 (tm-30) REVERT: B 77 VAL cc_start: 0.8807 (p) cc_final: 0.8599 (m) REVERT: B 83 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7509 (tt0) REVERT: B 188 ASN cc_start: 0.8923 (t0) cc_final: 0.8593 (t0) REVERT: B 199 LYS cc_start: 0.8146 (mtmm) cc_final: 0.7911 (mmtm) REVERT: B 277 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7460 (tt0) REVERT: B 384 LYS cc_start: 0.8079 (tppt) cc_final: 0.7849 (tptt) REVERT: B 491 LYS cc_start: 0.8922 (mttt) cc_final: 0.8652 (ttmm) REVERT: C 78 ILE cc_start: 0.8662 (mm) cc_final: 0.8300 (tt) REVERT: C 102 VAL cc_start: 0.8661 (p) cc_final: 0.8188 (t) REVERT: C 199 LYS cc_start: 0.8272 (mtmm) cc_final: 0.8015 (mttp) REVERT: C 207 VAL cc_start: 0.8575 (t) cc_final: 0.8243 (m) REVERT: C 274 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8142 (mt) REVERT: C 284 ILE cc_start: 0.8509 (mm) cc_final: 0.8235 (mt) REVERT: C 336 ASP cc_start: 0.8012 (t0) cc_final: 0.7593 (t0) REVERT: C 404 GLU cc_start: 0.8164 (tp30) cc_final: 0.7749 (tt0) REVERT: C 429 GLU cc_start: 0.8002 (tp30) cc_final: 0.7692 (tp30) REVERT: C 442 GLU cc_start: 0.7728 (pt0) cc_final: 0.7525 (mt-10) REVERT: D 59 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7973 (p0) REVERT: D 256 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8191 (tp) REVERT: D 283 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7920 (tp) REVERT: E 13 VAL cc_start: 0.8770 (OUTLIER) cc_final: 0.8458 (t) REVERT: E 221 ASP cc_start: 0.8616 (t70) cc_final: 0.8371 (t0) REVERT: E 277 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8713 (p) REVERT: E 413 SER cc_start: 0.8595 (m) cc_final: 0.8329 (t) REVERT: F 26 ARG cc_start: 0.8475 (tpp80) cc_final: 0.8046 (mmm-85) REVERT: F 70 THR cc_start: 0.8701 (p) cc_final: 0.8464 (p) REVERT: F 71 ASP cc_start: 0.8306 (t0) cc_final: 0.8055 (t0) REVERT: F 94 VAL cc_start: 0.8530 (t) cc_final: 0.8146 (p) REVERT: F 185 SER cc_start: 0.8506 (t) cc_final: 0.8018 (p) REVERT: F 196 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7195 (tm-30) REVERT: F 212 ASP cc_start: 0.8180 (t0) cc_final: 0.7881 (t0) REVERT: F 277 VAL cc_start: 0.9024 (m) cc_final: 0.8756 (p) REVERT: F 314 ASP cc_start: 0.7969 (t70) cc_final: 0.7538 (t70) REVERT: F 343 PHE cc_start: 0.8232 (m-80) cc_final: 0.7910 (m-80) REVERT: F 360 ILE cc_start: 0.8782 (mt) cc_final: 0.8562 (mt) REVERT: G 6 ARG cc_start: 0.8108 (mmm160) cc_final: 0.7329 (mtm-85) REVERT: G 79 VAL cc_start: 0.8107 (OUTLIER) cc_final: 0.7897 (m) REVERT: G 83 SER cc_start: 0.8812 (m) cc_final: 0.8498 (p) REVERT: G 96 VAL cc_start: 0.8051 (t) cc_final: 0.7769 (p) REVERT: G 162 MET cc_start: 0.7887 (tpp) cc_final: 0.7600 (mmt) REVERT: G 202 ARG cc_start: 0.8365 (ttm170) cc_final: 0.7669 (ttp-170) REVERT: H 7 GLU cc_start: 0.6816 (mt-10) cc_final: 0.6587 (mt-10) REVERT: a 146 HIS cc_start: 0.7265 (OUTLIER) cc_final: 0.6982 (m-70) REVERT: a 206 PHE cc_start: 0.6712 (m-80) cc_final: 0.6344 (m-80) REVERT: a 228 ILE cc_start: 0.8236 (mt) cc_final: 0.7924 (mt) REVERT: d 295 GLN cc_start: 0.8976 (tp40) cc_final: 0.8742 (tp40) REVERT: d 346 SER cc_start: 0.9127 (m) cc_final: 0.8769 (p) REVERT: d 400 ILE cc_start: 0.8938 (mt) cc_final: 0.8735 (mt) REVERT: 1 21 MET cc_start: 0.7433 (mmm) cc_final: 0.7068 (mmm) REVERT: 2 21 MET cc_start: 0.7720 (mmm) cc_final: 0.6937 (tpp) REVERT: 2 58 PHE cc_start: 0.6880 (OUTLIER) cc_final: 0.6489 (t80) REVERT: 3 75 MET cc_start: 0.6545 (tmm) cc_final: 0.6148 (tmm) REVERT: 4 21 MET cc_start: 0.8681 (tpp) cc_final: 0.8311 (tpp) REVERT: 4 54 PHE cc_start: 0.5075 (OUTLIER) cc_final: 0.4775 (m-80) REVERT: 4 75 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7805 (tmm) REVERT: 8 21 MET cc_start: 0.6957 (tpt) cc_final: 0.6677 (tpt) outliers start: 99 outliers final: 77 residues processed: 651 average time/residue: 0.1903 time to fit residues: 210.8985 Evaluate side-chains 666 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 577 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 452 GLU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 274 ILE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 146 HIS Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 53 ASP Chi-restraints excluded: chain d residue 66 LYS Chi-restraints excluded: chain d residue 80 SER Chi-restraints excluded: chain d residue 109 MET Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain d residue 351 LEU Chi-restraints excluded: chain d residue 397 LEU Chi-restraints excluded: chain d residue 423 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 54 PHE Chi-restraints excluded: chain 2 residue 58 PHE Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 6 residue 20 ILE Chi-restraints excluded: chain 9 residue 21 MET Chi-restraints excluded: chain 9 residue 82 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 315 optimal weight: 0.9990 chunk 170 optimal weight: 0.8980 chunk 436 optimal weight: 1.9990 chunk 256 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 466 optimal weight: 5.9990 chunk 303 optimal weight: 0.5980 chunk 311 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 219 GLN d 33 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.143995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.112383 restraints weight = 53555.231| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.88 r_work: 0.3228 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 36090 Z= 0.133 Angle : 0.541 9.417 49013 Z= 0.281 Chirality : 0.041 0.190 5781 Planarity : 0.004 0.057 6366 Dihedral : 5.568 86.109 5239 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.89 % Favored : 98.00 % Rotamer: Outliers : 3.10 % Allowed : 18.31 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 are not related in a simple way. whole: 1.72 (0.12), residues: 4761 helix: 2.25 (0.10), residues: 2593 sheet: -0.34 (0.21), residues: 580 loop : -0.08 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 122 TYR 0.012 0.001 TYR a 145 PHE 0.033 0.001 PHE D 456 TRP 0.048 0.001 TRP a 66 HIS 0.003 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00305 (36090) covalent geometry : angle 0.54104 (49013) hydrogen bonds : bond 0.03811 ( 2368) hydrogen bonds : angle 4.14113 ( 6939) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 610 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 LEU cc_start: 0.8656 (tm) cc_final: 0.8407 (tt) REVERT: A 308 LEU cc_start: 0.8149 (tp) cc_final: 0.7917 (tt) REVERT: A 490 LYS cc_start: 0.8544 (mmtt) cc_final: 0.8274 (mttm) REVERT: B 77 VAL cc_start: 0.8817 (p) cc_final: 0.8609 (m) REVERT: B 83 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7388 (tt0) REVERT: B 149 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8038 (tp) REVERT: B 188 ASN cc_start: 0.8910 (t0) cc_final: 0.8619 (t0) REVERT: B 199 LYS cc_start: 0.8157 (mtmm) cc_final: 0.7908 (mmtm) REVERT: B 277 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7460 (tt0) REVERT: B 384 LYS cc_start: 0.8068 (tppt) cc_final: 0.7836 (tptt) REVERT: B 491 LYS cc_start: 0.8901 (mttt) cc_final: 0.8637 (ttmm) REVERT: C 78 ILE cc_start: 0.8679 (mm) cc_final: 0.8353 (tt) REVERT: C 102 VAL cc_start: 0.8646 (p) cc_final: 0.8179 (t) REVERT: C 173 ASP cc_start: 0.7874 (t0) cc_final: 0.7561 (t0) REVERT: C 207 VAL cc_start: 0.8573 (t) cc_final: 0.8244 (m) REVERT: C 284 ILE cc_start: 0.8512 (mm) cc_final: 0.8262 (mt) REVERT: C 404 GLU cc_start: 0.8181 (tp30) cc_final: 0.7725 (tt0) REVERT: C 429 GLU cc_start: 0.7964 (tp30) cc_final: 0.7649 (tp30) REVERT: C 439 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7599 (mp) REVERT: C 442 GLU cc_start: 0.7704 (pt0) cc_final: 0.7500 (mt-10) REVERT: D 59 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7934 (p0) REVERT: D 256 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8163 (tp) REVERT: D 283 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7904 (tp) REVERT: D 305 MET cc_start: 0.8385 (tpp) cc_final: 0.8128 (ttm) REVERT: E 13 VAL cc_start: 0.8777 (OUTLIER) cc_final: 0.8452 (t) REVERT: E 77 VAL cc_start: 0.9169 (OUTLIER) cc_final: 0.8784 (m) REVERT: E 221 ASP cc_start: 0.8590 (t70) cc_final: 0.8327 (t0) REVERT: E 277 VAL cc_start: 0.8970 (OUTLIER) cc_final: 0.8722 (p) REVERT: E 327 LEU cc_start: 0.8248 (pp) cc_final: 0.7981 (mt) REVERT: E 413 SER cc_start: 0.8611 (m) cc_final: 0.8341 (t) REVERT: F 26 ARG cc_start: 0.8472 (tpp80) cc_final: 0.8051 (mmm-85) REVERT: F 70 THR cc_start: 0.8674 (p) cc_final: 0.8449 (p) REVERT: F 71 ASP cc_start: 0.8255 (t0) cc_final: 0.8023 (t0) REVERT: F 94 VAL cc_start: 0.8504 (t) cc_final: 0.8130 (p) REVERT: F 185 SER cc_start: 0.8539 (t) cc_final: 0.8009 (p) REVERT: F 196 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7205 (tm-30) REVERT: F 212 ASP cc_start: 0.8152 (t0) cc_final: 0.7799 (t0) REVERT: F 277 VAL cc_start: 0.8995 (m) cc_final: 0.8747 (p) REVERT: F 305 MET cc_start: 0.7726 (tpp) cc_final: 0.7421 (ttt) REVERT: F 314 ASP cc_start: 0.7956 (t70) cc_final: 0.7539 (t70) REVERT: F 333 LEU cc_start: 0.8800 (mt) cc_final: 0.8526 (mp) REVERT: F 343 PHE cc_start: 0.8293 (m-80) cc_final: 0.7970 (m-80) REVERT: F 360 ILE cc_start: 0.8776 (mt) cc_final: 0.8535 (mp) REVERT: G 6 ARG cc_start: 0.8096 (mmm160) cc_final: 0.7318 (mtm-85) REVERT: G 79 VAL cc_start: 0.8082 (OUTLIER) cc_final: 0.7877 (m) REVERT: G 83 SER cc_start: 0.8822 (m) cc_final: 0.8510 (p) REVERT: G 96 VAL cc_start: 0.8037 (t) cc_final: 0.7750 (p) REVERT: G 162 MET cc_start: 0.7876 (tpp) cc_final: 0.7622 (mmt) REVERT: G 202 ARG cc_start: 0.8396 (ttm170) cc_final: 0.7721 (ttp-170) REVERT: H 7 GLU cc_start: 0.6575 (mt-10) cc_final: 0.6374 (mt-10) REVERT: a 146 HIS cc_start: 0.7270 (OUTLIER) cc_final: 0.6978 (m-70) REVERT: a 206 PHE cc_start: 0.6715 (m-80) cc_final: 0.6336 (m-80) REVERT: a 228 ILE cc_start: 0.8271 (mt) cc_final: 0.7963 (mt) REVERT: d 346 SER cc_start: 0.9124 (m) cc_final: 0.8786 (p) REVERT: d 400 ILE cc_start: 0.8873 (mt) cc_final: 0.8670 (mt) REVERT: 1 21 MET cc_start: 0.7439 (mmm) cc_final: 0.7057 (mmm) REVERT: 2 21 MET cc_start: 0.7724 (mmm) cc_final: 0.6936 (tpp) REVERT: 2 58 PHE cc_start: 0.6902 (OUTLIER) cc_final: 0.6489 (t80) REVERT: 3 75 MET cc_start: 0.6493 (tmm) cc_final: 0.5370 (tpt) REVERT: 4 21 MET cc_start: 0.8653 (tpp) cc_final: 0.8327 (tpp) REVERT: 4 54 PHE cc_start: 0.5094 (OUTLIER) cc_final: 0.4815 (m-80) REVERT: 4 75 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7818 (tmm) REVERT: 7 75 MET cc_start: 0.6603 (tmm) cc_final: 0.6054 (tmm) REVERT: 8 21 MET cc_start: 0.6900 (tpt) cc_final: 0.6653 (tpt) outliers start: 108 outliers final: 79 residues processed: 676 average time/residue: 0.1883 time to fit residues: 216.1293 Evaluate side-chains 684 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 591 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 452 GLU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 274 ILE Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 146 HIS Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 53 ASP Chi-restraints excluded: chain d residue 66 LYS Chi-restraints excluded: chain d residue 72 VAL Chi-restraints excluded: chain d residue 80 SER Chi-restraints excluded: chain d residue 109 MET Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain d residue 351 LEU Chi-restraints excluded: chain d residue 397 LEU Chi-restraints excluded: chain d residue 423 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 54 PHE Chi-restraints excluded: chain 2 residue 58 PHE Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 6 residue 20 ILE Chi-restraints excluded: chain 9 residue 82 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 113 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 223 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 235 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 441 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.143364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.111742 restraints weight = 53297.522| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.89 r_work: 0.3218 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 36090 Z= 0.148 Angle : 0.557 9.857 49013 Z= 0.288 Chirality : 0.042 0.265 5781 Planarity : 0.004 0.057 6366 Dihedral : 5.514 84.251 5239 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.97 % Favored : 97.92 % Rotamer: Outliers : 2.84 % Allowed : 18.71 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 are not related in a simple way. whole: 1.74 (0.12), residues: 4761 helix: 2.25 (0.10), residues: 2596 sheet: -0.31 (0.21), residues: 580 loop : -0.06 (0.16), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 335 TYR 0.013 0.001 TYR a 145 PHE 0.035 0.001 PHE D 456 TRP 0.030 0.001 TRP a 66 HIS 0.004 0.001 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00346 (36090) covalent geometry : angle 0.55739 (49013) hydrogen bonds : bond 0.03879 ( 2368) hydrogen bonds : angle 4.15419 ( 6939) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 598 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8303 (mtmt) cc_final: 0.8072 (mttm) REVERT: A 149 LEU cc_start: 0.8678 (tm) cc_final: 0.8456 (tt) REVERT: A 308 LEU cc_start: 0.8164 (tp) cc_final: 0.7943 (tt) REVERT: A 490 LYS cc_start: 0.8490 (mmtt) cc_final: 0.8238 (mttm) REVERT: B 83 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7387 (tt0) REVERT: B 149 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8029 (tp) REVERT: B 188 ASN cc_start: 0.8906 (t0) cc_final: 0.8613 (t0) REVERT: B 199 LYS cc_start: 0.8185 (mtmm) cc_final: 0.7928 (mmtm) REVERT: B 277 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: B 384 LYS cc_start: 0.8022 (tppt) cc_final: 0.7806 (tptt) REVERT: B 491 LYS cc_start: 0.8898 (mttt) cc_final: 0.8631 (ttmm) REVERT: C 78 ILE cc_start: 0.8723 (mm) cc_final: 0.8391 (tp) REVERT: C 102 VAL cc_start: 0.8663 (p) cc_final: 0.8188 (t) REVERT: C 207 VAL cc_start: 0.8556 (t) cc_final: 0.8249 (m) REVERT: C 284 ILE cc_start: 0.8534 (mm) cc_final: 0.8283 (mt) REVERT: C 404 GLU cc_start: 0.8216 (tp30) cc_final: 0.7713 (tt0) REVERT: C 429 GLU cc_start: 0.8001 (tp30) cc_final: 0.7690 (tp30) REVERT: C 439 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7619 (mp) REVERT: D 59 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7878 (p0) REVERT: D 256 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8130 (tp) REVERT: D 305 MET cc_start: 0.8416 (tpp) cc_final: 0.8196 (ttm) REVERT: E 13 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8423 (t) REVERT: E 77 VAL cc_start: 0.9172 (OUTLIER) cc_final: 0.8799 (m) REVERT: E 221 ASP cc_start: 0.8585 (t70) cc_final: 0.8379 (t0) REVERT: E 272 ARG cc_start: 0.8338 (mtm-85) cc_final: 0.8063 (mtt180) REVERT: E 277 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8738 (p) REVERT: E 413 SER cc_start: 0.8653 (m) cc_final: 0.8371 (t) REVERT: F 26 ARG cc_start: 0.8505 (tpp80) cc_final: 0.8065 (mmm-85) REVERT: F 70 THR cc_start: 0.8676 (p) cc_final: 0.8215 (t) REVERT: F 71 ASP cc_start: 0.8253 (t0) cc_final: 0.8012 (t0) REVERT: F 94 VAL cc_start: 0.8516 (t) cc_final: 0.8150 (p) REVERT: F 185 SER cc_start: 0.8537 (t) cc_final: 0.8034 (p) REVERT: F 196 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7218 (tm-30) REVERT: F 212 ASP cc_start: 0.8164 (t0) cc_final: 0.7865 (t0) REVERT: F 277 VAL cc_start: 0.9010 (m) cc_final: 0.8763 (p) REVERT: F 305 MET cc_start: 0.7814 (tpp) cc_final: 0.7414 (ttt) REVERT: F 314 ASP cc_start: 0.7972 (t70) cc_final: 0.7547 (t70) REVERT: F 343 PHE cc_start: 0.8330 (m-80) cc_final: 0.7975 (m-80) REVERT: F 360 ILE cc_start: 0.8787 (mt) cc_final: 0.8547 (mp) REVERT: G 6 ARG cc_start: 0.8111 (mmm160) cc_final: 0.7327 (mtm-85) REVERT: G 79 VAL cc_start: 0.8065 (OUTLIER) cc_final: 0.7861 (m) REVERT: G 83 SER cc_start: 0.8809 (m) cc_final: 0.8492 (p) REVERT: G 96 VAL cc_start: 0.8044 (t) cc_final: 0.7755 (p) REVERT: G 162 MET cc_start: 0.7890 (tpp) cc_final: 0.7615 (mmt) REVERT: G 202 ARG cc_start: 0.8410 (ttm170) cc_final: 0.7737 (ttp-170) REVERT: G 263 MET cc_start: 0.7968 (mmp) cc_final: 0.7542 (mmp) REVERT: a 146 HIS cc_start: 0.7376 (OUTLIER) cc_final: 0.7066 (m-70) REVERT: a 228 ILE cc_start: 0.8253 (mt) cc_final: 0.7945 (mt) REVERT: d 295 GLN cc_start: 0.8802 (tp40) cc_final: 0.8563 (tp40) REVERT: d 346 SER cc_start: 0.9154 (m) cc_final: 0.8800 (p) REVERT: 1 21 MET cc_start: 0.7462 (mmm) cc_final: 0.7075 (mmm) REVERT: 2 21 MET cc_start: 0.7753 (mmm) cc_final: 0.6977 (tpp) REVERT: 2 58 PHE cc_start: 0.6876 (OUTLIER) cc_final: 0.6468 (t80) REVERT: 3 75 MET cc_start: 0.6521 (tmm) cc_final: 0.5173 (tpt) REVERT: 4 21 MET cc_start: 0.8591 (tpp) cc_final: 0.8254 (tpp) REVERT: 4 54 PHE cc_start: 0.5302 (OUTLIER) cc_final: 0.4986 (m-80) REVERT: 4 75 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7822 (tmm) REVERT: 8 21 MET cc_start: 0.6915 (tpt) cc_final: 0.6666 (tpt) outliers start: 99 outliers final: 78 residues processed: 655 average time/residue: 0.1951 time to fit residues: 216.8088 Evaluate side-chains 673 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 582 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 452 GLU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 274 ILE Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 146 HIS Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 53 ASP Chi-restraints excluded: chain d residue 80 SER Chi-restraints excluded: chain d residue 109 MET Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain d residue 351 LEU Chi-restraints excluded: chain d residue 397 LEU Chi-restraints excluded: chain d residue 423 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 54 PHE Chi-restraints excluded: chain 2 residue 58 PHE Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 9 residue 82 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 242 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 395 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 342 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 244 optimal weight: 0.0970 chunk 220 optimal weight: 0.5980 chunk 306 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN ** 6 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.144120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.112636 restraints weight = 53547.050| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.91 r_work: 0.3229 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 36090 Z= 0.131 Angle : 0.560 18.320 49013 Z= 0.288 Chirality : 0.042 0.265 5781 Planarity : 0.004 0.057 6366 Dihedral : 5.391 81.897 5239 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.95 % Favored : 97.94 % Rotamer: Outliers : 2.61 % Allowed : 19.32 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 are not related in a simple way. whole: 1.81 (0.12), residues: 4761 helix: 2.31 (0.10), residues: 2592 sheet: -0.25 (0.21), residues: 560 loop : -0.05 (0.16), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 426 TYR 0.012 0.001 TYR a 145 PHE 0.034 0.001 PHE D 456 TRP 0.026 0.001 TRP a 66 HIS 0.005 0.001 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00298 (36090) covalent geometry : angle 0.56036 (49013) hydrogen bonds : bond 0.03765 ( 2368) hydrogen bonds : angle 4.12829 ( 6939) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9522 Ramachandran restraints generated. 4761 Oldfield, 0 Emsley, 4761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 601 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8274 (mtmt) cc_final: 0.8073 (mttm) REVERT: A 149 LEU cc_start: 0.8651 (tm) cc_final: 0.8377 (tt) REVERT: A 308 LEU cc_start: 0.8161 (tp) cc_final: 0.7943 (tt) REVERT: A 490 LYS cc_start: 0.8492 (mmtt) cc_final: 0.8261 (mttm) REVERT: B 83 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7330 (tt0) REVERT: B 149 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.7999 (tp) REVERT: B 188 ASN cc_start: 0.8894 (t0) cc_final: 0.8615 (t0) REVERT: B 199 LYS cc_start: 0.8221 (mtmm) cc_final: 0.7974 (mmtm) REVERT: B 277 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7494 (tt0) REVERT: B 384 LYS cc_start: 0.8032 (tppt) cc_final: 0.7816 (tptt) REVERT: B 491 LYS cc_start: 0.8900 (mttt) cc_final: 0.8620 (ttmm) REVERT: C 78 ILE cc_start: 0.8733 (mm) cc_final: 0.8402 (tp) REVERT: C 102 VAL cc_start: 0.8642 (p) cc_final: 0.8190 (t) REVERT: C 173 ASP cc_start: 0.8120 (t0) cc_final: 0.7907 (t0) REVERT: C 284 ILE cc_start: 0.8512 (mm) cc_final: 0.8259 (mt) REVERT: C 310 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7751 (mm-30) REVERT: C 404 GLU cc_start: 0.8181 (tp30) cc_final: 0.7721 (tt0) REVERT: C 426 ARG cc_start: 0.7638 (mtt-85) cc_final: 0.7405 (ttm-80) REVERT: C 429 GLU cc_start: 0.8021 (tp30) cc_final: 0.7720 (tp30) REVERT: D 59 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7880 (p0) REVERT: D 415 ASN cc_start: 0.8882 (p0) cc_final: 0.8613 (p0) REVERT: E 13 VAL cc_start: 0.8800 (OUTLIER) cc_final: 0.8445 (t) REVERT: E 77 VAL cc_start: 0.9179 (OUTLIER) cc_final: 0.8796 (m) REVERT: E 272 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.8075 (mtt180) REVERT: E 277 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8729 (p) REVERT: E 327 LEU cc_start: 0.8233 (pp) cc_final: 0.7966 (mt) REVERT: E 413 SER cc_start: 0.8655 (m) cc_final: 0.8375 (t) REVERT: F 26 ARG cc_start: 0.8485 (tpp80) cc_final: 0.8052 (mmm-85) REVERT: F 70 THR cc_start: 0.8665 (p) cc_final: 0.8223 (t) REVERT: F 71 ASP cc_start: 0.8258 (t0) cc_final: 0.8018 (t0) REVERT: F 94 VAL cc_start: 0.8534 (t) cc_final: 0.8168 (p) REVERT: F 185 SER cc_start: 0.8525 (t) cc_final: 0.8006 (p) REVERT: F 196 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7193 (tm-30) REVERT: F 212 ASP cc_start: 0.8167 (t0) cc_final: 0.7813 (t0) REVERT: F 277 VAL cc_start: 0.8975 (m) cc_final: 0.8740 (p) REVERT: F 305 MET cc_start: 0.7794 (tpp) cc_final: 0.7418 (ttt) REVERT: F 314 ASP cc_start: 0.7974 (t70) cc_final: 0.7592 (t70) REVERT: F 343 PHE cc_start: 0.8335 (m-80) cc_final: 0.7994 (m-80) REVERT: F 360 ILE cc_start: 0.8790 (mt) cc_final: 0.8553 (mp) REVERT: G 6 ARG cc_start: 0.8072 (mmm160) cc_final: 0.7290 (mtm-85) REVERT: G 21 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8045 (mt) REVERT: G 79 VAL cc_start: 0.8100 (OUTLIER) cc_final: 0.7895 (m) REVERT: G 83 SER cc_start: 0.8820 (m) cc_final: 0.8508 (p) REVERT: G 96 VAL cc_start: 0.8041 (t) cc_final: 0.7747 (p) REVERT: G 162 MET cc_start: 0.7860 (tpp) cc_final: 0.7610 (mmt) REVERT: G 202 ARG cc_start: 0.8390 (ttm170) cc_final: 0.7732 (ttp-170) REVERT: G 263 MET cc_start: 0.7938 (mmp) cc_final: 0.7521 (mmp) REVERT: H 7 GLU cc_start: 0.6801 (mt-10) cc_final: 0.6489 (pt0) REVERT: a 146 HIS cc_start: 0.7259 (OUTLIER) cc_final: 0.6955 (m-70) REVERT: a 228 ILE cc_start: 0.8240 (mt) cc_final: 0.7936 (mt) REVERT: d 295 GLN cc_start: 0.8813 (tp40) cc_final: 0.8533 (tp40) REVERT: d 346 SER cc_start: 0.9135 (m) cc_final: 0.8784 (p) REVERT: 1 21 MET cc_start: 0.7436 (mmm) cc_final: 0.7048 (mmm) REVERT: 2 21 MET cc_start: 0.7721 (mmm) cc_final: 0.6941 (tpp) REVERT: 2 58 PHE cc_start: 0.6856 (OUTLIER) cc_final: 0.6446 (t80) REVERT: 3 75 MET cc_start: 0.6770 (tmm) cc_final: 0.6511 (tmm) REVERT: 4 21 MET cc_start: 0.8552 (tpp) cc_final: 0.8243 (tpp) REVERT: 4 54 PHE cc_start: 0.5310 (OUTLIER) cc_final: 0.4995 (m-80) REVERT: 4 75 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7819 (tmm) REVERT: 8 21 MET cc_start: 0.6858 (tpt) cc_final: 0.6603 (tpt) REVERT: 9 75 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7612 (ttp) outliers start: 91 outliers final: 70 residues processed: 652 average time/residue: 0.1957 time to fit residues: 215.9335 Evaluate side-chains 671 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 588 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 452 GLU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 193 ARG Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 274 ILE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain a residue 146 HIS Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 80 SER Chi-restraints excluded: chain d residue 109 MET Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain d residue 351 LEU Chi-restraints excluded: chain d residue 397 LEU Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 54 PHE Chi-restraints excluded: chain 2 residue 58 PHE Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 4 residue 75 MET Chi-restraints excluded: chain 9 residue 75 MET Chi-restraints excluded: chain 9 residue 82 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 106 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 392 optimal weight: 0.0980 chunk 105 optimal weight: 0.0010 chunk 321 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 424 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 394 optimal weight: 6.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 HIS ** 6 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.144944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.112671 restraints weight = 51937.665| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.75 r_work: 0.3231 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 36090 Z= 0.123 Angle : 0.558 18.532 49013 Z= 0.285 Chirality : 0.041 0.243 5781 Planarity : 0.004 0.057 6366 Dihedral : 5.244 79.195 5239 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.97 % Favored : 97.92 % Rotamer: Outliers : 2.35 % Allowed : 19.86 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 are not related in a simple way. whole: 1.88 (0.12), residues: 4761 helix: 2.37 (0.10), residues: 2590 sheet: -0.22 (0.21), residues: 562 loop : -0.02 (0.16), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 426 TYR 0.013 0.001 TYR a 145 PHE 0.046 0.001 PHE a 133 TRP 0.022 0.001 TRP a 66 HIS 0.005 0.001 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00278 (36090) covalent geometry : angle 0.55847 (49013) hydrogen bonds : bond 0.03689 ( 2368) hydrogen bonds : angle 4.10502 ( 6939) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9410.03 seconds wall clock time: 161 minutes 18.29 seconds (9678.29 seconds total)