Starting phenix.real_space_refine on Fri Mar 6 17:48:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kxr_23066/03_2026/7kxr_23066.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kxr_23066/03_2026/7kxr_23066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kxr_23066/03_2026/7kxr_23066.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kxr_23066/03_2026/7kxr_23066.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kxr_23066/03_2026/7kxr_23066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kxr_23066/03_2026/7kxr_23066.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.854 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 14 9.91 5 S 46 5.16 5 C 20535 2.51 5 N 5640 2.21 5 O 6591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s 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: 32826 Number of models: 1 Model: "" Number of chains: 15 Chain: "L" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1795 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 6, 'TRANS': 213} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 4431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4431 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 4431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4431 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 4431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4431 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 4431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4431 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 4431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4431 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 4431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4431 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 4431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4431 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.96, per 1000 atoms: 0.21 Number of scatterers: 32826 At special positions: 0 Unit cell: (174.945, 178.155, 237.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 14 19.99 S 46 16.00 O 6591 8.00 N 5640 7.00 C 20535 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: 2.25 Conformation dependent library (CDL) restraints added in 1.4 seconds 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7900 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 67 sheets defined 20.2% alpha, 39.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'L' and resid 31 through 43 Processing helix chain 'L' and resid 67 through 75 Processing helix chain 'L' and resid 140 through 153 Processing helix chain 'L' and resid 171 through 178 Processing helix chain 'L' and resid 209 through 224 removed outlier: 3.716A pdb=" N VAL L 213 " --> pdb=" O ASN L 209 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLN L 214 " --> pdb=" O SER L 210 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLU L 215 " --> pdb=" O ASN L 211 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE L 221 " --> pdb=" O PHE L 217 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR L 224 " --> pdb=" O ALA L 220 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 233 removed outlier: 4.199A pdb=" N HIS L 229 " --> pdb=" O ILE L 225 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG L 230 " --> pdb=" O GLU L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 250 removed outlier: 3.920A pdb=" N ALA L 240 " --> pdb=" O TYR L 236 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR L 243 " --> pdb=" O GLU L 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 191 Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'A' and resid 234 through 241 Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.947A pdb=" N HIS A 253 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 removed outlier: 3.684A pdb=" N LEU A 401 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 446 Processing helix chain 'A' and resid 480 through 486 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.611A pdb=" N LYS A 518 " --> pdb=" O GLU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 Processing helix chain 'A' and resid 555 through 570 Processing helix chain 'A' and resid 573 through 577 removed outlier: 3.586A pdb=" N THR A 576 " --> pdb=" O ASN A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 removed outlier: 3.556A pdb=" N LYS A 613 " --> pdb=" O GLU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 637 removed outlier: 3.855A pdb=" N LYS A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 191 Processing helix chain 'B' and resid 210 through 215 Processing helix chain 'B' and resid 234 through 241 Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.946A pdb=" N HIS B 253 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 401 removed outlier: 3.683A pdb=" N LEU B 401 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 446 Processing helix chain 'B' and resid 480 through 486 Processing helix chain 'B' and resid 514 through 518 removed outlier: 3.612A pdb=" N LYS B 518 " --> pdb=" O GLU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 532 Processing helix chain 'B' and resid 555 through 570 Processing helix chain 'B' and resid 573 through 577 removed outlier: 3.585A pdb=" N THR B 576 " --> pdb=" O ASN B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 617 removed outlier: 3.776A pdb=" N ALA B 615 " --> pdb=" O VAL B 612 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS B 616 " --> pdb=" O LYS B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 639 Processing helix chain 'B' and resid 660 through 664 removed outlier: 3.661A pdb=" N ASN B 664 " --> pdb=" O ASP B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 682 removed outlier: 4.576A pdb=" N TYR B 681 " --> pdb=" O ASP B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 735 removed outlier: 3.529A pdb=" N GLY B 735 " --> pdb=" O GLY B 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 191 Processing helix chain 'C' and resid 210 through 215 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 248 through 253 removed outlier: 3.946A pdb=" N HIS C 253 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 401 removed outlier: 3.682A pdb=" N LEU C 401 " --> pdb=" O GLU C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 446 Processing helix chain 'C' and resid 480 through 486 Processing helix chain 'C' and resid 514 through 518 removed outlier: 3.611A pdb=" N LYS C 518 " --> pdb=" O GLU C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 532 Processing helix chain 'C' and resid 555 through 570 Processing helix chain 'C' and resid 573 through 577 removed outlier: 3.585A pdb=" N THR C 576 " --> pdb=" O ASN C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 616 Processing helix chain 'C' and resid 634 through 637 Processing helix chain 'C' and resid 730 through 735 removed outlier: 3.604A pdb=" N GLY C 735 " --> pdb=" O GLY C 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 210 through 215 Processing helix chain 'D' and resid 234 through 241 Processing helix chain 'D' and resid 248 through 253 removed outlier: 3.946A pdb=" N HIS D 253 " --> pdb=" O GLU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 401 removed outlier: 3.682A pdb=" N LEU D 401 " --> pdb=" O GLU D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 446 Processing helix chain 'D' and resid 480 through 486 Processing helix chain 'D' and resid 514 through 518 removed outlier: 3.611A pdb=" N LYS D 518 " --> pdb=" O GLU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 532 Processing helix chain 'D' and resid 555 through 570 Processing helix chain 'D' and resid 573 through 577 removed outlier: 3.585A pdb=" N THR D 576 " --> pdb=" O ASN D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 613 removed outlier: 3.727A pdb=" N LYS D 613 " --> pdb=" O GLU D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 637 Processing helix chain 'E' and resid 184 through 191 Processing helix chain 'E' and resid 210 through 215 Processing helix chain 'E' and resid 234 through 241 Processing helix chain 'E' and resid 248 through 253 removed outlier: 3.946A pdb=" N HIS E 253 " --> pdb=" O GLU E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 401 removed outlier: 3.683A pdb=" N LEU E 401 " --> pdb=" O GLU E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 446 Processing helix chain 'E' and resid 480 through 486 Processing helix chain 'E' and resid 514 through 518 removed outlier: 3.611A pdb=" N LYS E 518 " --> pdb=" O GLU E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 532 Processing helix chain 'E' and resid 555 through 570 Processing helix chain 'E' and resid 573 through 577 removed outlier: 3.587A pdb=" N THR E 576 " --> pdb=" O ASN E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 613 Processing helix chain 'E' and resid 632 through 638 Processing helix chain 'E' and resid 679 through 682 Processing helix chain 'F' and resid 184 through 191 Processing helix chain 'F' and resid 210 through 215 Processing helix chain 'F' and resid 234 through 241 Processing helix chain 'F' and resid 248 through 253 removed outlier: 3.946A pdb=" N HIS F 253 " --> pdb=" O GLU F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 401 removed outlier: 3.682A pdb=" N LEU F 401 " --> pdb=" O GLU F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 446 Processing helix chain 'F' and resid 480 through 486 Processing helix chain 'F' and resid 514 through 518 removed outlier: 3.612A pdb=" N LYS F 518 " --> pdb=" O GLU F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 532 Processing helix chain 'F' and resid 555 through 570 Processing helix chain 'F' and resid 573 through 577 removed outlier: 3.585A pdb=" N THR F 576 " --> pdb=" O ASN F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 616 Processing helix chain 'F' and resid 632 through 637 removed outlier: 3.824A pdb=" N LYS F 637 " --> pdb=" O LYS F 633 " (cutoff:3.500A) Processing helix chain 'F' and resid 659 through 663 Processing helix chain 'F' and resid 677 through 682 Processing helix chain 'G' and resid 184 through 191 Processing helix chain 'G' and resid 210 through 215 Processing helix chain 'G' and resid 234 through 241 Processing helix chain 'G' and resid 248 through 253 removed outlier: 3.946A pdb=" N HIS G 253 " --> pdb=" O GLU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 401 removed outlier: 3.681A pdb=" N LEU G 401 " --> pdb=" O GLU G 398 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 446 Processing helix chain 'G' and resid 480 through 486 Processing helix chain 'G' and resid 514 through 518 removed outlier: 3.611A pdb=" N LYS G 518 " --> pdb=" O GLU G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 532 Processing helix chain 'G' and resid 555 through 570 Processing helix chain 'G' and resid 573 through 577 removed outlier: 3.587A pdb=" N THR G 576 " --> pdb=" O ASN G 573 " (cutoff:3.500A) Processing helix chain 'G' and resid 632 through 637 removed outlier: 3.856A pdb=" N LYS G 637 " --> pdb=" O LYS G 633 " (cutoff:3.500A) Processing helix chain 'G' and resid 660 through 664 removed outlier: 4.041A pdb=" N ASN G 664 " --> pdb=" O ASP G 661 " (cutoff:3.500A) Processing helix chain 'G' and resid 731 through 735 Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 196 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 273 removed outlier: 6.640A pdb=" N ASN A 363 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE A 269 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN A 361 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU A 271 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG A 359 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 409 through 411 removed outlier: 3.626A pdb=" N ASN A 409 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE A 432 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 339 through 352 removed outlier: 3.950A pdb=" N GLY A 318 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 311 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 320 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 309 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 322 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS A 336 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY B 318 " --> pdb=" O ALA C 311 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA C 311 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL B 320 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL C 309 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA B 322 " --> pdb=" O ALA C 307 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA C 307 " --> pdb=" O ALA B 322 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE B 324 " --> pdb=" O GLY C 305 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER B 330 " --> pdb=" O HIS C 299 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA C 322 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA D 307 " --> pdb=" O ALA C 322 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 324 " --> pdb=" O GLY D 305 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN C 328 " --> pdb=" O SER D 301 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS D 299 " --> pdb=" O SER C 330 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 334 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N HIS C 336 " --> pdb=" O THR D 293 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA D 322 " --> pdb=" O ALA E 307 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE D 324 " --> pdb=" O GLY E 305 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN D 328 " --> pdb=" O SER E 301 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS E 299 " --> pdb=" O SER D 330 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE D 334 " --> pdb=" O THR E 295 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS D 336 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA E 322 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE E 324 " --> pdb=" O GLY F 305 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN E 328 " --> pdb=" O SER F 301 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS F 299 " --> pdb=" O SER E 330 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE E 334 " --> pdb=" O THR F 295 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR F 295 " --> pdb=" O ILE E 334 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS E 336 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU E 338 " --> pdb=" O LYS F 291 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY F 318 " --> pdb=" O ALA G 311 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA G 311 " --> pdb=" O GLY F 318 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL F 320 " --> pdb=" O VAL G 309 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL G 309 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA F 322 " --> pdb=" O ALA G 307 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA G 307 " --> pdb=" O ALA F 322 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE F 324 " --> pdb=" O GLY G 305 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE F 334 " --> pdb=" O THR G 295 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS F 336 " --> pdb=" O THR G 293 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 316 through 330 removed outlier: 3.500A pdb=" N ALA G 322 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE G 324 " --> pdb=" O GLY A 305 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN G 328 " --> pdb=" O SER A 301 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 301 " --> pdb=" O ASN G 328 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER G 330 " --> pdb=" O HIS A 299 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N HIS A 299 " --> pdb=" O SER G 330 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR A 293 " --> pdb=" O HIS G 336 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N HIS G 336 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR A 295 " --> pdb=" O ILE G 334 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE G 334 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A 297 " --> pdb=" O VAL G 332 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 332 through 337 removed outlier: 3.589A pdb=" N ARG A 297 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE G 334 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR A 295 " --> pdb=" O ILE G 334 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N HIS G 336 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR A 293 " --> pdb=" O HIS G 336 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 279 " --> pdb=" O MET G 350 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN A 285 " --> pdb=" O ARG G 344 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG G 344 " --> pdb=" O GLN A 285 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 287 " --> pdb=" O GLY G 342 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY G 342 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 289 " --> pdb=" O LEU G 340 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU G 340 " --> pdb=" O ILE A 289 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 339 through 352 current: chain 'A' and resid 339 through 352 Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 395 removed outlier: 6.607A pdb=" N LEU A 383 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR A 393 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR A 381 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS A 395 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TYR A 375 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE A 404 " --> pdb=" O TYR A 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 395 removed outlier: 6.607A pdb=" N LEU A 383 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR A 393 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR A 381 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS A 395 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL A 377 " --> pdb=" O TYR A 456 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR A 456 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLN A 454 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR A 381 " --> pdb=" O THR A 452 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR A 452 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU A 383 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU A 450 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU A 385 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU A 448 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N VAL A 455 " --> pdb=" O ASN A 476 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N ASN A 476 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N GLY A 457 " --> pdb=" O GLY A 474 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N GLY A 474 " --> pdb=" O GLY A 457 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE A 459 " --> pdb=" O ASP A 472 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 501 through 506 removed outlier: 8.838A pdb=" N ILE A 589 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG A 490 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE A 591 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE A 492 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N ASP A 593 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AB2, first strand: chain 'A' and resid 596 through 598 removed outlier: 3.988A pdb=" N GLY A 606 " --> pdb=" O HIS A 597 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 627 through 629 Processing sheet with id=AB4, first strand: chain 'A' and resid 639 through 645 removed outlier: 3.599A pdb=" N GLY A 641 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ALA A 700 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU A 725 " --> pdb=" O ALA A 700 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 192 through 194 Processing sheet with id=AB6, first strand: chain 'B' and resid 262 through 273 removed outlier: 6.640A pdb=" N ASN B 363 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE B 269 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN B 361 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU B 271 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG B 359 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 409 through 411 removed outlier: 3.628A pdb=" N ASN B 409 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE B 432 " --> pdb=" O LEU B 360 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 389 through 395 removed outlier: 6.605A pdb=" N LEU B 383 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR B 393 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR B 381 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS B 395 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TYR B 375 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE B 404 " --> pdb=" O TYR B 375 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 389 through 395 removed outlier: 6.605A pdb=" N LEU B 383 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR B 393 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR B 381 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS B 395 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL B 377 " --> pdb=" O TYR B 456 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR B 456 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLN B 454 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR B 381 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR B 452 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU B 383 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU B 450 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU B 385 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU B 448 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 10.812A pdb=" N VAL B 455 " --> pdb=" O ASN B 476 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N ASN B 476 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N GLY B 457 " --> pdb=" O GLY B 474 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N GLY B 474 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE B 459 " --> pdb=" O ASP B 472 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 501 through 506 removed outlier: 8.838A pdb=" N ILE B 589 " --> pdb=" O THR B 488 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG B 490 " --> pdb=" O ILE B 589 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE B 591 " --> pdb=" O ARG B 490 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE B 492 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N ASP B 593 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 541 through 542 Processing sheet with id=AC3, first strand: chain 'B' and resid 642 through 645 removed outlier: 3.686A pdb=" N VAL B 696 " --> pdb=" O LYS B 729 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS B 729 " --> pdb=" O VAL B 696 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 195 through 196 Processing sheet with id=AC5, first strand: chain 'C' and resid 262 through 273 removed outlier: 6.640A pdb=" N ASN C 363 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE C 269 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN C 361 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU C 271 " --> pdb=" O ARG C 359 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG C 359 " --> pdb=" O LEU C 271 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 409 through 411 removed outlier: 3.629A pdb=" N ASN C 409 " --> pdb=" O ASN C 368 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE C 432 " --> pdb=" O LEU C 360 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 389 through 395 removed outlier: 6.606A pdb=" N LEU C 383 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR C 393 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR C 381 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS C 395 " --> pdb=" O PRO C 379 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR C 375 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE C 404 " --> pdb=" O TYR C 375 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 389 through 395 removed outlier: 6.606A pdb=" N LEU C 383 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR C 393 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR C 381 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS C 395 " --> pdb=" O PRO C 379 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL C 377 " --> pdb=" O TYR C 456 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR C 456 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLN C 454 " --> pdb=" O PRO C 379 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR C 381 " --> pdb=" O THR C 452 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR C 452 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU C 383 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU C 450 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU C 385 " --> pdb=" O LEU C 448 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU C 448 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N VAL C 455 " --> pdb=" O ASN C 476 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N ASN C 476 " --> pdb=" O VAL C 455 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N GLY C 457 " --> pdb=" O GLY C 474 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N GLY C 474 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE C 459 " --> pdb=" O ASP C 472 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 501 through 506 removed outlier: 8.837A pdb=" N ILE C 589 " --> pdb=" O THR C 488 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG C 490 " --> pdb=" O ILE C 589 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ILE C 591 " --> pdb=" O ARG C 490 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE C 492 " --> pdb=" O ILE C 591 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ASP C 593 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 541 through 542 Processing sheet with id=AD2, first strand: chain 'C' and resid 597 through 598 removed outlier: 3.572A pdb=" N GLY C 606 " --> pdb=" O HIS C 597 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 628 through 629 Processing sheet with id=AD4, first strand: chain 'C' and resid 653 through 655 removed outlier: 3.934A pdb=" N GLU C 654 " --> pdb=" O ILE C 646 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY C 641 " --> pdb=" O VAL C 701 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ALA C 700 " --> pdb=" O LEU C 725 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU C 725 " --> pdb=" O ALA C 700 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 192 through 196 Processing sheet with id=AD6, first strand: chain 'D' and resid 262 through 273 removed outlier: 6.640A pdb=" N ASN D 363 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE D 269 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN D 361 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU D 271 " --> pdb=" O ARG D 359 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG D 359 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 409 through 411 removed outlier: 3.628A pdb=" N ASN D 409 " --> pdb=" O ASN D 368 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE D 432 " --> pdb=" O LEU D 360 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 389 through 395 removed outlier: 6.607A pdb=" N LEU D 383 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR D 393 " --> pdb=" O THR D 381 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR D 381 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS D 395 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR D 375 " --> pdb=" O ILE D 404 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE D 404 " --> pdb=" O TYR D 375 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 389 through 395 removed outlier: 6.607A pdb=" N LEU D 383 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR D 393 " --> pdb=" O THR D 381 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR D 381 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS D 395 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL D 377 " --> pdb=" O TYR D 456 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR D 456 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLN D 454 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR D 381 " --> pdb=" O THR D 452 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR D 452 " --> pdb=" O THR D 381 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU D 383 " --> pdb=" O LEU D 450 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU D 450 " --> pdb=" O LEU D 383 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU D 385 " --> pdb=" O LEU D 448 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU D 448 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N VAL D 455 " --> pdb=" O ASN D 476 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N ASN D 476 " --> pdb=" O VAL D 455 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N GLY D 457 " --> pdb=" O GLY D 474 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N GLY D 474 " --> pdb=" O GLY D 457 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE D 459 " --> pdb=" O ASP D 472 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 501 through 506 removed outlier: 8.837A pdb=" N ILE D 589 " --> pdb=" O THR D 488 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG D 490 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ILE D 591 " --> pdb=" O ARG D 490 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE D 492 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N ASP D 593 " --> pdb=" O ILE D 492 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 541 through 542 Processing sheet with id=AE3, first strand: chain 'D' and resid 597 through 598 removed outlier: 6.205A pdb=" N HIS D 597 " --> pdb=" O VAL D 605 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 654 through 655 removed outlier: 3.599A pdb=" N GLY D 641 " --> pdb=" O VAL D 701 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS D 695 " --> pdb=" O GLU D 647 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS D 729 " --> pdb=" O VAL D 696 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA D 700 " --> pdb=" O LEU D 725 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU D 725 " --> pdb=" O ALA D 700 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 667 through 669 removed outlier: 3.788A pdb=" N LYS D 673 " --> pdb=" O ARG D 669 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 192 through 196 Processing sheet with id=AE7, first strand: chain 'E' and resid 262 through 273 removed outlier: 6.639A pdb=" N ASN E 363 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE E 269 " --> pdb=" O ASN E 361 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN E 361 " --> pdb=" O ILE E 269 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU E 271 " --> pdb=" O ARG E 359 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG E 359 " --> pdb=" O LEU E 271 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 409 through 411 removed outlier: 3.628A pdb=" N ASN E 409 " --> pdb=" O ASN E 368 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 389 through 395 removed outlier: 6.607A pdb=" N LEU E 383 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR E 393 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR E 381 " --> pdb=" O THR E 393 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS E 395 " --> pdb=" O PRO E 379 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR E 375 " --> pdb=" O ILE E 404 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE E 404 " --> pdb=" O TYR E 375 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 389 through 395 removed outlier: 6.607A pdb=" N LEU E 383 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR E 393 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR E 381 " --> pdb=" O THR E 393 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS E 395 " --> pdb=" O PRO E 379 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL E 377 " --> pdb=" O TYR E 456 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR E 456 " --> pdb=" O VAL E 377 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLN E 454 " --> pdb=" O PRO E 379 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR E 381 " --> pdb=" O THR E 452 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR E 452 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU E 383 " --> pdb=" O LEU E 450 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU E 450 " --> pdb=" O LEU E 383 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU E 385 " --> pdb=" O LEU E 448 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU E 448 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N VAL E 455 " --> pdb=" O ASN E 476 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N ASN E 476 " --> pdb=" O VAL E 455 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N GLY E 457 " --> pdb=" O GLY E 474 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N GLY E 474 " --> pdb=" O GLY E 457 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE E 459 " --> pdb=" O ASP E 472 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 501 through 506 removed outlier: 8.837A pdb=" N ILE E 589 " --> pdb=" O THR E 488 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG E 490 " --> pdb=" O ILE E 589 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE E 591 " --> pdb=" O ARG E 490 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE E 492 " --> pdb=" O ILE E 591 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N ASP E 593 " --> pdb=" O ILE E 492 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 541 through 542 Processing sheet with id=AF4, first strand: chain 'E' and resid 619 through 622 removed outlier: 6.573A pdb=" N LEU E 628 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N SER E 622 " --> pdb=" O GLY E 626 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLY E 626 " --> pdb=" O SER E 622 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 654 through 655 removed outlier: 3.544A pdb=" N GLU E 654 " --> pdb=" O ILE E 646 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLY E 641 " --> pdb=" O VAL E 701 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS E 729 " --> pdb=" O VAL E 696 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA E 700 " --> pdb=" O LEU E 725 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU E 725 " --> pdb=" O ALA E 700 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 192 through 196 Processing sheet with id=AF7, first strand: chain 'F' and resid 262 through 273 removed outlier: 6.640A pdb=" N ASN F 363 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE F 269 " --> pdb=" O ASN F 361 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN F 361 " --> pdb=" O ILE F 269 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU F 271 " --> pdb=" O ARG F 359 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG F 359 " --> pdb=" O LEU F 271 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 409 through 411 removed outlier: 3.628A pdb=" N ASN F 409 " --> pdb=" O ASN F 368 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE F 432 " --> pdb=" O LEU F 360 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 389 through 395 removed outlier: 6.606A pdb=" N LEU F 383 " --> pdb=" O LEU F 391 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR F 393 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR F 381 " --> pdb=" O THR F 393 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS F 395 " --> pdb=" O PRO F 379 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TYR F 375 " --> pdb=" O ILE F 404 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE F 404 " --> pdb=" O TYR F 375 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 389 through 395 removed outlier: 6.606A pdb=" N LEU F 383 " --> pdb=" O LEU F 391 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR F 393 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR F 381 " --> pdb=" O THR F 393 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS F 395 " --> pdb=" O PRO F 379 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL F 377 " --> pdb=" O TYR F 456 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR F 456 " --> pdb=" O VAL F 377 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLN F 454 " --> pdb=" O PRO F 379 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR F 381 " --> pdb=" O THR F 452 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR F 452 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU F 383 " --> pdb=" O LEU F 450 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU F 450 " --> pdb=" O LEU F 383 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU F 385 " --> pdb=" O LEU F 448 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU F 448 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 10.812A pdb=" N VAL F 455 " --> pdb=" O ASN F 476 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N ASN F 476 " --> pdb=" O VAL F 455 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N GLY F 457 " --> pdb=" O GLY F 474 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N GLY F 474 " --> pdb=" O GLY F 457 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE F 459 " --> pdb=" O ASP F 472 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 501 through 506 removed outlier: 8.838A pdb=" N ILE F 589 " --> pdb=" O THR F 488 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG F 490 " --> pdb=" O ILE F 589 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ILE F 591 " --> pdb=" O ARG F 490 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE F 492 " --> pdb=" O ILE F 591 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N ASP F 593 " --> pdb=" O ILE F 492 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 541 through 542 Processing sheet with id=AG4, first strand: chain 'F' and resid 621 through 622 Processing sheet with id=AG5, first strand: chain 'F' and resid 654 through 655 removed outlier: 3.542A pdb=" N GLU F 654 " --> pdb=" O ILE F 646 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY F 641 " --> pdb=" O VAL F 701 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS F 729 " --> pdb=" O VAL F 696 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA F 700 " --> pdb=" O LEU F 725 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU F 725 " --> pdb=" O ALA F 700 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 192 through 196 Processing sheet with id=AG7, first strand: chain 'G' and resid 262 through 273 removed outlier: 6.639A pdb=" N ASN G 363 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE G 269 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN G 361 " --> pdb=" O ILE G 269 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU G 271 " --> pdb=" O ARG G 359 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG G 359 " --> pdb=" O LEU G 271 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 409 through 411 removed outlier: 3.628A pdb=" N ASN G 409 " --> pdb=" O ASN G 368 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 389 through 395 removed outlier: 6.606A pdb=" N LEU G 383 " --> pdb=" O LEU G 391 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR G 393 " --> pdb=" O THR G 381 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR G 381 " --> pdb=" O THR G 393 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS G 395 " --> pdb=" O PRO G 379 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TYR G 375 " --> pdb=" O ILE G 404 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE G 404 " --> pdb=" O TYR G 375 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 389 through 395 removed outlier: 6.606A pdb=" N LEU G 383 " --> pdb=" O LEU G 391 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR G 393 " --> pdb=" O THR G 381 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR G 381 " --> pdb=" O THR G 393 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS G 395 " --> pdb=" O PRO G 379 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL G 377 " --> pdb=" O TYR G 456 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR G 456 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLN G 454 " --> pdb=" O PRO G 379 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR G 381 " --> pdb=" O THR G 452 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR G 452 " --> pdb=" O THR G 381 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU G 383 " --> pdb=" O LEU G 450 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU G 450 " --> pdb=" O LEU G 383 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU G 385 " --> pdb=" O LEU G 448 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU G 448 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N VAL G 455 " --> pdb=" O ASN G 476 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N ASN G 476 " --> pdb=" O VAL G 455 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N GLY G 457 " --> pdb=" O GLY G 474 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N GLY G 474 " --> pdb=" O GLY G 457 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE G 459 " --> pdb=" O ASP G 472 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 501 through 506 removed outlier: 8.839A pdb=" N ILE G 589 " --> pdb=" O THR G 488 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG G 490 " --> pdb=" O ILE G 589 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ILE G 591 " --> pdb=" O ARG G 490 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE G 492 " --> pdb=" O ILE G 591 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ASP G 593 " --> pdb=" O ILE G 492 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 541 through 542 Processing sheet with id=AH4, first strand: chain 'G' and resid 639 through 647 removed outlier: 3.887A pdb=" N GLY G 641 " --> pdb=" O VAL G 701 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS G 729 " --> pdb=" O VAL G 696 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE G 727 " --> pdb=" O VAL G 698 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ALA G 700 " --> pdb=" O LEU G 725 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU G 725 " --> pdb=" O ALA G 700 " (cutoff:3.500A) 1205 hydrogen bonds defined for protein. 3228 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.69 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 5776 1.28 - 1.41: 7729 1.41 - 1.55: 19765 1.55 - 1.68: 24 1.68 - 1.82: 91 Bond restraints: 33385 Sorted by residual: bond pdb=" C PRO G 431 " pdb=" O PRO G 431 " ideal model delta sigma weight residual 1.233 1.142 0.091 1.18e-02 7.18e+03 6.00e+01 bond pdb=" C PHE G 427 " pdb=" O PHE G 427 " ideal model delta sigma weight residual 1.235 1.148 0.087 1.32e-02 5.74e+03 4.38e+01 bond pdb=" C ASP C 425 " pdb=" O ASP C 425 " ideal model delta sigma weight residual 1.233 1.152 0.082 1.28e-02 6.10e+03 4.06e+01 bond pdb=" C ILE G 432 " pdb=" O ILE G 432 " ideal model delta sigma weight residual 1.239 1.175 0.064 1.22e-02 6.72e+03 2.73e+01 bond pdb=" CA SER D 429 " pdb=" CB SER D 429 " ideal model delta sigma weight residual 1.537 1.465 0.072 1.41e-02 5.03e+03 2.63e+01 ... (remaining 33380 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 43863 2.95 - 5.89: 1304 5.89 - 8.84: 107 8.84 - 11.78: 16 11.78 - 14.73: 1 Bond angle restraints: 45291 Sorted by residual: angle pdb=" CA PHE C 427 " pdb=" CB PHE C 427 " pdb=" CG PHE C 427 " ideal model delta sigma weight residual 113.80 103.38 10.42 1.00e+00 1.00e+00 1.09e+02 angle pdb=" N THR B 300 " pdb=" CA THR B 300 " pdb=" C THR B 300 " ideal model delta sigma weight residual 108.52 123.25 -14.73 1.63e+00 3.76e-01 8.16e+01 angle pdb=" N GLU E 614 " pdb=" CA GLU E 614 " pdb=" C GLU E 614 " ideal model delta sigma weight residual 111.69 122.27 -10.58 1.23e+00 6.61e-01 7.39e+01 angle pdb=" N PHE E 427 " pdb=" CA PHE E 427 " pdb=" C PHE E 427 " ideal model delta sigma weight residual 112.92 102.61 10.31 1.23e+00 6.61e-01 7.03e+01 angle pdb=" O LYS L 90 " pdb=" C LYS L 90 " pdb=" N HIS L 91 " ideal model delta sigma weight residual 120.71 127.52 -6.81 9.00e-01 1.23e+00 5.72e+01 ... (remaining 45286 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 19460 17.51 - 35.02: 712 35.02 - 52.53: 183 52.53 - 70.05: 26 70.05 - 87.56: 25 Dihedral angle restraints: 20406 sinusoidal: 8199 harmonic: 12207 Sorted by residual: dihedral pdb=" C ASP A 683 " pdb=" N ASP A 683 " pdb=" CA ASP A 683 " pdb=" CB ASP A 683 " ideal model delta harmonic sigma weight residual -122.60 -140.15 17.55 0 2.50e+00 1.60e-01 4.93e+01 dihedral pdb=" C PHE L 205 " pdb=" N PHE L 205 " pdb=" CA PHE L 205 " pdb=" CB PHE L 205 " ideal model delta harmonic sigma weight residual -122.60 -138.30 15.70 0 2.50e+00 1.60e-01 3.95e+01 dihedral pdb=" C PHE L 170 " pdb=" N PHE L 170 " pdb=" CA PHE L 170 " pdb=" CB PHE L 170 " ideal model delta harmonic sigma weight residual -122.60 -137.26 14.66 0 2.50e+00 1.60e-01 3.44e+01 ... (remaining 20403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 4641 0.122 - 0.244: 468 0.244 - 0.366: 55 0.366 - 0.488: 9 0.488 - 0.610: 5 Chirality restraints: 5178 Sorted by residual: chirality pdb=" CA ASP A 683 " pdb=" N ASP A 683 " pdb=" C ASP A 683 " pdb=" CB ASP A 683 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.29e+00 chirality pdb=" CA PHE L 170 " pdb=" N PHE L 170 " pdb=" C PHE L 170 " pdb=" CB PHE L 170 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.27e+00 chirality pdb=" CA PHE L 205 " pdb=" N PHE L 205 " pdb=" C PHE L 205 " pdb=" CB PHE L 205 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.76e+00 ... (remaining 5175 not shown) Planarity restraints: 5938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU G 614 " -0.026 2.00e-02 2.50e+03 5.43e-02 2.95e+01 pdb=" C GLU G 614 " 0.094 2.00e-02 2.50e+03 pdb=" O GLU G 614 " -0.035 2.00e-02 2.50e+03 pdb=" N ALA G 615 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE G 427 " 0.024 2.00e-02 2.50e+03 5.01e-02 2.51e+01 pdb=" C PHE G 427 " -0.087 2.00e-02 2.50e+03 pdb=" O PHE G 427 " 0.033 2.00e-02 2.50e+03 pdb=" N SER G 428 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 664 " -0.024 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C ASN G 664 " 0.085 2.00e-02 2.50e+03 pdb=" O ASN G 664 " -0.032 2.00e-02 2.50e+03 pdb=" N ILE G 665 " -0.029 2.00e-02 2.50e+03 ... (remaining 5935 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 238 2.49 - 3.09: 23615 3.09 - 3.70: 48470 3.70 - 4.30: 71233 4.30 - 4.90: 117606 Nonbonded interactions: 261162 Sorted by model distance: nonbonded pdb=" OD1 ASN C 691 " pdb=" CD PRO C 692 " model vdw 1.888 3.440 nonbonded pdb=" N ASP C 426 " pdb=" OD1 ASP C 426 " model vdw 2.060 3.120 nonbonded pdb=" O ASN G 601 " pdb=" ND2 ASN G 601 " model vdw 2.083 3.120 nonbonded pdb=" O ILE D 183 " pdb="CA CA D 801 " model vdw 2.107 2.510 nonbonded pdb=" O ILE E 183 " pdb="CA CA E 801 " model vdw 2.107 2.510 ... (remaining 261157 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 28.140 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 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 : 0.009 0.091 33385 Z= 0.599 Angle : 1.186 14.728 45291 Z= 0.795 Chirality : 0.080 0.610 5178 Planarity : 0.007 0.070 5938 Dihedral : 10.613 87.558 12506 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 26.42 Ramachandran Plot: Outliers : 0.58 % Allowed : 5.24 % Favored : 94.18 % Rotamer: Outliers : 4.01 % Allowed : 4.82 % Favored : 91.17 % Cbeta Deviations : 0.51 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.12), residues: 4138 helix: -1.51 (0.19), residues: 601 sheet: -0.24 (0.14), residues: 1194 loop : -1.78 (0.11), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 592 TYR 0.047 0.002 TYR F 694 PHE 0.024 0.003 PHE C 427 TRP 0.016 0.003 TRP F 226 HIS 0.017 0.003 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00873 (33385) covalent geometry : angle 1.18606 (45291) hydrogen bonds : bond 0.22789 ( 1183) hydrogen bonds : angle 9.72077 ( 3228) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1742 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 1594 time to evaluate : 1.134 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: 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: 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: symmetry clash REVERT: A 180 ASN cc_start: 0.9366 (t0) cc_final: 0.9062 (t0) REVERT: A 195 ASP cc_start: 0.8017 (t70) cc_final: 0.7741 (t70) REVERT: A 200 ARG cc_start: 0.6598 (mpp80) cc_final: 0.6105 (mtt90) REVERT: A 220 LYS cc_start: 0.6681 (mttm) cc_final: 0.6462 (mttm) REVERT: A 265 ASP cc_start: 0.6462 (p0) cc_final: 0.6148 (p0) REVERT: A 274 ASN cc_start: 0.8940 (t0) cc_final: 0.8438 (t0) REVERT: A 281 ASN cc_start: 0.6689 (t160) cc_final: 0.6200 (t0) REVERT: A 287 ARG cc_start: 0.4231 (mtt90) cc_final: 0.3993 (mtt90) REVERT: A 296 SER cc_start: 0.5006 (m) cc_final: 0.4458 (p) REVERT: A 346 TRP cc_start: 0.7120 (t-100) cc_final: 0.6658 (t-100) REVERT: A 350 MET cc_start: 0.7603 (mtt) cc_final: 0.7329 (mtt) REVERT: A 364 ILE cc_start: 0.7591 (pt) cc_final: 0.6623 (mp) REVERT: A 366 TYR cc_start: 0.8534 (m-10) cc_final: 0.8232 (m-10) REVERT: A 368 ASN cc_start: 0.8646 (t0) cc_final: 0.7618 (t0) REVERT: A 371 THR cc_start: 0.8768 (p) cc_final: 0.8380 (p) REVERT: A 398 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8143 (mt-10) REVERT: A 403 GLN cc_start: 0.8438 (mt0) cc_final: 0.7954 (mt0) REVERT: A 410 TYR cc_start: 0.8849 (m-10) cc_final: 0.8275 (m-80) REVERT: A 439 PHE cc_start: 0.9377 (t80) cc_final: 0.9066 (t80) REVERT: A 447 GLN cc_start: 0.8383 (mt0) cc_final: 0.8133 (mt0) REVERT: A 483 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8574 (mm-40) REVERT: A 487 THR cc_start: 0.9338 (p) cc_final: 0.9122 (p) REVERT: A 504 ARG cc_start: 0.8231 (mtt-85) cc_final: 0.7867 (mmt90) REVERT: A 508 VAL cc_start: 0.8246 (t) cc_final: 0.7906 (t) REVERT: A 515 GLU cc_start: 0.8387 (tp30) cc_final: 0.6769 (tp30) REVERT: A 535 GLU cc_start: 0.8725 (pt0) cc_final: 0.8465 (pt0) REVERT: A 543 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8382 (mm110) REVERT: A 580 LYS cc_start: 0.9031 (mttp) cc_final: 0.8673 (mmtp) REVERT: A 582 LYS cc_start: 0.8581 (mmtt) cc_final: 0.8310 (mtpp) REVERT: A 586 LYS cc_start: 0.8319 (mtpp) cc_final: 0.7806 (mtpp) REVERT: A 597 HIS cc_start: 0.7574 (m170) cc_final: 0.7202 (m-70) REVERT: A 662 MET cc_start: -0.0855 (mtp) cc_final: -0.1383 (ttp) REVERT: B 207 ILE cc_start: 0.9146 (mt) cc_final: 0.8762 (mp) REVERT: B 210 ILE cc_start: 0.9303 (mt) cc_final: 0.9051 (mm) REVERT: B 211 HIS cc_start: 0.8588 (m90) cc_final: 0.7897 (m90) REVERT: B 228 THR cc_start: 0.6789 (m) cc_final: 0.6229 (m) REVERT: B 273 LYS cc_start: 0.8848 (tttt) cc_final: 0.8322 (ttmm) REVERT: B 274 ASN cc_start: 0.8406 (t0) cc_final: 0.7814 (t0) REVERT: B 287 ARG cc_start: 0.6775 (mtt90) cc_final: 0.6572 (mtt90) REVERT: B 365 ARG cc_start: 0.8004 (mtt-85) cc_final: 0.7459 (mtt-85) REVERT: B 393 THR cc_start: 0.7455 (m) cc_final: 0.7171 (m) REVERT: B 403 GLN cc_start: 0.8583 (mt0) cc_final: 0.8066 (mt0) REVERT: B 408 ASN cc_start: 0.9101 (m-40) cc_final: 0.8858 (m-40) REVERT: B 445 THR cc_start: 0.9098 (p) cc_final: 0.8575 (p) REVERT: B 451 ASP cc_start: 0.6760 (m-30) cc_final: 0.6500 (m-30) REVERT: B 452 THR cc_start: 0.9381 (m) cc_final: 0.9028 (p) REVERT: B 475 SER cc_start: 0.8189 (m) cc_final: 0.7689 (m) REVERT: B 486 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8384 (mm-30) REVERT: B 525 GLU cc_start: 0.8795 (tp30) cc_final: 0.8099 (tp30) REVERT: B 529 ILE cc_start: 0.8235 (pt) cc_final: 0.7663 (pt) REVERT: B 543 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.6515 (mp10) REVERT: B 548 THR cc_start: 0.8792 (p) cc_final: 0.8439 (p) REVERT: B 553 ASN cc_start: 0.7734 (m-40) cc_final: 0.7013 (m110) REVERT: B 597 HIS cc_start: 0.6975 (OUTLIER) cc_final: 0.6751 (t-170) REVERT: C 192 TYR cc_start: 0.8297 (p90) cc_final: 0.8069 (p90) REVERT: C 197 LYS cc_start: 0.8623 (tttt) cc_final: 0.8101 (mttm) REVERT: C 200 ARG cc_start: 0.7523 (mpp80) cc_final: 0.7236 (mtm180) REVERT: C 274 ASN cc_start: 0.8713 (t0) cc_final: 0.8157 (t0) REVERT: C 275 GLU cc_start: 0.8332 (tt0) cc_final: 0.8092 (tt0) REVERT: C 279 THR cc_start: 0.8503 (p) cc_final: 0.8292 (t) REVERT: C 302 GLU cc_start: 0.6443 (OUTLIER) cc_final: 0.5916 (mp0) REVERT: C 344 ARG cc_start: 0.7342 (ttp-110) cc_final: 0.7109 (ttp-110) REVERT: C 346 TRP cc_start: 0.6954 (t-100) cc_final: 0.6723 (t-100) REVERT: C 350 MET cc_start: 0.7965 (mtt) cc_final: 0.7535 (mtt) REVERT: C 409 ASN cc_start: 0.8082 (m110) cc_final: 0.7585 (m-40) REVERT: C 436 TYR cc_start: 0.8063 (t80) cc_final: 0.7756 (t80) REVERT: C 447 GLN cc_start: 0.8068 (mt0) cc_final: 0.7669 (mt0) REVERT: C 472 ASP cc_start: 0.7528 (t0) cc_final: 0.7250 (t0) REVERT: C 518 LYS cc_start: 0.7483 (mtmt) cc_final: 0.7106 (mtmt) REVERT: C 522 THR cc_start: 0.7278 (p) cc_final: 0.6799 (p) REVERT: C 545 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.7873 (ttpt) REVERT: C 549 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8388 (mt-10) REVERT: C 559 SER cc_start: 0.8765 (t) cc_final: 0.8544 (p) REVERT: C 563 LYS cc_start: 0.9109 (tppt) cc_final: 0.8877 (ttmt) REVERT: C 581 ILE cc_start: 0.6551 (mm) cc_final: 0.6290 (mm) REVERT: C 586 LYS cc_start: 0.7118 (mtpp) cc_final: 0.6518 (mtmm) REVERT: C 593 ASP cc_start: 0.8207 (t70) cc_final: 0.7625 (t0) REVERT: C 595 ARG cc_start: 0.8554 (mtm180) cc_final: 0.8133 (mpp80) REVERT: C 598 TYR cc_start: 0.5520 (m-80) cc_final: 0.4787 (m-80) REVERT: C 662 MET cc_start: 0.3354 (mtp) cc_final: 0.3015 (ttm) REVERT: D 178 ARG cc_start: 0.6783 (mtt180) cc_final: 0.6575 (mtt180) REVERT: D 180 ASN cc_start: 0.8861 (t0) cc_final: 0.8294 (t0) REVERT: D 195 ASP cc_start: 0.7653 (t70) cc_final: 0.7336 (t0) REVERT: D 197 LYS cc_start: 0.8974 (tttt) cc_final: 0.8682 (tppt) REVERT: D 200 ARG cc_start: 0.6851 (mpp80) cc_final: 0.6431 (mtt180) REVERT: D 212 GLU cc_start: 0.8372 (tt0) cc_final: 0.7978 (tt0) REVERT: D 213 LYS cc_start: 0.9203 (mttt) cc_final: 0.8785 (mttt) REVERT: D 244 ASP cc_start: 0.7736 (t0) cc_final: 0.7371 (t0) REVERT: D 246 ASN cc_start: 0.8763 (m110) cc_final: 0.8162 (m110) REVERT: D 263 HIS cc_start: 0.7523 (p-80) cc_final: 0.7310 (p-80) REVERT: D 275 GLU cc_start: 0.8499 (tt0) cc_final: 0.8217 (tt0) REVERT: D 283 ASP cc_start: 0.6909 (m-30) cc_final: 0.6676 (m-30) REVERT: D 287 ARG cc_start: 0.7830 (mtt90) cc_final: 0.7375 (mtt90) REVERT: D 387 LYS cc_start: 0.9242 (tptp) cc_final: 0.8787 (tppp) REVERT: D 441 GLU cc_start: 0.8949 (tt0) cc_final: 0.8606 (tt0) REVERT: D 445 THR cc_start: 0.8389 (p) cc_final: 0.8125 (t) REVERT: D 447 GLN cc_start: 0.8508 (mt0) cc_final: 0.7862 (mt0) REVERT: D 472 ASP cc_start: 0.8161 (t0) cc_final: 0.7439 (t0) REVERT: D 486 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7682 (mm-30) REVERT: D 491 ILE cc_start: 0.6994 (mt) cc_final: 0.6775 (mt) REVERT: D 508 VAL cc_start: 0.8196 (t) cc_final: 0.7885 (m) REVERT: D 541 GLN cc_start: 0.8264 (mt0) cc_final: 0.7920 (tt0) REVERT: D 543 GLN cc_start: 0.9329 (OUTLIER) cc_final: 0.8246 (mp10) REVERT: D 549 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8438 (pt0) REVERT: D 563 LYS cc_start: 0.8834 (tppt) cc_final: 0.8552 (mtpp) REVERT: D 584 ASN cc_start: 0.7544 (m-40) cc_final: 0.7340 (m-40) REVERT: D 586 LYS cc_start: 0.6867 (mtpp) cc_final: 0.6522 (mttp) REVERT: D 587 MET cc_start: 0.7378 (mtt) cc_final: 0.6912 (mtt) REVERT: D 589 ILE cc_start: 0.7291 (mt) cc_final: 0.7039 (mm) REVERT: D 596 PHE cc_start: 0.7973 (m-80) cc_final: 0.7301 (m-80) REVERT: E 202 PHE cc_start: 0.6329 (m-10) cc_final: 0.6042 (m-10) REVERT: E 217 THR cc_start: 0.8082 (m) cc_final: 0.7729 (p) REVERT: E 219 TYR cc_start: 0.8393 (m-10) cc_final: 0.8008 (m-10) REVERT: E 243 ILE cc_start: 0.9052 (tt) cc_final: 0.8795 (tt) REVERT: E 283 ASP cc_start: 0.5137 (m-30) cc_final: 0.4922 (m-30) REVERT: E 284 SER cc_start: 0.6588 (m) cc_final: 0.6040 (t) REVERT: E 286 THR cc_start: 0.7861 (m) cc_final: 0.7655 (t) REVERT: E 339 SER cc_start: 0.7886 (m) cc_final: 0.7666 (m) REVERT: E 387 LYS cc_start: 0.9126 (tptp) cc_final: 0.8601 (tppt) REVERT: E 403 GLN cc_start: 0.8360 (mt0) cc_final: 0.7809 (mt0) REVERT: E 422 ASN cc_start: 0.8009 (p0) cc_final: 0.7693 (p0) REVERT: E 462 TYR cc_start: 0.8272 (t80) cc_final: 0.7879 (t80) REVERT: E 475 SER cc_start: 0.7808 (m) cc_final: 0.7362 (m) REVERT: E 476 ASN cc_start: 0.8118 (p0) cc_final: 0.7518 (p0) REVERT: E 485 GLN cc_start: 0.8780 (mt0) cc_final: 0.8514 (mt0) REVERT: E 504 ARG cc_start: 0.7297 (mtt-85) cc_final: 0.7000 (mtt-85) REVERT: E 515 GLU cc_start: 0.7985 (tp30) cc_final: 0.6634 (tp30) REVERT: E 518 LYS cc_start: 0.8415 (mtmt) cc_final: 0.6660 (mtmt) REVERT: E 525 GLU cc_start: 0.8696 (tp30) cc_final: 0.7910 (tp30) REVERT: E 537 ASN cc_start: 0.8401 (t0) cc_final: 0.7746 (p0) REVERT: E 543 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7798 (mp10) REVERT: E 563 LYS cc_start: 0.8989 (tppt) cc_final: 0.8680 (mtpt) REVERT: E 587 MET cc_start: 0.7712 (mtt) cc_final: 0.7320 (mtt) REVERT: E 598 TYR cc_start: 0.4706 (m-80) cc_final: 0.4105 (m-80) REVERT: E 602 ASN cc_start: 0.5599 (OUTLIER) cc_final: 0.4920 (m-40) REVERT: E 608 ASP cc_start: 0.8649 (m-30) cc_final: 0.8173 (m-30) REVERT: F 197 LYS cc_start: 0.8856 (tttt) cc_final: 0.8599 (ttmm) REVERT: F 207 ILE cc_start: 0.8515 (mt) cc_final: 0.8274 (mm) REVERT: F 211 HIS cc_start: 0.8350 (m90) cc_final: 0.7684 (m90) REVERT: F 237 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8671 (mt-10) REVERT: F 290 SER cc_start: 0.6837 (m) cc_final: 0.6569 (t) REVERT: F 350 MET cc_start: 0.7774 (mtt) cc_final: 0.7516 (mtt) REVERT: F 387 LYS cc_start: 0.9235 (tptp) cc_final: 0.8860 (ttmm) REVERT: F 398 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7877 (mt-10) REVERT: F 403 GLN cc_start: 0.8451 (mt0) cc_final: 0.8225 (mt0) REVERT: F 426 ASP cc_start: 0.9046 (m-30) cc_final: 0.8807 (m-30) REVERT: F 486 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7547 (mm-30) REVERT: F 496 LYS cc_start: 0.8269 (tttt) cc_final: 0.7960 (tppt) REVERT: F 535 GLU cc_start: 0.7974 (pt0) cc_final: 0.7637 (pt0) REVERT: F 543 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8548 (mp10) REVERT: F 573 ASN cc_start: 0.7974 (t0) cc_final: 0.7561 (t0) REVERT: F 584 ASN cc_start: 0.7768 (m-40) cc_final: 0.7439 (m-40) REVERT: F 587 MET cc_start: 0.6849 (mtt) cc_final: 0.6285 (mtt) REVERT: F 593 ASP cc_start: 0.6954 (t0) cc_final: 0.6706 (t0) REVERT: F 595 ARG cc_start: 0.8558 (mtm180) cc_final: 0.8228 (mtm-85) REVERT: F 718 THR cc_start: -0.1006 (OUTLIER) cc_final: -0.1504 (m) REVERT: G 195 ASP cc_start: 0.7720 (t70) cc_final: 0.7285 (p0) REVERT: G 199 LYS cc_start: 0.6828 (mmtt) cc_final: 0.6608 (mmmm) REVERT: G 212 GLU cc_start: 0.7577 (tt0) cc_final: 0.7348 (tp30) REVERT: G 238 LYS cc_start: 0.8545 (ttmp) cc_final: 0.7839 (mtpp) REVERT: G 259 TYR cc_start: 0.7293 (p90) cc_final: 0.6416 (p90) REVERT: G 267 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8285 (mt-10) REVERT: G 269 ILE cc_start: 0.8754 (pp) cc_final: 0.8542 (mm) REVERT: G 275 GLU cc_start: 0.7514 (tt0) cc_final: 0.7114 (tt0) REVERT: G 277 GLN cc_start: 0.8235 (pt0) cc_final: 0.7900 (pt0) REVERT: G 281 ASN cc_start: 0.6144 (t160) cc_final: 0.5733 (t0) REVERT: G 346 TRP cc_start: 0.6717 (t-100) cc_final: 0.6346 (m-90) REVERT: G 348 GLU cc_start: 0.7278 (tt0) cc_final: 0.7011 (tt0) REVERT: G 350 MET cc_start: 0.8275 (mtt) cc_final: 0.7890 (mtt) REVERT: G 356 ASP cc_start: 0.8331 (t0) cc_final: 0.7837 (t0) REVERT: G 388 ASN cc_start: 0.8008 (p0) cc_final: 0.7794 (p0) REVERT: G 403 GLN cc_start: 0.8329 (mt0) cc_final: 0.7925 (mt0) REVERT: G 425 ASP cc_start: 0.7275 (m-30) cc_final: 0.6781 (m-30) REVERT: G 478 SER cc_start: 0.9313 (m) cc_final: 0.8813 (m) REVERT: G 512 ASP cc_start: 0.7616 (t0) cc_final: 0.7015 (t0) REVERT: G 524 LYS cc_start: 0.8387 (ttpt) cc_final: 0.7946 (tttm) REVERT: G 525 GLU cc_start: 0.8406 (tp30) cc_final: 0.7371 (tp30) REVERT: G 531 PHE cc_start: 0.7352 (m-10) cc_final: 0.6922 (m-80) REVERT: G 543 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7739 (mp10) REVERT: G 556 GLN cc_start: 0.8751 (tt0) cc_final: 0.8496 (tm-30) REVERT: G 564 ASN cc_start: 0.8898 (m-40) cc_final: 0.8562 (m-40) REVERT: G 568 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8078 (mt-10) REVERT: G 582 LYS cc_start: 0.8267 (mmtt) cc_final: 0.7924 (mtmm) REVERT: G 586 LYS cc_start: 0.8310 (mtpp) cc_final: 0.7725 (mtmm) REVERT: G 587 MET cc_start: 0.7445 (mtt) cc_final: 0.7120 (mtm) REVERT: G 612 VAL cc_start: 0.8362 (t) cc_final: 0.8123 (m) REVERT: G 616 HIS cc_start: 0.6538 (t70) cc_final: 0.6202 (t70) REVERT: G 658 ASP cc_start: 0.6107 (t0) cc_final: 0.5884 (t70) outliers start: 148 outliers final: 60 residues processed: 1720 average time/residue: 0.2071 time to fit residues: 566.2397 Evaluate side-chains 1261 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 1190 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain L residue 102 LYS Chi-restraints excluded: chain L residue 104 ILE Chi-restraints excluded: chain L residue 122 LYS Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 165 GLN Chi-restraints excluded: chain L residue 167 TYR Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain L residue 197 HIS Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain L residue 244 MET Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 678 PHE Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain B residue 543 GLN Chi-restraints excluded: chain B residue 596 PHE Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 665 ILE Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 678 PHE Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 545 LYS Chi-restraints excluded: chain C residue 636 ARG Chi-restraints excluded: chain C residue 638 ILE Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 703 LYS Chi-restraints excluded: chain D residue 543 GLN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain D residue 638 ILE Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain E residue 543 GLN Chi-restraints excluded: chain E residue 602 ASN Chi-restraints excluded: chain E residue 634 ASP Chi-restraints excluded: chain E residue 709 ASN Chi-restraints excluded: chain F residue 543 GLN Chi-restraints excluded: chain F residue 596 PHE Chi-restraints excluded: chain F residue 629 LEU Chi-restraints excluded: chain F residue 708 ILE Chi-restraints excluded: chain F residue 718 THR Chi-restraints excluded: chain G residue 543 GLN Chi-restraints excluded: chain G residue 605 VAL Chi-restraints excluded: chain G residue 620 ILE Chi-restraints excluded: chain G residue 636 ARG Chi-restraints excluded: chain G residue 657 ASN Chi-restraints excluded: chain G residue 662 MET Chi-restraints excluded: chain G residue 665 ILE Chi-restraints excluded: chain G residue 675 PHE Chi-restraints excluded: chain G residue 708 ILE Chi-restraints excluded: chain G residue 724 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 GLN L 42 HIS L 132 GLN L 146 ASN L 165 GLN L 168 GLN L 175 ASN L 186 GLN L 192 ASN L 211 ASN L 214 GLN L 234 GLN L 248 ASN A 281 ASN A 292 ASN A 389 GLN A 408 ASN A 556 GLN A 621 ASN ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 ASN B 336 HIS B 424 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 553 ASN ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 ASN B 691 ASN B 713 ASN C 281 ASN C 292 ASN C 363 ASN ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 GLN C 584 ASN ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 HIS C 682 ASN C 693 ASN C 709 ASN D 292 ASN ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 GLN D 483 GLN D 556 GLN D 570 ASN D 584 ASN E 292 ASN ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 483 GLN E 541 GLN E 557 GLN E 584 ASN E 693 ASN E 705 ASN E 719 ASN F 281 ASN F 292 ASN F 553 ASN F 584 ASN F 597 HIS F 601 ASN G 281 ASN ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 408 ASN G 483 GLN G 601 ASN ** G 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 657 ASN G 693 ASN G 719 ASN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.200578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.133149 restraints weight = 47370.275| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 3.70 r_work: 0.3418 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 33385 Z= 0.152 Angle : 0.691 11.706 45291 Z= 0.360 Chirality : 0.049 0.304 5178 Planarity : 0.005 0.058 5938 Dihedral : 7.796 85.928 4638 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.41 % Favored : 96.45 % Rotamer: Outliers : 4.25 % Allowed : 16.34 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.13), residues: 4138 helix: -0.00 (0.22), residues: 600 sheet: 0.37 (0.14), residues: 1247 loop : -1.11 (0.13), residues: 2291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 592 TYR 0.021 0.002 TYR F 462 PHE 0.026 0.002 PHE E 678 TRP 0.010 0.001 TRP C 346 HIS 0.012 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00330 (33385) covalent geometry : angle 0.69073 (45291) hydrogen bonds : bond 0.03893 ( 1183) hydrogen bonds : angle 6.89172 ( 3228) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1481 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 1324 time to evaluate : 1.216 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: 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: 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 180 ASN cc_start: 0.9130 (t0) cc_final: 0.8788 (t0) REVERT: A 237 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8653 (mt-10) REVERT: A 256 VAL cc_start: 0.9514 (t) cc_final: 0.9157 (p) REVERT: A 274 ASN cc_start: 0.8995 (t0) cc_final: 0.8403 (t0) REVERT: A 287 ARG cc_start: 0.6533 (mtt90) cc_final: 0.6039 (mtt90) REVERT: A 296 SER cc_start: 0.8954 (m) cc_final: 0.8447 (p) REVERT: A 343 GLU cc_start: 0.7067 (mp0) cc_final: 0.6799 (mp0) REVERT: A 344 ARG cc_start: 0.7711 (ttp-110) cc_final: 0.6930 (ttp-110) REVERT: A 350 MET cc_start: 0.8263 (mtt) cc_final: 0.7955 (mtt) REVERT: A 368 ASN cc_start: 0.8930 (t0) cc_final: 0.8344 (t0) REVERT: A 384 VAL cc_start: 0.9078 (t) cc_final: 0.8812 (m) REVERT: A 400 GLN cc_start: 0.9077 (mp10) cc_final: 0.8840 (mp10) REVERT: A 411 TYR cc_start: 0.9085 (t80) cc_final: 0.8345 (t80) REVERT: A 454 GLN cc_start: 0.8559 (pt0) cc_final: 0.7909 (pt0) REVERT: A 486 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8754 (mm-30) REVERT: A 508 VAL cc_start: 0.8823 (t) cc_final: 0.8512 (t) REVERT: A 515 GLU cc_start: 0.8915 (tp30) cc_final: 0.7049 (tp30) REVERT: A 582 LYS cc_start: 0.8576 (mmtt) cc_final: 0.8290 (mtpp) REVERT: A 597 HIS cc_start: 0.8071 (m170) cc_final: 0.7594 (m-70) REVERT: A 662 MET cc_start: 0.1386 (mtp) cc_final: 0.0581 (ttp) REVERT: B 211 HIS cc_start: 0.8731 (m90) cc_final: 0.8492 (m90) REVERT: B 274 ASN cc_start: 0.9070 (t0) cc_final: 0.8455 (t0) REVERT: B 287 ARG cc_start: 0.7606 (mtt90) cc_final: 0.7261 (mtt90) REVERT: B 344 ARG cc_start: 0.7470 (ttp-110) cc_final: 0.6889 (mtp-110) REVERT: B 368 ASN cc_start: 0.8781 (t0) cc_final: 0.8389 (t0) REVERT: B 375 TYR cc_start: 0.8609 (m-80) cc_final: 0.8321 (m-80) REVERT: B 403 GLN cc_start: 0.8944 (mt0) cc_final: 0.8484 (mt0) REVERT: B 408 ASN cc_start: 0.9282 (m-40) cc_final: 0.9045 (m-40) REVERT: B 445 THR cc_start: 0.9257 (p) cc_final: 0.9022 (p) REVERT: B 451 ASP cc_start: 0.7518 (m-30) cc_final: 0.6902 (m-30) REVERT: B 452 THR cc_start: 0.9364 (m) cc_final: 0.8970 (p) REVERT: B 470 ARG cc_start: 0.9009 (ttm110) cc_final: 0.8579 (ttm110) REVERT: B 475 SER cc_start: 0.8191 (m) cc_final: 0.7743 (m) REVERT: B 486 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8707 (mm-30) REVERT: B 525 GLU cc_start: 0.9142 (tp30) cc_final: 0.8361 (tp30) REVERT: B 529 ILE cc_start: 0.8830 (pt) cc_final: 0.8317 (pt) REVERT: B 543 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7852 (mm110) REVERT: B 546 ASP cc_start: 0.8307 (t0) cc_final: 0.7990 (t0) REVERT: B 548 THR cc_start: 0.8996 (p) cc_final: 0.8706 (p) REVERT: B 553 ASN cc_start: 0.8177 (m110) cc_final: 0.7828 (m110) REVERT: B 586 LYS cc_start: 0.8838 (ttmm) cc_final: 0.8381 (ttmm) REVERT: B 587 MET cc_start: 0.8656 (mtt) cc_final: 0.8225 (mtm) REVERT: C 208 SER cc_start: 0.9280 (OUTLIER) cc_final: 0.8941 (t) REVERT: C 226 TRP cc_start: 0.8925 (t60) cc_final: 0.8573 (t60) REVERT: C 344 ARG cc_start: 0.8210 (ttp-110) cc_final: 0.7820 (ttp-110) REVERT: C 350 MET cc_start: 0.8473 (mtt) cc_final: 0.8157 (mtt) REVERT: C 375 TYR cc_start: 0.8961 (m-10) cc_final: 0.8742 (m-10) REVERT: C 401 LEU cc_start: 0.9473 (tt) cc_final: 0.9257 (tt) REVERT: C 405 LEU cc_start: 0.8789 (tp) cc_final: 0.8476 (tp) REVERT: C 409 ASN cc_start: 0.8541 (m110) cc_final: 0.8025 (m-40) REVERT: C 436 TYR cc_start: 0.8370 (t80) cc_final: 0.8079 (t80) REVERT: C 496 LYS cc_start: 0.9119 (ttmm) cc_final: 0.8880 (tppt) REVERT: C 545 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8343 (ttpt) REVERT: C 549 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8607 (mt-10) REVERT: C 555 ASP cc_start: 0.8329 (p0) cc_final: 0.7955 (p0) REVERT: C 563 LYS cc_start: 0.9295 (tppt) cc_final: 0.8999 (ttmt) REVERT: C 593 ASP cc_start: 0.8444 (t70) cc_final: 0.7727 (t0) REVERT: D 180 ASN cc_start: 0.9247 (t0) cc_final: 0.8617 (t0) REVERT: D 195 ASP cc_start: 0.8245 (t70) cc_final: 0.7970 (t0) REVERT: D 244 ASP cc_start: 0.8398 (t0) cc_final: 0.7928 (t0) REVERT: D 246 ASN cc_start: 0.9086 (m110) cc_final: 0.8600 (m110) REVERT: D 280 GLN cc_start: 0.8477 (tt0) cc_final: 0.8151 (tp-100) REVERT: D 287 ARG cc_start: 0.8262 (mtt90) cc_final: 0.7896 (mtt90) REVERT: D 344 ARG cc_start: 0.8024 (ttp-170) cc_final: 0.7697 (ttp-170) REVERT: D 356 ASP cc_start: 0.8483 (t70) cc_final: 0.8212 (t70) REVERT: D 387 LYS cc_start: 0.9276 (tptp) cc_final: 0.8927 (tppp) REVERT: D 401 LEU cc_start: 0.9103 (tt) cc_final: 0.8787 (tt) REVERT: D 411 TYR cc_start: 0.9023 (t80) cc_final: 0.8456 (t80) REVERT: D 414 LYS cc_start: 0.9221 (tptm) cc_final: 0.8952 (tppp) REVERT: D 472 ASP cc_start: 0.8581 (t0) cc_final: 0.7992 (t0) REVERT: D 541 GLN cc_start: 0.8681 (mt0) cc_final: 0.8481 (tt0) REVERT: D 543 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8518 (mm-40) REVERT: D 549 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8630 (mt-10) REVERT: D 560 GLN cc_start: 0.8173 (tp-100) cc_final: 0.7873 (tm-30) REVERT: D 586 LYS cc_start: 0.8698 (mtpp) cc_final: 0.8470 (mttp) REVERT: D 589 ILE cc_start: 0.8687 (mt) cc_final: 0.8326 (mm) REVERT: D 593 ASP cc_start: 0.8050 (t0) cc_final: 0.7796 (t0) REVERT: D 596 PHE cc_start: 0.8809 (m-80) cc_final: 0.7927 (m-80) REVERT: E 206 TRP cc_start: 0.8719 (t-100) cc_final: 0.8096 (t-100) REVERT: E 217 THR cc_start: 0.8839 (m) cc_final: 0.8371 (p) REVERT: E 218 LYS cc_start: 0.9317 (ttpt) cc_final: 0.8516 (mtpt) REVERT: E 219 TYR cc_start: 0.8832 (m-10) cc_final: 0.8411 (m-10) REVERT: E 236 PHE cc_start: 0.9130 (t80) cc_final: 0.8924 (t80) REVERT: E 287 ARG cc_start: 0.8259 (mtt90) cc_final: 0.7781 (mtt90) REVERT: E 339 SER cc_start: 0.9418 (m) cc_final: 0.9023 (p) REVERT: E 366 TYR cc_start: 0.8818 (m-10) cc_final: 0.8490 (m-10) REVERT: E 387 LYS cc_start: 0.9140 (tptp) cc_final: 0.8692 (tppt) REVERT: E 403 GLN cc_start: 0.9011 (mt0) cc_final: 0.8691 (mt0) REVERT: E 422 ASN cc_start: 0.8794 (p0) cc_final: 0.8185 (p0) REVERT: E 447 GLN cc_start: 0.8887 (mt0) cc_final: 0.8459 (mm-40) REVERT: E 462 TYR cc_start: 0.8822 (t80) cc_final: 0.8481 (t80) REVERT: E 475 SER cc_start: 0.8497 (m) cc_final: 0.8177 (m) REVERT: E 476 ASN cc_start: 0.8909 (p0) cc_final: 0.8300 (p0) REVERT: E 485 GLN cc_start: 0.9294 (mt0) cc_final: 0.9087 (mt0) REVERT: E 486 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8338 (mm-30) REVERT: E 499 ASN cc_start: 0.8355 (m-40) cc_final: 0.7775 (m-40) REVERT: E 512 ASP cc_start: 0.8323 (t0) cc_final: 0.7740 (t0) REVERT: E 515 GLU cc_start: 0.8233 (tp30) cc_final: 0.6472 (tp30) REVERT: E 518 LYS cc_start: 0.9225 (mtmt) cc_final: 0.8852 (mtmt) REVERT: E 525 GLU cc_start: 0.8936 (tp30) cc_final: 0.8156 (tp30) REVERT: E 537 ASN cc_start: 0.8603 (t0) cc_final: 0.8057 (p0) REVERT: E 556 GLN cc_start: 0.8546 (pm20) cc_final: 0.8269 (pm20) REVERT: E 563 LYS cc_start: 0.9217 (tppt) cc_final: 0.8907 (mtpt) REVERT: E 584 ASN cc_start: 0.9081 (m110) cc_final: 0.8807 (m-40) REVERT: E 587 MET cc_start: 0.8981 (mtt) cc_final: 0.8661 (mtm) REVERT: E 593 ASP cc_start: 0.8697 (t0) cc_final: 0.8345 (t0) REVERT: E 603 ILE cc_start: 0.8131 (mm) cc_final: 0.7926 (mm) REVERT: F 197 LYS cc_start: 0.9095 (tttt) cc_final: 0.8845 (ttmm) REVERT: F 211 HIS cc_start: 0.8524 (m90) cc_final: 0.8208 (m-70) REVERT: F 276 ASP cc_start: 0.7851 (p0) cc_final: 0.7562 (p0) REVERT: F 281 ASN cc_start: 0.7522 (t0) cc_final: 0.7315 (m-40) REVERT: F 426 ASP cc_start: 0.8984 (m-30) cc_final: 0.8698 (m-30) REVERT: F 443 GLU cc_start: 0.8648 (mt-10) cc_final: 0.7991 (mt-10) REVERT: F 486 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8131 (mm-30) REVERT: F 496 LYS cc_start: 0.9306 (tttt) cc_final: 0.8792 (ttmm) REVERT: F 515 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8273 (mp0) REVERT: F 535 GLU cc_start: 0.8260 (pt0) cc_final: 0.7899 (pt0) REVERT: F 543 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8521 (mp10) REVERT: F 573 ASN cc_start: 0.8549 (t0) cc_final: 0.8100 (t0) REVERT: F 575 TYR cc_start: 0.9240 (m-10) cc_final: 0.8967 (m-80) REVERT: F 593 ASP cc_start: 0.7918 (t0) cc_final: 0.7120 (t0) REVERT: F 662 MET cc_start: 0.5527 (ttp) cc_final: 0.4714 (ptm) REVERT: F 703 LYS cc_start: 0.8855 (mmtp) cc_final: 0.8544 (mmtp) REVERT: G 189 VAL cc_start: 0.9430 (t) cc_final: 0.9120 (m) REVERT: G 212 GLU cc_start: 0.7881 (tt0) cc_final: 0.7578 (tp30) REVERT: G 259 TYR cc_start: 0.8771 (p90) cc_final: 0.8436 (p90) REVERT: G 264 VAL cc_start: 0.9387 (t) cc_final: 0.9166 (p) REVERT: G 266 MET cc_start: 0.8966 (ttt) cc_final: 0.8696 (ttt) REVERT: G 275 GLU cc_start: 0.8299 (tt0) cc_final: 0.8081 (tt0) REVERT: G 277 GLN cc_start: 0.8899 (pt0) cc_final: 0.8686 (pt0) REVERT: G 346 TRP cc_start: 0.7756 (t-100) cc_final: 0.7294 (m-90) REVERT: G 350 MET cc_start: 0.8352 (mtt) cc_final: 0.7978 (mtt) REVERT: G 353 ASN cc_start: 0.8418 (t0) cc_final: 0.8194 (t0) REVERT: G 356 ASP cc_start: 0.8698 (t0) cc_final: 0.8040 (t0) REVERT: G 368 ASN cc_start: 0.8975 (t0) cc_final: 0.8505 (t0) REVERT: G 375 TYR cc_start: 0.8389 (m-10) cc_final: 0.8067 (m-80) REVERT: G 402 SER cc_start: 0.9356 (t) cc_final: 0.9101 (t) REVERT: G 442 LEU cc_start: 0.9391 (tp) cc_final: 0.9170 (tp) REVERT: G 468 ARG cc_start: 0.8823 (ttp80) cc_final: 0.8600 (ttp80) REVERT: G 512 ASP cc_start: 0.8778 (t0) cc_final: 0.8184 (t0) REVERT: G 525 GLU cc_start: 0.8835 (tp30) cc_final: 0.7785 (tp30) REVERT: G 529 ILE cc_start: 0.8654 (pt) cc_final: 0.8008 (pt) REVERT: G 556 GLN cc_start: 0.9346 (tt0) cc_final: 0.8944 (tm-30) REVERT: G 564 ASN cc_start: 0.9234 (m-40) cc_final: 0.8783 (m-40) REVERT: G 565 GLN cc_start: 0.9093 (mt0) cc_final: 0.8822 (mt0) REVERT: G 568 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8166 (mt-10) REVERT: G 582 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8262 (mtmm) outliers start: 157 outliers final: 101 residues processed: 1410 average time/residue: 0.1863 time to fit residues: 436.5547 Evaluate side-chains 1332 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 1225 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain L residue 102 LYS Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 122 LYS Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 167 TYR Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain L residue 250 GLN Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 543 GLN Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 665 ILE Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 545 LYS Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 636 ARG Chi-restraints excluded: chain C residue 638 ILE Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 703 LYS Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 492 ILE Chi-restraints excluded: chain D residue 543 GLN Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain E residue 444 LYS Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 589 ILE Chi-restraints excluded: chain E residue 610 SER Chi-restraints excluded: chain E residue 634 ASP Chi-restraints excluded: chain E residue 706 THR Chi-restraints excluded: chain E residue 709 ASN Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 468 ARG Chi-restraints excluded: chain F residue 497 ASP Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 515 GLU Chi-restraints excluded: chain F residue 543 GLN Chi-restraints excluded: chain F residue 582 LYS Chi-restraints excluded: chain F residue 713 ASN Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 263 HIS Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 605 VAL Chi-restraints excluded: chain G residue 620 ILE Chi-restraints excluded: chain G residue 636 ARG Chi-restraints excluded: chain G residue 657 ASN Chi-restraints excluded: chain G residue 665 ILE Chi-restraints excluded: chain G residue 683 ASP Chi-restraints excluded: chain G residue 708 ILE Chi-restraints excluded: chain G residue 724 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 228 optimal weight: 0.9980 chunk 366 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 377 optimal weight: 2.9990 chunk 362 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 268 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 251 optimal weight: 0.0020 chunk 163 optimal weight: 8.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 42 HIS A 408 ASN A 447 GLN A 556 GLN A 584 ASN A 630 ASN B 263 HIS B 336 HIS B 368 ASN B 541 GLN ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 HIS C 281 ASN C 485 GLN C 588 ASN C 682 ASN D 299 HIS ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 556 GLN D 565 GLN E 268 ASN F 499 ASN F 597 HIS ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 GLN G 584 ASN ** G 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.198501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.131396 restraints weight = 47134.251| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 3.64 r_work: 0.3398 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 33385 Z= 0.127 Angle : 0.611 11.342 45291 Z= 0.319 Chirality : 0.047 0.210 5178 Planarity : 0.004 0.073 5938 Dihedral : 6.590 89.703 4559 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.62 % Favored : 96.23 % Rotamer: Outliers : 4.96 % Allowed : 18.78 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.13), residues: 4138 helix: 0.44 (0.23), residues: 599 sheet: 0.80 (0.15), residues: 1211 loop : -0.83 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 592 TYR 0.027 0.001 TYR F 411 PHE 0.024 0.002 PHE E 439 TRP 0.015 0.002 TRP B 206 HIS 0.009 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00277 (33385) covalent geometry : angle 0.61113 (45291) hydrogen bonds : bond 0.03284 ( 1183) hydrogen bonds : angle 6.08180 ( 3228) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1465 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 1282 time to evaluate : 1.049 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: 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: L 167 TYR cc_start: 0.2899 (OUTLIER) cc_final: 0.1649 (p90) REVERT: A 202 PHE cc_start: 0.8121 (m-10) cc_final: 0.7892 (m-10) REVERT: A 256 VAL cc_start: 0.9535 (t) cc_final: 0.9242 (p) REVERT: A 274 ASN cc_start: 0.8963 (t0) cc_final: 0.8417 (t0) REVERT: A 275 GLU cc_start: 0.8422 (tt0) cc_final: 0.8174 (tt0) REVERT: A 287 ARG cc_start: 0.6866 (mtt90) cc_final: 0.6266 (mtt90) REVERT: A 296 SER cc_start: 0.9342 (m) cc_final: 0.8987 (p) REVERT: A 343 GLU cc_start: 0.7278 (mp0) cc_final: 0.6922 (mp0) REVERT: A 344 ARG cc_start: 0.7761 (ttp-110) cc_final: 0.6917 (ttp-110) REVERT: A 368 ASN cc_start: 0.8956 (t0) cc_final: 0.8462 (t0) REVERT: A 384 VAL cc_start: 0.9176 (t) cc_final: 0.8956 (m) REVERT: A 454 GLN cc_start: 0.8634 (pt0) cc_final: 0.7881 (pt0) REVERT: A 486 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8631 (mm-30) REVERT: A 508 VAL cc_start: 0.8902 (t) cc_final: 0.8599 (t) REVERT: A 515 GLU cc_start: 0.8867 (tp30) cc_final: 0.6997 (tp30) REVERT: A 582 LYS cc_start: 0.8606 (mmtt) cc_final: 0.8356 (mtpp) REVERT: A 587 MET cc_start: 0.8671 (mtm) cc_final: 0.8440 (mtt) REVERT: A 597 HIS cc_start: 0.8067 (m170) cc_final: 0.7637 (m-70) REVERT: A 636 ARG cc_start: 0.9218 (ppp-140) cc_final: 0.8459 (ttp-110) REVERT: A 662 MET cc_start: 0.2002 (mtp) cc_final: 0.0847 (ttp) REVERT: B 207 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8852 (pt) REVERT: B 211 HIS cc_start: 0.9013 (m90) cc_final: 0.8519 (m-70) REVERT: B 274 ASN cc_start: 0.9080 (t0) cc_final: 0.8491 (t0) REVERT: B 283 ASP cc_start: 0.7576 (m-30) cc_final: 0.6952 (m-30) REVERT: B 287 ARG cc_start: 0.7782 (mtt90) cc_final: 0.7472 (mtt90) REVERT: B 291 LYS cc_start: 0.7554 (tptm) cc_final: 0.7169 (tptt) REVERT: B 344 ARG cc_start: 0.7561 (ttp-110) cc_final: 0.7267 (mtp-110) REVERT: B 348 GLU cc_start: 0.8422 (tt0) cc_final: 0.8005 (tt0) REVERT: B 368 ASN cc_start: 0.8649 (t0) cc_final: 0.8229 (t0) REVERT: B 375 TYR cc_start: 0.8731 (m-80) cc_final: 0.8329 (m-80) REVERT: B 403 GLN cc_start: 0.8976 (mt0) cc_final: 0.8472 (mt0) REVERT: B 408 ASN cc_start: 0.9325 (m-40) cc_final: 0.9091 (m-40) REVERT: B 443 GLU cc_start: 0.9381 (tp30) cc_final: 0.9123 (tp30) REVERT: B 450 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7929 (mm) REVERT: B 451 ASP cc_start: 0.7276 (m-30) cc_final: 0.6802 (m-30) REVERT: B 452 THR cc_start: 0.9331 (m) cc_final: 0.8922 (p) REVERT: B 470 ARG cc_start: 0.9021 (ttm110) cc_final: 0.8724 (ttm110) REVERT: B 486 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8687 (mm-30) REVERT: B 496 LYS cc_start: 0.8800 (tttt) cc_final: 0.8500 (tppt) REVERT: B 521 MET cc_start: 0.8326 (tpp) cc_final: 0.8075 (tpp) REVERT: B 525 GLU cc_start: 0.9019 (tp30) cc_final: 0.8035 (tp30) REVERT: B 529 ILE cc_start: 0.8981 (pt) cc_final: 0.8137 (pt) REVERT: B 546 ASP cc_start: 0.8500 (t0) cc_final: 0.8171 (t0) REVERT: B 548 THR cc_start: 0.9148 (p) cc_final: 0.8694 (p) REVERT: B 586 LYS cc_start: 0.8891 (ttmm) cc_final: 0.8429 (ttmm) REVERT: B 587 MET cc_start: 0.8781 (mtt) cc_final: 0.8410 (mtt) REVERT: B 593 ASP cc_start: 0.5685 (t0) cc_final: 0.5470 (t70) REVERT: B 596 PHE cc_start: 0.8230 (m-10) cc_final: 0.8019 (m-10) REVERT: B 662 MET cc_start: 0.8100 (ttm) cc_final: 0.7197 (ttm) REVERT: B 676 ILE cc_start: 0.4699 (OUTLIER) cc_final: 0.4451 (pp) REVERT: C 226 TRP cc_start: 0.8968 (t60) cc_final: 0.8739 (t60) REVERT: C 344 ARG cc_start: 0.8215 (ttp-110) cc_final: 0.7539 (ttp-110) REVERT: C 350 MET cc_start: 0.8570 (mtt) cc_final: 0.8190 (mtt) REVERT: C 401 LEU cc_start: 0.9347 (tt) cc_final: 0.9125 (tt) REVERT: C 405 LEU cc_start: 0.8812 (tp) cc_final: 0.8602 (tp) REVERT: C 436 TYR cc_start: 0.8459 (t80) cc_final: 0.8143 (t80) REVERT: C 496 LYS cc_start: 0.9110 (ttmm) cc_final: 0.8883 (tppt) REVERT: C 545 LYS cc_start: 0.8907 (ttmm) cc_final: 0.8441 (ttpt) REVERT: C 546 ASP cc_start: 0.8787 (t0) cc_final: 0.8430 (t0) REVERT: C 549 GLU cc_start: 0.9220 (mt-10) cc_final: 0.8606 (mt-10) REVERT: C 563 LYS cc_start: 0.9262 (tppt) cc_final: 0.9006 (ttmt) REVERT: C 586 LYS cc_start: 0.8548 (mtpp) cc_final: 0.8190 (mtmt) REVERT: C 593 ASP cc_start: 0.8384 (t70) cc_final: 0.7902 (t0) REVERT: C 596 PHE cc_start: 0.9166 (m-80) cc_final: 0.8908 (m-10) REVERT: C 662 MET cc_start: 0.5378 (mtp) cc_final: 0.4687 (ttp) REVERT: D 180 ASN cc_start: 0.9276 (t0) cc_final: 0.8743 (t0) REVERT: D 195 ASP cc_start: 0.8152 (t70) cc_final: 0.7896 (t0) REVERT: D 280 GLN cc_start: 0.8514 (tt0) cc_final: 0.8106 (tp40) REVERT: D 287 ARG cc_start: 0.8312 (mtt90) cc_final: 0.7940 (mtt90) REVERT: D 344 ARG cc_start: 0.7863 (ttp-170) cc_final: 0.7377 (ttp-170) REVERT: D 356 ASP cc_start: 0.8598 (t70) cc_final: 0.8151 (t70) REVERT: D 387 LYS cc_start: 0.9338 (tptp) cc_final: 0.9032 (tppp) REVERT: D 401 LEU cc_start: 0.9166 (tt) cc_final: 0.8884 (tt) REVERT: D 411 TYR cc_start: 0.9061 (t80) cc_final: 0.8552 (t80) REVERT: D 414 LYS cc_start: 0.9261 (tptm) cc_final: 0.8980 (tppp) REVERT: D 447 GLN cc_start: 0.8840 (mt0) cc_final: 0.8544 (mt0) REVERT: D 543 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8620 (mp10) REVERT: D 549 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8665 (mt-10) REVERT: D 557 GLN cc_start: 0.9225 (tp-100) cc_final: 0.8778 (tp-100) REVERT: D 558 THR cc_start: 0.9108 (m) cc_final: 0.8719 (p) REVERT: D 586 LYS cc_start: 0.8739 (mtpp) cc_final: 0.8434 (mttp) REVERT: D 593 ASP cc_start: 0.7995 (t0) cc_final: 0.7668 (t0) REVERT: D 596 PHE cc_start: 0.8726 (m-80) cc_final: 0.7875 (m-80) REVERT: D 637 LYS cc_start: 0.8789 (ttpp) cc_final: 0.8271 (ttpp) REVERT: E 217 THR cc_start: 0.8971 (m) cc_final: 0.8713 (p) REVERT: E 218 LYS cc_start: 0.9310 (ttpt) cc_final: 0.8744 (mtpp) REVERT: E 219 TYR cc_start: 0.8918 (m-10) cc_final: 0.8351 (m-10) REVERT: E 236 PHE cc_start: 0.9130 (t80) cc_final: 0.8924 (t80) REVERT: E 287 ARG cc_start: 0.8201 (mtt90) cc_final: 0.7972 (mtt90) REVERT: E 339 SER cc_start: 0.9414 (m) cc_final: 0.9004 (p) REVERT: E 366 TYR cc_start: 0.8563 (m-10) cc_final: 0.8192 (m-10) REVERT: E 387 LYS cc_start: 0.9158 (tptp) cc_final: 0.8715 (tppt) REVERT: E 403 GLN cc_start: 0.9045 (mt0) cc_final: 0.8677 (mt0) REVERT: E 422 ASN cc_start: 0.9095 (p0) cc_final: 0.8567 (p0) REVERT: E 447 GLN cc_start: 0.8927 (mt0) cc_final: 0.8467 (mm110) REVERT: E 462 TYR cc_start: 0.8798 (t80) cc_final: 0.8484 (t80) REVERT: E 475 SER cc_start: 0.8485 (m) cc_final: 0.7914 (m) REVERT: E 476 ASN cc_start: 0.8798 (p0) cc_final: 0.8261 (p0) REVERT: E 486 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8026 (mm-30) REVERT: E 499 ASN cc_start: 0.8343 (m-40) cc_final: 0.7680 (m-40) REVERT: E 512 ASP cc_start: 0.8622 (t0) cc_final: 0.7817 (t0) REVERT: E 514 LEU cc_start: 0.9206 (tp) cc_final: 0.8935 (tt) REVERT: E 515 GLU cc_start: 0.8141 (tp30) cc_final: 0.6646 (tp30) REVERT: E 525 GLU cc_start: 0.8773 (tp30) cc_final: 0.7980 (tp30) REVERT: E 563 LYS cc_start: 0.9225 (tppt) cc_final: 0.8913 (mtpt) REVERT: E 577 VAL cc_start: 0.9478 (m) cc_final: 0.9276 (p) REVERT: E 586 LYS cc_start: 0.9089 (mtpp) cc_final: 0.8646 (mtpp) REVERT: E 587 MET cc_start: 0.8956 (mtt) cc_final: 0.8717 (mtm) REVERT: F 180 ASN cc_start: 0.9576 (t0) cc_final: 0.9316 (t0) REVERT: F 197 LYS cc_start: 0.9099 (tttt) cc_final: 0.8746 (ttpp) REVERT: F 207 ILE cc_start: 0.9153 (tp) cc_final: 0.8721 (tp) REVERT: F 211 HIS cc_start: 0.8576 (m90) cc_final: 0.8230 (m90) REVERT: F 245 LYS cc_start: 0.9424 (mmtm) cc_final: 0.9211 (mmtm) REVERT: F 252 ARG cc_start: 0.9145 (mmm-85) cc_final: 0.8769 (mmm-85) REVERT: F 276 ASP cc_start: 0.7901 (p0) cc_final: 0.7570 (p0) REVERT: F 343 GLU cc_start: 0.7809 (mp0) cc_final: 0.7564 (mp0) REVERT: F 443 GLU cc_start: 0.8598 (mt-10) cc_final: 0.7898 (mt-10) REVERT: F 479 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8097 (mt-10) REVERT: F 496 LYS cc_start: 0.9343 (tttt) cc_final: 0.8708 (tppp) REVERT: F 515 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: F 535 GLU cc_start: 0.8302 (pt0) cc_final: 0.7964 (pt0) REVERT: F 573 ASN cc_start: 0.8599 (t0) cc_final: 0.8153 (t0) REVERT: F 575 TYR cc_start: 0.9220 (m-10) cc_final: 0.8843 (m-10) REVERT: F 587 MET cc_start: 0.8918 (mtt) cc_final: 0.8254 (mtt) REVERT: F 593 ASP cc_start: 0.8087 (t0) cc_final: 0.7507 (t0) REVERT: F 662 MET cc_start: 0.5451 (ttp) cc_final: 0.4468 (ptm) REVERT: F 703 LYS cc_start: 0.8867 (mmtp) cc_final: 0.8495 (mmtp) REVERT: G 212 GLU cc_start: 0.7870 (tt0) cc_final: 0.7629 (tp30) REVERT: G 264 VAL cc_start: 0.9434 (t) cc_final: 0.9196 (p) REVERT: G 346 TRP cc_start: 0.7699 (t-100) cc_final: 0.7418 (m-90) REVERT: G 353 ASN cc_start: 0.8401 (t0) cc_final: 0.8068 (t0) REVERT: G 356 ASP cc_start: 0.8645 (t0) cc_final: 0.8017 (t0) REVERT: G 368 ASN cc_start: 0.9002 (t0) cc_final: 0.8550 (t0) REVERT: G 442 LEU cc_start: 0.9353 (tp) cc_final: 0.9145 (tp) REVERT: G 454 GLN cc_start: 0.8553 (pt0) cc_final: 0.8330 (pt0) REVERT: G 483 GLN cc_start: 0.8862 (mm110) cc_final: 0.8363 (mm110) REVERT: G 512 ASP cc_start: 0.8874 (t0) cc_final: 0.8336 (t0) REVERT: G 518 LYS cc_start: 0.8886 (mtmm) cc_final: 0.8632 (mtmm) REVERT: G 525 GLU cc_start: 0.8856 (tp30) cc_final: 0.7885 (tp30) REVERT: G 556 GLN cc_start: 0.9387 (tt0) cc_final: 0.9013 (tm-30) REVERT: G 560 GLN cc_start: 0.8853 (tp40) cc_final: 0.8267 (tp-100) REVERT: G 565 GLN cc_start: 0.9144 (mt0) cc_final: 0.8830 (mt0) REVERT: G 568 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8201 (mt-10) REVERT: G 582 LYS cc_start: 0.8782 (mmtt) cc_final: 0.8376 (mtmm) REVERT: G 586 LYS cc_start: 0.9129 (mtpp) cc_final: 0.8608 (mttm) REVERT: G 657 ASN cc_start: 0.8168 (OUTLIER) cc_final: 0.7426 (m-40) outliers start: 183 outliers final: 123 residues processed: 1367 average time/residue: 0.1873 time to fit residues: 426.2793 Evaluate side-chains 1368 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 1238 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain L residue 102 LYS Chi-restraints excluded: chain L residue 122 LYS Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 167 TYR Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain L residue 250 GLN Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain B residue 543 GLN Chi-restraints excluded: chain B residue 665 ILE Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 636 ARG Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 703 LYS Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 492 ILE Chi-restraints excluded: chain D residue 543 GLN Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 610 SER Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain E residue 444 LYS Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 610 SER Chi-restraints excluded: chain E residue 636 ARG Chi-restraints excluded: chain E residue 709 ASN Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 263 HIS Chi-restraints excluded: chain F residue 468 ARG Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 515 GLU Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 713 ASN Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 227 SER Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 263 HIS Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain G residue 594 LYS Chi-restraints excluded: chain G residue 605 VAL Chi-restraints excluded: chain G residue 620 ILE Chi-restraints excluded: chain G residue 657 ASN Chi-restraints excluded: chain G residue 665 ILE Chi-restraints excluded: chain G residue 708 ILE Chi-restraints excluded: chain G residue 724 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 237 optimal weight: 20.0000 chunk 268 optimal weight: 0.0010 chunk 149 optimal weight: 9.9990 chunk 317 optimal weight: 6.9990 chunk 199 optimal weight: 7.9990 chunk 227 optimal weight: 4.9990 chunk 298 optimal weight: 20.0000 chunk 349 optimal weight: 0.3980 chunk 81 optimal weight: 3.9990 chunk 352 optimal weight: 20.0000 chunk 10 optimal weight: 0.2980 overall best weight: 1.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 42 HIS A 438 GLN A 556 GLN A 565 GLN B 561 ASN C 485 GLN ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 GLN E 268 ASN ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 HIS F 376 ASN ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 ASN F 539 ASN F 597 HIS ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 GLN G 541 GLN ** G 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.191928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.124188 restraints weight = 46881.600| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.52 r_work: 0.3287 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 33385 Z= 0.195 Angle : 0.632 12.816 45291 Z= 0.331 Chirality : 0.048 0.291 5178 Planarity : 0.004 0.077 5938 Dihedral : 5.995 88.395 4537 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.94 % Favored : 95.92 % Rotamer: Outliers : 5.93 % Allowed : 19.62 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.13), residues: 4138 helix: 0.57 (0.23), residues: 597 sheet: 0.88 (0.16), residues: 1045 loop : -0.83 (0.13), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 592 TYR 0.034 0.002 TYR B 542 PHE 0.028 0.002 PHE E 439 TRP 0.015 0.002 TRP G 206 HIS 0.007 0.001 HIS L 42 Details of bonding type rmsd covalent geometry : bond 0.00428 (33385) covalent geometry : angle 0.63167 (45291) hydrogen bonds : bond 0.03359 ( 1183) hydrogen bonds : angle 5.67377 ( 3228) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1502 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 1283 time to evaluate : 1.182 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: 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: symmetry clash REVERT: A 256 VAL cc_start: 0.9629 (t) cc_final: 0.9351 (p) REVERT: A 274 ASN cc_start: 0.9195 (t0) cc_final: 0.8979 (t0) REVERT: A 275 GLU cc_start: 0.8435 (tt0) cc_final: 0.8101 (tt0) REVERT: A 284 SER cc_start: 0.8602 (m) cc_final: 0.7325 (t) REVERT: A 287 ARG cc_start: 0.7595 (mtt90) cc_final: 0.7247 (mtt90) REVERT: A 296 SER cc_start: 0.9431 (m) cc_final: 0.9124 (p) REVERT: A 343 GLU cc_start: 0.7435 (mp0) cc_final: 0.7009 (mp0) REVERT: A 346 TRP cc_start: 0.7789 (t-100) cc_final: 0.7346 (t-100) REVERT: A 368 ASN cc_start: 0.9067 (t0) cc_final: 0.8449 (t0) REVERT: A 438 GLN cc_start: 0.8730 (mt0) cc_final: 0.8463 (mt0) REVERT: A 448 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8687 (tm) REVERT: A 454 GLN cc_start: 0.8634 (pt0) cc_final: 0.7924 (pt0) REVERT: A 486 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8619 (mm-30) REVERT: A 508 VAL cc_start: 0.9122 (t) cc_final: 0.8893 (t) REVERT: A 515 GLU cc_start: 0.8928 (tp30) cc_final: 0.7225 (tp30) REVERT: A 545 LYS cc_start: 0.8947 (mmmt) cc_final: 0.8222 (tppp) REVERT: A 594 LYS cc_start: 0.8957 (ttpp) cc_final: 0.8600 (ttmm) REVERT: A 597 HIS cc_start: 0.8360 (m170) cc_final: 0.7852 (m-70) REVERT: A 636 ARG cc_start: 0.9223 (ppp-140) cc_final: 0.8487 (ttp-110) REVERT: A 662 MET cc_start: 0.3808 (mtp) cc_final: 0.2131 (ttp) REVERT: B 207 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8731 (pt) REVERT: B 209 ASN cc_start: 0.8934 (p0) cc_final: 0.8547 (p0) REVERT: B 211 HIS cc_start: 0.9009 (m90) cc_final: 0.8311 (m90) REVERT: B 230 SER cc_start: 0.9577 (m) cc_final: 0.9242 (p) REVERT: B 245 LYS cc_start: 0.9247 (mmtm) cc_final: 0.8943 (mmmm) REVERT: B 267 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8113 (mt-10) REVERT: B 274 ASN cc_start: 0.9175 (t0) cc_final: 0.8529 (t0) REVERT: B 283 ASP cc_start: 0.7666 (m-30) cc_final: 0.7249 (m-30) REVERT: B 287 ARG cc_start: 0.7980 (mtt90) cc_final: 0.7642 (mtt90) REVERT: B 291 LYS cc_start: 0.7811 (tptm) cc_final: 0.7369 (tptt) REVERT: B 364 ILE cc_start: 0.9040 (pt) cc_final: 0.8548 (mp) REVERT: B 368 ASN cc_start: 0.8877 (t0) cc_final: 0.8601 (t0) REVERT: B 375 TYR cc_start: 0.8965 (m-80) cc_final: 0.8475 (m-80) REVERT: B 388 ASN cc_start: 0.8533 (p0) cc_final: 0.7771 (p0) REVERT: B 403 GLN cc_start: 0.9084 (mt0) cc_final: 0.8412 (mt0) REVERT: B 425 ASP cc_start: 0.8484 (m-30) cc_final: 0.8050 (m-30) REVERT: B 430 THR cc_start: 0.8948 (m) cc_final: 0.8701 (m) REVERT: B 443 GLU cc_start: 0.9341 (tp30) cc_final: 0.9097 (tp30) REVERT: B 450 LEU cc_start: 0.8327 (mm) cc_final: 0.8061 (mm) REVERT: B 451 ASP cc_start: 0.7422 (m-30) cc_final: 0.6963 (m-30) REVERT: B 452 THR cc_start: 0.9415 (m) cc_final: 0.9151 (p) REVERT: B 470 ARG cc_start: 0.9072 (ttm110) cc_final: 0.8812 (ttm110) REVERT: B 486 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8739 (mm-30) REVERT: B 525 GLU cc_start: 0.9075 (tp30) cc_final: 0.8098 (tp30) REVERT: B 529 ILE cc_start: 0.9142 (pt) cc_final: 0.8433 (pt) REVERT: B 541 GLN cc_start: 0.8674 (tt0) cc_final: 0.8412 (tt0) REVERT: B 546 ASP cc_start: 0.8763 (t0) cc_final: 0.8531 (t0) REVERT: B 548 THR cc_start: 0.9284 (p) cc_final: 0.8879 (t) REVERT: B 584 ASN cc_start: 0.8811 (m-40) cc_final: 0.8610 (m-40) REVERT: B 586 LYS cc_start: 0.9006 (ttmm) cc_final: 0.8460 (ttmm) REVERT: B 587 MET cc_start: 0.8934 (mtt) cc_final: 0.8543 (mtm) REVERT: C 202 PHE cc_start: 0.8357 (m-10) cc_final: 0.8079 (m-10) REVERT: C 274 ASN cc_start: 0.9020 (t0) cc_final: 0.8426 (t0) REVERT: C 281 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7291 (p0) REVERT: C 335 ASP cc_start: 0.7906 (m-30) cc_final: 0.7664 (m-30) REVERT: C 344 ARG cc_start: 0.8293 (ttp-110) cc_final: 0.7642 (ttp-170) REVERT: C 348 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7525 (mt-10) REVERT: C 350 MET cc_start: 0.8518 (mtt) cc_final: 0.8221 (mtt) REVERT: C 356 ASP cc_start: 0.8096 (t0) cc_final: 0.7416 (t0) REVERT: C 436 TYR cc_start: 0.8613 (t80) cc_final: 0.8177 (t80) REVERT: C 443 GLU cc_start: 0.8526 (tt0) cc_final: 0.8311 (tt0) REVERT: C 447 GLN cc_start: 0.8929 (mt0) cc_final: 0.8633 (mt0) REVERT: C 496 LYS cc_start: 0.9098 (ttmm) cc_final: 0.8886 (tppt) REVERT: C 515 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8807 (mp0) REVERT: C 545 LYS cc_start: 0.8945 (ttmm) cc_final: 0.8431 (ttpt) REVERT: C 546 ASP cc_start: 0.8840 (t0) cc_final: 0.8363 (t0) REVERT: C 549 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8254 (mt-10) REVERT: C 563 LYS cc_start: 0.9282 (tppt) cc_final: 0.9009 (ttmt) REVERT: C 586 LYS cc_start: 0.8802 (mtpp) cc_final: 0.8537 (mttp) REVERT: C 587 MET cc_start: 0.8455 (mtt) cc_final: 0.8127 (mtt) REVERT: C 593 ASP cc_start: 0.8812 (t70) cc_final: 0.8059 (t0) REVERT: C 596 PHE cc_start: 0.9266 (m-80) cc_final: 0.8608 (m-10) REVERT: C 662 MET cc_start: 0.5354 (mtp) cc_final: 0.4260 (ttp) REVERT: D 180 ASN cc_start: 0.9362 (t0) cc_final: 0.9045 (t0) REVERT: D 195 ASP cc_start: 0.8197 (t70) cc_final: 0.7949 (t0) REVERT: D 200 ARG cc_start: 0.8125 (mpp-170) cc_final: 0.7895 (mpp-170) REVERT: D 274 ASN cc_start: 0.9330 (t0) cc_final: 0.8506 (t0) REVERT: D 287 ARG cc_start: 0.8420 (mtt90) cc_final: 0.8079 (mtt90) REVERT: D 356 ASP cc_start: 0.8760 (t70) cc_final: 0.8122 (t70) REVERT: D 387 LYS cc_start: 0.9379 (tptp) cc_final: 0.9107 (tppp) REVERT: D 401 LEU cc_start: 0.9303 (tt) cc_final: 0.9068 (tt) REVERT: D 499 ASN cc_start: 0.8744 (m-40) cc_final: 0.8354 (m-40) REVERT: D 543 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8902 (mp10) REVERT: D 549 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8662 (mt-10) REVERT: D 558 THR cc_start: 0.9157 (m) cc_final: 0.8741 (p) REVERT: D 559 SER cc_start: 0.8579 (t) cc_final: 0.8200 (p) REVERT: D 586 LYS cc_start: 0.9009 (mtpp) cc_final: 0.8742 (mtmm) REVERT: D 593 ASP cc_start: 0.8221 (t0) cc_final: 0.7527 (t0) REVERT: D 596 PHE cc_start: 0.8783 (m-80) cc_final: 0.6933 (m-80) REVERT: D 611 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8920 (p) REVERT: D 614 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8388 (mp0) REVERT: D 637 LYS cc_start: 0.8964 (ttpp) cc_final: 0.8623 (ttpp) REVERT: E 200 ARG cc_start: 0.7094 (mpp80) cc_final: 0.6707 (mpp80) REVERT: E 217 THR cc_start: 0.8902 (m) cc_final: 0.8590 (p) REVERT: E 218 LYS cc_start: 0.9373 (ttpt) cc_final: 0.9116 (ttmt) REVERT: E 219 TYR cc_start: 0.8951 (m-10) cc_final: 0.8453 (m-10) REVERT: E 236 PHE cc_start: 0.9266 (t80) cc_final: 0.9047 (t80) REVERT: E 361 ASN cc_start: 0.8976 (t0) cc_final: 0.8737 (m-40) REVERT: E 366 TYR cc_start: 0.8755 (m-10) cc_final: 0.8377 (m-10) REVERT: E 393 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.9013 (p) REVERT: E 410 TYR cc_start: 0.8842 (m-10) cc_final: 0.8481 (m-10) REVERT: E 422 ASN cc_start: 0.9207 (p0) cc_final: 0.8974 (p0) REVERT: E 435 ASN cc_start: 0.8044 (p0) cc_final: 0.7691 (p0) REVERT: E 436 TYR cc_start: 0.8495 (t80) cc_final: 0.8292 (t80) REVERT: E 443 GLU cc_start: 0.9295 (mt-10) cc_final: 0.9084 (mt-10) REVERT: E 447 GLN cc_start: 0.8993 (mt0) cc_final: 0.8568 (mm110) REVERT: E 462 TYR cc_start: 0.8836 (t80) cc_final: 0.8459 (t80) REVERT: E 464 PHE cc_start: 0.9128 (m-80) cc_final: 0.8908 (m-80) REVERT: E 486 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7956 (mm-30) REVERT: E 494 ASN cc_start: 0.9145 (p0) cc_final: 0.8874 (p0) REVERT: E 499 ASN cc_start: 0.8410 (m-40) cc_final: 0.7720 (m-40) REVERT: E 515 GLU cc_start: 0.8240 (tp30) cc_final: 0.6490 (tp30) REVERT: E 525 GLU cc_start: 0.8843 (tp30) cc_final: 0.8548 (tp30) REVERT: E 541 GLN cc_start: 0.9095 (tt0) cc_final: 0.8641 (tp40) REVERT: E 546 ASP cc_start: 0.8187 (t0) cc_final: 0.7879 (t70) REVERT: E 557 GLN cc_start: 0.8985 (mp-120) cc_final: 0.8724 (mp10) REVERT: E 563 LYS cc_start: 0.9247 (tppt) cc_final: 0.8970 (mtpt) REVERT: E 586 LYS cc_start: 0.9115 (mtpp) cc_final: 0.8528 (mtpp) REVERT: E 587 MET cc_start: 0.9072 (mtt) cc_final: 0.8866 (mtm) REVERT: F 180 ASN cc_start: 0.9586 (t0) cc_final: 0.9294 (t0) REVERT: F 197 LYS cc_start: 0.9137 (tttt) cc_final: 0.8910 (ttmm) REVERT: F 207 ILE cc_start: 0.9181 (tp) cc_final: 0.8824 (tp) REVERT: F 211 HIS cc_start: 0.8767 (m90) cc_final: 0.8294 (m90) REVERT: F 276 ASP cc_start: 0.8014 (p0) cc_final: 0.7653 (p0) REVERT: F 343 GLU cc_start: 0.7637 (mp0) cc_final: 0.7280 (mp0) REVERT: F 391 LEU cc_start: 0.9188 (mt) cc_final: 0.8891 (mt) REVERT: F 430 THR cc_start: 0.9079 (m) cc_final: 0.8419 (p) REVERT: F 443 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8185 (mt-10) REVERT: F 476 ASN cc_start: 0.8971 (p0) cc_final: 0.8580 (p0) REVERT: F 479 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8133 (mt-10) REVERT: F 486 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8243 (mm-30) REVERT: F 496 LYS cc_start: 0.9412 (tttt) cc_final: 0.8764 (tppp) REVERT: F 515 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.7973 (mp0) REVERT: F 535 GLU cc_start: 0.8311 (pt0) cc_final: 0.8008 (pt0) REVERT: F 541 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7524 (tp40) REVERT: F 593 ASP cc_start: 0.8132 (t0) cc_final: 0.7871 (t0) REVERT: F 637 LYS cc_start: 0.9438 (ttmt) cc_final: 0.8894 (ptmt) REVERT: F 703 LYS cc_start: 0.8897 (mmtp) cc_final: 0.8467 (mmtt) REVERT: G 212 GLU cc_start: 0.7887 (tt0) cc_final: 0.7648 (tp30) REVERT: G 238 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8633 (mtpp) REVERT: G 264 VAL cc_start: 0.9561 (t) cc_final: 0.9248 (p) REVERT: G 289 ILE cc_start: 0.7935 (mt) cc_final: 0.7632 (mt) REVERT: G 346 TRP cc_start: 0.7927 (t-100) cc_final: 0.7438 (m-90) REVERT: G 348 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: G 353 ASN cc_start: 0.8569 (t0) cc_final: 0.8172 (t0) REVERT: G 356 ASP cc_start: 0.8604 (t0) cc_final: 0.7988 (t0) REVERT: G 368 ASN cc_start: 0.9123 (t0) cc_final: 0.8851 (t0) REVERT: G 472 ASP cc_start: 0.7603 (t0) cc_final: 0.6985 (t0) REVERT: G 501 VAL cc_start: 0.8030 (t) cc_final: 0.7783 (m) REVERT: G 512 ASP cc_start: 0.8744 (t0) cc_final: 0.8351 (t0) REVERT: G 518 LYS cc_start: 0.8701 (mtmm) cc_final: 0.8426 (mtmm) REVERT: G 525 GLU cc_start: 0.8861 (tp30) cc_final: 0.7787 (tp30) REVERT: G 541 GLN cc_start: 0.7958 (tt0) cc_final: 0.7704 (tt0) REVERT: G 543 GLN cc_start: 0.9444 (mm-40) cc_final: 0.8558 (mm-40) REVERT: G 556 GLN cc_start: 0.9361 (tt0) cc_final: 0.8981 (tm-30) REVERT: G 560 GLN cc_start: 0.8987 (tp40) cc_final: 0.8370 (tp-100) REVERT: G 568 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8291 (mt-10) REVERT: G 573 ASN cc_start: 0.8114 (t0) cc_final: 0.7548 (t0) REVERT: G 582 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8665 (mtmm) REVERT: G 586 LYS cc_start: 0.8965 (mtpp) cc_final: 0.8304 (mttm) REVERT: G 657 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.7497 (m-40) outliers start: 219 outliers final: 157 residues processed: 1378 average time/residue: 0.1815 time to fit residues: 418.8975 Evaluate side-chains 1392 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 1223 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain L residue 102 LYS Chi-restraints excluded: chain L residue 122 LYS Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 250 GLN Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 543 GLN Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 665 ILE Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 636 ARG Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 682 ASN Chi-restraints excluded: chain C residue 703 LYS Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 543 GLN Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain D residue 638 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 537 ASN Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 610 SER Chi-restraints excluded: chain E residue 636 ARG Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 709 ASN Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 263 HIS Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 377 VAL Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 497 ASP Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 515 GLU Chi-restraints excluded: chain F residue 541 GLN Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 713 ASN Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 227 SER Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 263 HIS Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 425 ASP Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain G residue 452 THR Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 594 LYS Chi-restraints excluded: chain G residue 620 ILE Chi-restraints excluded: chain G residue 657 ASN Chi-restraints excluded: chain G residue 665 ILE Chi-restraints excluded: chain G residue 708 ILE Chi-restraints excluded: chain G residue 724 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 199 optimal weight: 0.0980 chunk 202 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 252 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 chunk 334 optimal weight: 5.9990 chunk 105 optimal weight: 0.0770 chunk 371 optimal weight: 20.0000 chunk 375 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 ASN A 556 GLN B 561 ASN B 565 GLN C 198 ASN ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 588 ASN D 198 ASN ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 HIS E 299 HIS ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 GLN F 597 HIS ** G 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 403 GLN G 584 ASN G 616 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.191313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.123805 restraints weight = 46688.948| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.51 r_work: 0.3281 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33385 Z= 0.161 Angle : 0.606 11.796 45291 Z= 0.315 Chirality : 0.047 0.250 5178 Planarity : 0.004 0.079 5938 Dihedral : 5.836 87.613 4532 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.99 % Favored : 95.87 % Rotamer: Outliers : 5.77 % Allowed : 21.21 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.13), residues: 4138 helix: 0.44 (0.22), residues: 638 sheet: 0.98 (0.16), residues: 1055 loop : -0.84 (0.13), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 595 TYR 0.031 0.001 TYR F 411 PHE 0.020 0.002 PHE A 554 TRP 0.012 0.002 TRP F 346 HIS 0.007 0.001 HIS E 263 Details of bonding type rmsd covalent geometry : bond 0.00353 (33385) covalent geometry : angle 0.60589 (45291) hydrogen bonds : bond 0.03109 ( 1183) hydrogen bonds : angle 5.47646 ( 3228) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1493 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 1280 time to evaluate : 1.217 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 LYS cc_start: 0.9413 (mmtm) cc_final: 0.9132 (mmtm) REVERT: A 256 VAL cc_start: 0.9660 (t) cc_final: 0.9388 (p) REVERT: A 274 ASN cc_start: 0.9190 (t0) cc_final: 0.8701 (t0) REVERT: A 275 GLU cc_start: 0.8565 (tt0) cc_final: 0.8292 (tt0) REVERT: A 284 SER cc_start: 0.8807 (m) cc_final: 0.7816 (t) REVERT: A 287 ARG cc_start: 0.7719 (mtt90) cc_final: 0.7393 (mtt90) REVERT: A 296 SER cc_start: 0.9455 (m) cc_final: 0.9170 (p) REVERT: A 343 GLU cc_start: 0.7604 (mp0) cc_final: 0.7154 (mp0) REVERT: A 364 ILE cc_start: 0.9047 (pt) cc_final: 0.8626 (mp) REVERT: A 368 ASN cc_start: 0.9059 (t0) cc_final: 0.8461 (t0) REVERT: A 389 GLN cc_start: 0.8159 (tt0) cc_final: 0.7861 (tt0) REVERT: A 448 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8511 (tm) REVERT: A 454 GLN cc_start: 0.8577 (pt0) cc_final: 0.7634 (pt0) REVERT: A 486 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8535 (mm-30) REVERT: A 515 GLU cc_start: 0.9009 (tp30) cc_final: 0.7367 (tp30) REVERT: A 545 LYS cc_start: 0.8952 (mmmt) cc_final: 0.8149 (tptp) REVERT: A 549 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8523 (mt-10) REVERT: A 587 MET cc_start: 0.8907 (mtp) cc_final: 0.8352 (mtp) REVERT: A 594 LYS cc_start: 0.9001 (ttpp) cc_final: 0.8689 (ttmm) REVERT: A 597 HIS cc_start: 0.8376 (m170) cc_final: 0.7941 (m90) REVERT: A 662 MET cc_start: 0.3965 (mtp) cc_final: 0.2334 (ttp) REVERT: B 211 HIS cc_start: 0.8966 (m90) cc_final: 0.8447 (m90) REVERT: B 230 SER cc_start: 0.9583 (m) cc_final: 0.9223 (p) REVERT: B 245 LYS cc_start: 0.9329 (mmtm) cc_final: 0.9071 (mmmm) REVERT: B 253 HIS cc_start: 0.9164 (t-90) cc_final: 0.8917 (t-90) REVERT: B 259 TYR cc_start: 0.9259 (p90) cc_final: 0.9001 (p90) REVERT: B 274 ASN cc_start: 0.9167 (t0) cc_final: 0.8644 (t0) REVERT: B 287 ARG cc_start: 0.8163 (mtt90) cc_final: 0.7833 (mtt90) REVERT: B 291 LYS cc_start: 0.7925 (tptm) cc_final: 0.7462 (tptt) REVERT: B 364 ILE cc_start: 0.9069 (pt) cc_final: 0.8678 (mp) REVERT: B 365 ARG cc_start: 0.9089 (mtt-85) cc_final: 0.8867 (mtt-85) REVERT: B 368 ASN cc_start: 0.8919 (t0) cc_final: 0.8699 (t0) REVERT: B 375 TYR cc_start: 0.8994 (m-80) cc_final: 0.8589 (m-80) REVERT: B 388 ASN cc_start: 0.8546 (p0) cc_final: 0.7878 (p0) REVERT: B 399 ASN cc_start: 0.9429 (m-40) cc_final: 0.9204 (m-40) REVERT: B 403 GLN cc_start: 0.9039 (mt0) cc_final: 0.8216 (mt0) REVERT: B 425 ASP cc_start: 0.8519 (m-30) cc_final: 0.7977 (m-30) REVERT: B 430 THR cc_start: 0.9038 (m) cc_final: 0.8771 (m) REVERT: B 443 GLU cc_start: 0.9317 (tp30) cc_final: 0.9053 (tp30) REVERT: B 470 ARG cc_start: 0.9094 (ttm110) cc_final: 0.8870 (ttm110) REVERT: B 486 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8840 (mm-30) REVERT: B 525 GLU cc_start: 0.9005 (tp30) cc_final: 0.8013 (tp30) REVERT: B 529 ILE cc_start: 0.9144 (pt) cc_final: 0.8371 (pt) REVERT: B 546 ASP cc_start: 0.8838 (t0) cc_final: 0.8625 (t0) REVERT: B 548 THR cc_start: 0.9252 (p) cc_final: 0.8788 (t) REVERT: B 553 ASN cc_start: 0.8121 (m-40) cc_final: 0.7716 (m-40) REVERT: B 586 LYS cc_start: 0.9072 (ttmm) cc_final: 0.8527 (ttmm) REVERT: B 587 MET cc_start: 0.8915 (mtt) cc_final: 0.8675 (mtt) REVERT: B 662 MET cc_start: 0.8479 (ttm) cc_final: 0.8202 (ttm) REVERT: B 689 ILE cc_start: 0.6447 (OUTLIER) cc_final: 0.6223 (mp) REVERT: B 718 THR cc_start: 0.5674 (OUTLIER) cc_final: 0.5420 (m) REVERT: C 185 ASP cc_start: 0.8786 (p0) cc_final: 0.8571 (p0) REVERT: C 202 PHE cc_start: 0.8459 (m-10) cc_final: 0.8135 (m-10) REVERT: C 227 SER cc_start: 0.9291 (OUTLIER) cc_final: 0.9087 (p) REVERT: C 274 ASN cc_start: 0.9021 (t0) cc_final: 0.8395 (t0) REVERT: C 281 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7260 (p0) REVERT: C 344 ARG cc_start: 0.8331 (ttp-110) cc_final: 0.7814 (ttp-170) REVERT: C 348 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7397 (mt-10) REVERT: C 356 ASP cc_start: 0.8183 (t0) cc_final: 0.7505 (t0) REVERT: C 436 TYR cc_start: 0.8690 (t80) cc_final: 0.8177 (t80) REVERT: C 443 GLU cc_start: 0.8508 (tt0) cc_final: 0.8260 (tt0) REVERT: C 447 GLN cc_start: 0.9058 (mt0) cc_final: 0.8728 (mt0) REVERT: C 496 LYS cc_start: 0.9084 (ttmm) cc_final: 0.8878 (tppt) REVERT: C 515 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8728 (mp0) REVERT: C 545 LYS cc_start: 0.8972 (ttmm) cc_final: 0.8425 (ttpt) REVERT: C 546 ASP cc_start: 0.8784 (t0) cc_final: 0.8478 (t0) REVERT: C 549 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8218 (mt-10) REVERT: C 555 ASP cc_start: 0.8238 (p0) cc_final: 0.7859 (p0) REVERT: C 563 LYS cc_start: 0.9245 (tppt) cc_final: 0.8982 (ttmt) REVERT: C 586 LYS cc_start: 0.8847 (mtpp) cc_final: 0.8585 (mttp) REVERT: C 587 MET cc_start: 0.8306 (mtt) cc_final: 0.8044 (mtt) REVERT: C 593 ASP cc_start: 0.8767 (t70) cc_final: 0.8276 (t0) REVERT: C 662 MET cc_start: 0.5332 (mtp) cc_final: 0.4233 (ttp) REVERT: D 180 ASN cc_start: 0.9380 (t0) cc_final: 0.9067 (t0) REVERT: D 195 ASP cc_start: 0.8158 (t70) cc_final: 0.7911 (t0) REVERT: D 259 TYR cc_start: 0.9294 (p90) cc_final: 0.9075 (p90) REVERT: D 274 ASN cc_start: 0.9268 (t0) cc_final: 0.8507 (t0) REVERT: D 297 ARG cc_start: 0.8386 (tpp80) cc_final: 0.7606 (mmm-85) REVERT: D 356 ASP cc_start: 0.8835 (t70) cc_final: 0.8187 (t70) REVERT: D 387 LYS cc_start: 0.9367 (tptp) cc_final: 0.9122 (tppp) REVERT: D 401 LEU cc_start: 0.9270 (tt) cc_final: 0.9035 (tt) REVERT: D 499 ASN cc_start: 0.8740 (m-40) cc_final: 0.8340 (m-40) REVERT: D 549 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8596 (mt-10) REVERT: D 559 SER cc_start: 0.8602 (t) cc_final: 0.8276 (p) REVERT: D 586 LYS cc_start: 0.9048 (mtpp) cc_final: 0.8841 (mtmm) REVERT: D 593 ASP cc_start: 0.8200 (t0) cc_final: 0.7928 (t0) REVERT: D 596 PHE cc_start: 0.8539 (m-80) cc_final: 0.7957 (m-80) REVERT: D 637 LYS cc_start: 0.8954 (ttpp) cc_final: 0.8661 (ttpp) REVERT: E 180 ASN cc_start: 0.9493 (t0) cc_final: 0.9102 (t0) REVERT: E 200 ARG cc_start: 0.7144 (mpp80) cc_final: 0.6668 (mpp80) REVERT: E 217 THR cc_start: 0.8934 (m) cc_final: 0.8602 (p) REVERT: E 218 LYS cc_start: 0.9337 (ttpt) cc_final: 0.9091 (ttmt) REVERT: E 219 TYR cc_start: 0.8968 (m-10) cc_final: 0.8326 (m-10) REVERT: E 236 PHE cc_start: 0.9299 (t80) cc_final: 0.9085 (t80) REVERT: E 285 GLN cc_start: 0.8407 (mt0) cc_final: 0.8180 (mt0) REVERT: E 287 ARG cc_start: 0.8274 (mtt90) cc_final: 0.8035 (mtt90) REVERT: E 366 TYR cc_start: 0.8714 (m-10) cc_final: 0.8317 (m-10) REVERT: E 393 THR cc_start: 0.9350 (OUTLIER) cc_final: 0.9104 (p) REVERT: E 422 ASN cc_start: 0.9130 (p0) cc_final: 0.8803 (p0) REVERT: E 447 GLN cc_start: 0.8978 (mt0) cc_final: 0.8570 (mm110) REVERT: E 462 TYR cc_start: 0.8786 (t80) cc_final: 0.8373 (t80) REVERT: E 464 PHE cc_start: 0.9134 (m-80) cc_final: 0.8918 (m-10) REVERT: E 476 ASN cc_start: 0.9002 (p0) cc_final: 0.8754 (p0) REVERT: E 486 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7912 (mm-30) REVERT: E 494 ASN cc_start: 0.9192 (p0) cc_final: 0.8908 (p0) REVERT: E 496 LYS cc_start: 0.8389 (tppt) cc_final: 0.8111 (ttmm) REVERT: E 499 ASN cc_start: 0.8474 (m-40) cc_final: 0.7775 (m-40) REVERT: E 514 LEU cc_start: 0.9287 (tp) cc_final: 0.9036 (tt) REVERT: E 515 GLU cc_start: 0.8150 (tp30) cc_final: 0.6669 (tp30) REVERT: E 518 LYS cc_start: 0.8827 (mtmt) cc_final: 0.7791 (ptpp) REVERT: E 525 GLU cc_start: 0.8819 (tp30) cc_final: 0.8511 (tp30) REVERT: E 541 GLN cc_start: 0.9039 (tt0) cc_final: 0.8625 (tp40) REVERT: E 546 ASP cc_start: 0.8315 (t0) cc_final: 0.8005 (t70) REVERT: E 557 GLN cc_start: 0.8976 (mp-120) cc_final: 0.8699 (mp10) REVERT: E 563 LYS cc_start: 0.9257 (tppt) cc_final: 0.8978 (mtpt) REVERT: E 586 LYS cc_start: 0.9065 (mtpp) cc_final: 0.8400 (mtpp) REVERT: E 587 MET cc_start: 0.9019 (mtt) cc_final: 0.8816 (mtm) REVERT: E 593 ASP cc_start: 0.8750 (t0) cc_final: 0.8334 (t0) REVERT: F 180 ASN cc_start: 0.9580 (t0) cc_final: 0.9303 (t0) REVERT: F 207 ILE cc_start: 0.9167 (tp) cc_final: 0.8819 (tp) REVERT: F 211 HIS cc_start: 0.8775 (m90) cc_final: 0.8321 (m90) REVERT: F 228 THR cc_start: 0.9422 (OUTLIER) cc_final: 0.9097 (p) REVERT: F 276 ASP cc_start: 0.8406 (p0) cc_final: 0.8043 (p0) REVERT: F 430 THR cc_start: 0.9102 (m) cc_final: 0.8473 (p) REVERT: F 443 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8174 (mt-10) REVERT: F 476 ASN cc_start: 0.8979 (p0) cc_final: 0.8632 (p0) REVERT: F 479 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8113 (mt-10) REVERT: F 486 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8296 (mm-30) REVERT: F 496 LYS cc_start: 0.9375 (tttt) cc_final: 0.8755 (tppp) REVERT: F 535 GLU cc_start: 0.8287 (pt0) cc_final: 0.8014 (pt0) REVERT: F 587 MET cc_start: 0.8997 (mtt) cc_final: 0.8260 (mtt) REVERT: F 593 ASP cc_start: 0.8177 (t0) cc_final: 0.7773 (t0) REVERT: F 637 LYS cc_start: 0.9405 (ttmt) cc_final: 0.8864 (ptmt) REVERT: F 662 MET cc_start: 0.3393 (ttt) cc_final: 0.2499 (ttp) REVERT: F 703 LYS cc_start: 0.8832 (mmtp) cc_final: 0.8615 (mmtm) REVERT: G 178 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8535 (mtt180) REVERT: G 212 GLU cc_start: 0.7859 (tt0) cc_final: 0.7631 (tp30) REVERT: G 238 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8663 (mtpp) REVERT: G 264 VAL cc_start: 0.9579 (t) cc_final: 0.9265 (p) REVERT: G 346 TRP cc_start: 0.8047 (t-100) cc_final: 0.7635 (m-90) REVERT: G 348 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7902 (tt0) REVERT: G 353 ASN cc_start: 0.8477 (t0) cc_final: 0.8096 (t0) REVERT: G 356 ASP cc_start: 0.8661 (t0) cc_final: 0.7921 (t0) REVERT: G 368 ASN cc_start: 0.9021 (t0) cc_final: 0.8797 (t0) REVERT: G 472 ASP cc_start: 0.7653 (t0) cc_final: 0.6984 (t0) REVERT: G 501 VAL cc_start: 0.8156 (t) cc_final: 0.7890 (m) REVERT: G 512 ASP cc_start: 0.8823 (t0) cc_final: 0.8481 (t0) REVERT: G 518 LYS cc_start: 0.9035 (mtmm) cc_final: 0.8788 (mtmm) REVERT: G 525 GLU cc_start: 0.8778 (tp30) cc_final: 0.7792 (tp30) REVERT: G 541 GLN cc_start: 0.8017 (tt0) cc_final: 0.7752 (tt0) REVERT: G 543 GLN cc_start: 0.9395 (mm-40) cc_final: 0.8968 (mm-40) REVERT: G 556 GLN cc_start: 0.9339 (tt0) cc_final: 0.9018 (tm-30) REVERT: G 560 GLN cc_start: 0.8999 (tp40) cc_final: 0.8323 (tp-100) REVERT: G 568 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8332 (mt-10) REVERT: G 573 ASN cc_start: 0.8304 (t0) cc_final: 0.7739 (t0) REVERT: G 582 LYS cc_start: 0.8970 (mmtt) cc_final: 0.8719 (mtmm) REVERT: G 586 LYS cc_start: 0.9005 (mtpp) cc_final: 0.8255 (mttm) REVERT: G 595 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7312 (ptm160) REVERT: G 657 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.7491 (m-40) outliers start: 213 outliers final: 160 residues processed: 1363 average time/residue: 0.1808 time to fit residues: 413.3451 Evaluate side-chains 1385 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 1212 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 40 MET Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain L residue 102 LYS Chi-restraints excluded: chain L residue 120 TYR Chi-restraints excluded: chain L residue 122 LYS Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 250 GLN Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 543 GLN Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 636 ARG Chi-restraints excluded: chain C residue 703 LYS Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 374 ILE Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 537 ASN Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 709 ASN Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 263 HIS Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 410 TYR Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 515 GLU Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 713 ASN Chi-restraints excluded: chain G residue 178 ARG Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 227 SER Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 263 HIS Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain G residue 452 THR Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 569 LEU Chi-restraints excluded: chain G residue 595 ARG Chi-restraints excluded: chain G residue 620 ILE Chi-restraints excluded: chain G residue 657 ASN Chi-restraints excluded: chain G residue 665 ILE Chi-restraints excluded: chain G residue 724 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 70 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 337 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 297 optimal weight: 30.0000 chunk 215 optimal weight: 3.9990 chunk 361 optimal weight: 0.2980 chunk 382 optimal weight: 0.0000 chunk 90 optimal weight: 8.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 ASN A 556 GLN A 557 GLN A 565 GLN A 584 ASN B 180 ASN B 438 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 ASN B 565 GLN ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN D 280 GLN ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 HIS ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 363 ASN ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 403 GLN G 458 ASN G 616 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.193660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.126900 restraints weight = 46533.828| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 3.51 r_work: 0.3324 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 33385 Z= 0.105 Angle : 0.586 11.066 45291 Z= 0.301 Chirality : 0.047 0.188 5178 Planarity : 0.003 0.079 5938 Dihedral : 5.444 70.883 4524 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.70 % Favored : 96.16 % Rotamer: Outliers : 5.01 % Allowed : 22.79 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.13), residues: 4138 helix: 0.55 (0.22), residues: 639 sheet: 1.25 (0.16), residues: 974 loop : -0.86 (0.13), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 595 TYR 0.022 0.001 TYR F 411 PHE 0.027 0.001 PHE E 439 TRP 0.016 0.001 TRP F 346 HIS 0.007 0.001 HIS E 263 Details of bonding type rmsd covalent geometry : bond 0.00231 (33385) covalent geometry : angle 0.58604 (45291) hydrogen bonds : bond 0.02804 ( 1183) hydrogen bonds : angle 5.29237 ( 3228) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1488 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 1303 time to evaluate : 1.266 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 LYS cc_start: 0.9419 (mmtm) cc_final: 0.9142 (mmtm) REVERT: A 256 VAL cc_start: 0.9655 (t) cc_final: 0.9374 (p) REVERT: A 274 ASN cc_start: 0.9159 (t0) cc_final: 0.8948 (t0) REVERT: A 275 GLU cc_start: 0.8545 (tt0) cc_final: 0.8208 (tt0) REVERT: A 287 ARG cc_start: 0.7632 (mtt90) cc_final: 0.7276 (mtt90) REVERT: A 296 SER cc_start: 0.9449 (m) cc_final: 0.9160 (p) REVERT: A 364 ILE cc_start: 0.9085 (pt) cc_final: 0.8568 (mp) REVERT: A 368 ASN cc_start: 0.9022 (t0) cc_final: 0.8509 (t0) REVERT: A 448 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8447 (tm) REVERT: A 454 GLN cc_start: 0.8616 (pt0) cc_final: 0.7697 (pt0) REVERT: A 486 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8563 (mm-30) REVERT: A 545 LYS cc_start: 0.8843 (mmmt) cc_final: 0.8053 (tptp) REVERT: A 549 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8423 (mt-10) REVERT: A 587 MET cc_start: 0.8911 (mtp) cc_final: 0.8292 (mtp) REVERT: A 597 HIS cc_start: 0.8339 (m170) cc_final: 0.7935 (m90) REVERT: A 662 MET cc_start: 0.4006 (mtp) cc_final: 0.2335 (ttp) REVERT: B 200 ARG cc_start: 0.8795 (mpp-170) cc_final: 0.8497 (mtm180) REVERT: B 211 HIS cc_start: 0.8939 (m90) cc_final: 0.8395 (m90) REVERT: B 219 TYR cc_start: 0.8791 (m-80) cc_final: 0.8494 (m-10) REVERT: B 253 HIS cc_start: 0.9124 (t-90) cc_final: 0.8788 (t-90) REVERT: B 267 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8167 (mt-10) REVERT: B 274 ASN cc_start: 0.9186 (t0) cc_final: 0.8640 (t0) REVERT: B 287 ARG cc_start: 0.8066 (mtt90) cc_final: 0.7784 (mtt90) REVERT: B 291 LYS cc_start: 0.8017 (tptm) cc_final: 0.7506 (tptt) REVERT: B 364 ILE cc_start: 0.8977 (pt) cc_final: 0.8567 (mp) REVERT: B 375 TYR cc_start: 0.8952 (m-80) cc_final: 0.8473 (m-80) REVERT: B 388 ASN cc_start: 0.8501 (p0) cc_final: 0.7892 (p0) REVERT: B 399 ASN cc_start: 0.9418 (m-40) cc_final: 0.9184 (m-40) REVERT: B 403 GLN cc_start: 0.9049 (mt0) cc_final: 0.8215 (mt0) REVERT: B 425 ASP cc_start: 0.8541 (m-30) cc_final: 0.7736 (m-30) REVERT: B 430 THR cc_start: 0.8751 (m) cc_final: 0.8461 (m) REVERT: B 470 ARG cc_start: 0.9080 (ttm110) cc_final: 0.8864 (ttm110) REVERT: B 486 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8727 (mm-30) REVERT: B 525 GLU cc_start: 0.8979 (tp30) cc_final: 0.7977 (tp30) REVERT: B 529 ILE cc_start: 0.9114 (pt) cc_final: 0.8334 (pt) REVERT: B 541 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8171 (tt0) REVERT: B 543 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8290 (mm-40) REVERT: B 546 ASP cc_start: 0.8649 (t0) cc_final: 0.8421 (t0) REVERT: B 548 THR cc_start: 0.9239 (p) cc_final: 0.8789 (t) REVERT: B 553 ASN cc_start: 0.8064 (m-40) cc_final: 0.7619 (m-40) REVERT: B 586 LYS cc_start: 0.9086 (ttmm) cc_final: 0.8508 (ttmm) REVERT: B 587 MET cc_start: 0.8943 (mtt) cc_final: 0.8729 (mtt) REVERT: B 662 MET cc_start: 0.8316 (ttm) cc_final: 0.7702 (ttt) REVERT: B 718 THR cc_start: 0.5662 (OUTLIER) cc_final: 0.5436 (m) REVERT: C 185 ASP cc_start: 0.8813 (p0) cc_final: 0.8537 (p0) REVERT: C 202 PHE cc_start: 0.8422 (m-10) cc_final: 0.8112 (m-10) REVERT: C 348 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7413 (mt-10) REVERT: C 356 ASP cc_start: 0.8149 (t0) cc_final: 0.7509 (t0) REVERT: C 438 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8634 (mt0) REVERT: C 443 GLU cc_start: 0.8465 (tt0) cc_final: 0.8211 (tt0) REVERT: C 496 LYS cc_start: 0.9058 (ttmm) cc_final: 0.8851 (tppt) REVERT: C 515 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8745 (mp0) REVERT: C 545 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8429 (ttpt) REVERT: C 546 ASP cc_start: 0.8751 (t0) cc_final: 0.8444 (t0) REVERT: C 549 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8418 (mt-10) REVERT: C 563 LYS cc_start: 0.9204 (tppt) cc_final: 0.8958 (ttmt) REVERT: C 586 LYS cc_start: 0.8783 (mtpp) cc_final: 0.8542 (mttp) REVERT: C 587 MET cc_start: 0.8194 (mtt) cc_final: 0.7867 (mtt) REVERT: C 592 ARG cc_start: 0.8018 (mtm-85) cc_final: 0.7756 (mtm-85) REVERT: C 593 ASP cc_start: 0.8707 (t70) cc_final: 0.8175 (t0) REVERT: C 595 ARG cc_start: 0.8976 (mtm180) cc_final: 0.8744 (mtm-85) REVERT: C 662 MET cc_start: 0.5357 (mtp) cc_final: 0.4262 (ttp) REVERT: D 180 ASN cc_start: 0.9388 (t0) cc_final: 0.9058 (t0) REVERT: D 195 ASP cc_start: 0.8130 (t70) cc_final: 0.7895 (t0) REVERT: D 212 GLU cc_start: 0.9130 (tt0) cc_final: 0.8918 (tt0) REVERT: D 216 LEU cc_start: 0.9015 (mt) cc_final: 0.8765 (mp) REVERT: D 297 ARG cc_start: 0.8400 (tpp80) cc_final: 0.7580 (mmm-85) REVERT: D 344 ARG cc_start: 0.8039 (ttp-170) cc_final: 0.7740 (ttp-170) REVERT: D 356 ASP cc_start: 0.8803 (t70) cc_final: 0.8312 (t70) REVERT: D 387 LYS cc_start: 0.9389 (tptp) cc_final: 0.9148 (tppp) REVERT: D 401 LEU cc_start: 0.9174 (tt) cc_final: 0.8861 (tt) REVERT: D 476 ASN cc_start: 0.9165 (p0) cc_final: 0.8494 (p0) REVERT: D 499 ASN cc_start: 0.8635 (m-40) cc_final: 0.8208 (m-40) REVERT: D 549 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8618 (mt-10) REVERT: D 586 LYS cc_start: 0.9001 (mtpp) cc_final: 0.8768 (mtmm) REVERT: D 593 ASP cc_start: 0.8034 (t0) cc_final: 0.7637 (t0) REVERT: D 596 PHE cc_start: 0.8476 (m-80) cc_final: 0.7803 (m-80) REVERT: D 614 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8567 (mp0) REVERT: D 637 LYS cc_start: 0.8905 (ttpp) cc_final: 0.8641 (ttpp) REVERT: E 180 ASN cc_start: 0.9490 (t0) cc_final: 0.9052 (t0) REVERT: E 184 PRO cc_start: 0.8913 (Cg_exo) cc_final: 0.8642 (Cg_endo) REVERT: E 200 ARG cc_start: 0.7104 (mpp80) cc_final: 0.6608 (mpp80) REVERT: E 217 THR cc_start: 0.8926 (m) cc_final: 0.8572 (p) REVERT: E 218 LYS cc_start: 0.9318 (ttpt) cc_final: 0.9044 (ttmt) REVERT: E 219 TYR cc_start: 0.8935 (m-10) cc_final: 0.8322 (m-10) REVERT: E 236 PHE cc_start: 0.9258 (t80) cc_final: 0.9047 (t80) REVERT: E 289 ILE cc_start: 0.8871 (mt) cc_final: 0.8646 (mt) REVERT: E 366 TYR cc_start: 0.8707 (m-10) cc_final: 0.8357 (m-10) REVERT: E 393 THR cc_start: 0.9289 (OUTLIER) cc_final: 0.9066 (p) REVERT: E 422 ASN cc_start: 0.9104 (p0) cc_final: 0.8744 (p0) REVERT: E 447 GLN cc_start: 0.8952 (mt0) cc_final: 0.8516 (mm110) REVERT: E 462 TYR cc_start: 0.8803 (t80) cc_final: 0.8464 (t80) REVERT: E 476 ASN cc_start: 0.8973 (p0) cc_final: 0.8712 (p0) REVERT: E 486 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7808 (mm-30) REVERT: E 494 ASN cc_start: 0.9103 (p0) cc_final: 0.8842 (p0) REVERT: E 499 ASN cc_start: 0.8330 (m-40) cc_final: 0.7647 (m-40) REVERT: E 514 LEU cc_start: 0.9276 (tp) cc_final: 0.9050 (tt) REVERT: E 515 GLU cc_start: 0.8030 (tp30) cc_final: 0.6551 (tp30) REVERT: E 518 LYS cc_start: 0.8845 (mtmt) cc_final: 0.7911 (ptpp) REVERT: E 525 GLU cc_start: 0.8675 (tp30) cc_final: 0.8330 (tp30) REVERT: E 541 GLN cc_start: 0.9017 (tt0) cc_final: 0.8606 (tp40) REVERT: E 546 ASP cc_start: 0.8135 (t0) cc_final: 0.7783 (t70) REVERT: E 563 LYS cc_start: 0.9225 (tppt) cc_final: 0.8942 (mtpt) REVERT: E 586 LYS cc_start: 0.9058 (mtpp) cc_final: 0.8446 (mtpp) REVERT: E 587 MET cc_start: 0.9035 (mtt) cc_final: 0.8766 (mtm) REVERT: E 588 ASN cc_start: 0.8851 (m-40) cc_final: 0.8471 (m-40) REVERT: E 593 ASP cc_start: 0.8900 (t0) cc_final: 0.8461 (t0) REVERT: F 180 ASN cc_start: 0.9573 (t0) cc_final: 0.9274 (t0) REVERT: F 276 ASP cc_start: 0.8457 (p0) cc_final: 0.8042 (p0) REVERT: F 430 THR cc_start: 0.9121 (m) cc_final: 0.8524 (p) REVERT: F 443 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8179 (mt-10) REVERT: F 476 ASN cc_start: 0.8889 (p0) cc_final: 0.8557 (p0) REVERT: F 479 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7812 (mt-10) REVERT: F 496 LYS cc_start: 0.9361 (tttt) cc_final: 0.8741 (tppp) REVERT: F 535 GLU cc_start: 0.8331 (pt0) cc_final: 0.8045 (pt0) REVERT: F 575 TYR cc_start: 0.9054 (m-10) cc_final: 0.8468 (m-10) REVERT: F 587 MET cc_start: 0.8956 (mtt) cc_final: 0.8183 (mtt) REVERT: F 593 ASP cc_start: 0.8177 (t0) cc_final: 0.7710 (t0) REVERT: F 662 MET cc_start: 0.3398 (ttt) cc_final: 0.2539 (ttp) REVERT: F 703 LYS cc_start: 0.8876 (mmtp) cc_final: 0.8503 (mmtm) REVERT: G 178 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8518 (mtt90) REVERT: G 264 VAL cc_start: 0.9560 (t) cc_final: 0.9290 (p) REVERT: G 346 TRP cc_start: 0.8005 (t-100) cc_final: 0.7597 (m-90) REVERT: G 348 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7832 (tt0) REVERT: G 353 ASN cc_start: 0.8384 (t0) cc_final: 0.7981 (t0) REVERT: G 356 ASP cc_start: 0.8606 (t0) cc_final: 0.7860 (t0) REVERT: G 368 ASN cc_start: 0.9015 (t0) cc_final: 0.8726 (t0) REVERT: G 403 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8759 (mt0) REVERT: G 419 ILE cc_start: 0.8893 (pp) cc_final: 0.8501 (pp) REVERT: G 430 THR cc_start: 0.8865 (m) cc_final: 0.8437 (p) REVERT: G 472 ASP cc_start: 0.7634 (t0) cc_final: 0.6860 (t0) REVERT: G 512 ASP cc_start: 0.8806 (t0) cc_final: 0.8446 (t0) REVERT: G 518 LYS cc_start: 0.8993 (mtmm) cc_final: 0.8738 (mtmm) REVERT: G 525 GLU cc_start: 0.8791 (tp30) cc_final: 0.7770 (tp30) REVERT: G 541 GLN cc_start: 0.8043 (tt0) cc_final: 0.7759 (tt0) REVERT: G 543 GLN cc_start: 0.9404 (mm-40) cc_final: 0.8963 (mm-40) REVERT: G 556 GLN cc_start: 0.9329 (tt0) cc_final: 0.9017 (tm-30) REVERT: G 560 GLN cc_start: 0.8997 (tp40) cc_final: 0.8307 (tp-100) REVERT: G 568 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8266 (mt-10) REVERT: G 573 ASN cc_start: 0.8275 (t0) cc_final: 0.7677 (t0) REVERT: G 582 LYS cc_start: 0.9020 (mmtt) cc_final: 0.8719 (mtmm) REVERT: G 595 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7219 (ptm160) REVERT: G 657 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7500 (m-40) outliers start: 185 outliers final: 139 residues processed: 1369 average time/residue: 0.1845 time to fit residues: 423.6700 Evaluate side-chains 1409 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 1257 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 40 MET Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain L residue 102 LYS Chi-restraints excluded: chain L residue 120 TYR Chi-restraints excluded: chain L residue 122 LYS Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 250 GLN Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain B residue 543 GLN Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 545 LYS Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 636 ARG Chi-restraints excluded: chain C residue 703 LYS Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain D residue 638 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 374 ILE Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 537 ASN Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 263 HIS Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 515 GLU Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 713 ASN Chi-restraints excluded: chain G residue 178 ARG Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain G residue 425 ASP Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain G residue 452 THR Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 569 LEU Chi-restraints excluded: chain G residue 595 ARG Chi-restraints excluded: chain G residue 620 ILE Chi-restraints excluded: chain G residue 657 ASN Chi-restraints excluded: chain G residue 665 ILE Chi-restraints excluded: chain G residue 675 PHE Chi-restraints excluded: chain G residue 724 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 400 optimal weight: 1.9990 chunk 314 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 346 optimal weight: 8.9990 chunk 370 optimal weight: 20.0000 chunk 100 optimal weight: 0.8980 chunk 360 optimal weight: 3.9990 chunk 289 optimal weight: 0.6980 chunk 200 optimal weight: 2.9990 chunk 331 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN A 408 ASN A 556 GLN A 565 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 GLN B 584 ASN B 693 ASN ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 HIS ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 556 GLN E 299 HIS ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 616 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.188747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.120773 restraints weight = 46729.789| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.48 r_work: 0.3238 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 33385 Z= 0.201 Angle : 0.625 10.824 45291 Z= 0.328 Chirality : 0.048 0.215 5178 Planarity : 0.004 0.080 5938 Dihedral : 5.492 69.712 4522 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.52 % Favored : 95.31 % Rotamer: Outliers : 6.29 % Allowed : 22.84 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.13), residues: 4138 helix: 0.49 (0.22), residues: 644 sheet: 1.30 (0.16), residues: 982 loop : -0.89 (0.13), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 595 TYR 0.034 0.002 TYR F 411 PHE 0.034 0.002 PHE E 439 TRP 0.025 0.002 TRP A 206 HIS 0.006 0.001 HIS F 211 Details of bonding type rmsd covalent geometry : bond 0.00435 (33385) covalent geometry : angle 0.62543 (45291) hydrogen bonds : bond 0.03235 ( 1183) hydrogen bonds : angle 5.33195 ( 3228) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1478 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 1246 time to evaluate : 1.210 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: 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 245 LYS cc_start: 0.9482 (mmtm) cc_final: 0.9166 (mmtm) REVERT: A 250 GLU cc_start: 0.8945 (pm20) cc_final: 0.8705 (pm20) REVERT: A 256 VAL cc_start: 0.9683 (t) cc_final: 0.9419 (p) REVERT: A 274 ASN cc_start: 0.9204 (t0) cc_final: 0.8696 (t0) REVERT: A 275 GLU cc_start: 0.8594 (tt0) cc_final: 0.8351 (tt0) REVERT: A 287 ARG cc_start: 0.7827 (mtt90) cc_final: 0.7498 (mtt90) REVERT: A 290 SER cc_start: 0.9023 (m) cc_final: 0.8805 (t) REVERT: A 296 SER cc_start: 0.9437 (m) cc_final: 0.9220 (p) REVERT: A 368 ASN cc_start: 0.9002 (t0) cc_final: 0.8525 (t0) REVERT: A 389 GLN cc_start: 0.8432 (tt0) cc_final: 0.8197 (tt0) REVERT: A 411 TYR cc_start: 0.8954 (t80) cc_final: 0.8446 (t80) REVERT: A 448 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8534 (tm) REVERT: A 451 ASP cc_start: 0.7593 (m-30) cc_final: 0.7078 (m-30) REVERT: A 486 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8727 (mm-30) REVERT: A 587 MET cc_start: 0.8961 (mtp) cc_final: 0.8134 (mtm) REVERT: A 594 LYS cc_start: 0.8962 (ttpp) cc_final: 0.8713 (ttmm) REVERT: A 597 HIS cc_start: 0.8399 (m170) cc_final: 0.7861 (m90) REVERT: A 662 MET cc_start: 0.4568 (mtp) cc_final: 0.3150 (ttp) REVERT: B 200 ARG cc_start: 0.8967 (mpp-170) cc_final: 0.8608 (mtm180) REVERT: B 211 HIS cc_start: 0.8990 (m90) cc_final: 0.8490 (m90) REVERT: B 219 TYR cc_start: 0.8882 (m-80) cc_final: 0.8577 (m-10) REVERT: B 259 TYR cc_start: 0.9326 (p90) cc_final: 0.8944 (p90) REVERT: B 274 ASN cc_start: 0.9186 (t0) cc_final: 0.8717 (t0) REVERT: B 281 ASN cc_start: 0.8930 (t0) cc_final: 0.8661 (m-40) REVERT: B 287 ARG cc_start: 0.8240 (mtt90) cc_final: 0.7990 (mtt90) REVERT: B 291 LYS cc_start: 0.8243 (tptm) cc_final: 0.7623 (tptt) REVERT: B 361 ASN cc_start: 0.9032 (t0) cc_final: 0.8640 (t0) REVERT: B 364 ILE cc_start: 0.9129 (pt) cc_final: 0.8709 (mp) REVERT: B 375 TYR cc_start: 0.9091 (m-80) cc_final: 0.8705 (m-80) REVERT: B 388 ASN cc_start: 0.8638 (p0) cc_final: 0.8032 (p0) REVERT: B 399 ASN cc_start: 0.9490 (m-40) cc_final: 0.9290 (m-40) REVERT: B 403 GLN cc_start: 0.9042 (mt0) cc_final: 0.8324 (mt0) REVERT: B 425 ASP cc_start: 0.8494 (m-30) cc_final: 0.8080 (m-30) REVERT: B 440 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9231 (mm) REVERT: B 450 LEU cc_start: 0.8498 (mm) cc_final: 0.8297 (mm) REVERT: B 486 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8876 (mm-30) REVERT: B 525 GLU cc_start: 0.9040 (tp30) cc_final: 0.8083 (tp30) REVERT: B 529 ILE cc_start: 0.9280 (pt) cc_final: 0.8605 (pt) REVERT: B 546 ASP cc_start: 0.8711 (t0) cc_final: 0.8087 (t0) REVERT: B 553 ASN cc_start: 0.8014 (m-40) cc_final: 0.7658 (m-40) REVERT: B 586 LYS cc_start: 0.9154 (ttmm) cc_final: 0.8601 (ttmm) REVERT: B 662 MET cc_start: 0.8409 (ttm) cc_final: 0.7773 (ttt) REVERT: B 689 ILE cc_start: 0.6519 (OUTLIER) cc_final: 0.6282 (mp) REVERT: B 718 THR cc_start: 0.5540 (OUTLIER) cc_final: 0.5330 (m) REVERT: C 185 ASP cc_start: 0.8936 (p0) cc_final: 0.8647 (p0) REVERT: C 202 PHE cc_start: 0.8300 (m-10) cc_final: 0.8011 (m-10) REVERT: C 274 ASN cc_start: 0.9055 (t0) cc_final: 0.8562 (t0) REVERT: C 281 ASN cc_start: 0.8276 (OUTLIER) cc_final: 0.7417 (p0) REVERT: C 348 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7444 (mt-10) REVERT: C 356 ASP cc_start: 0.8267 (t0) cc_final: 0.7550 (t0) REVERT: C 438 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8631 (mt0) REVERT: C 443 GLU cc_start: 0.8505 (tt0) cc_final: 0.8250 (tt0) REVERT: C 515 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8587 (mp0) REVERT: C 525 GLU cc_start: 0.9074 (tp30) cc_final: 0.8014 (tp30) REVERT: C 545 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8442 (ttpt) REVERT: C 546 ASP cc_start: 0.8760 (t0) cc_final: 0.8482 (t0) REVERT: C 549 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8193 (mt-10) REVERT: C 550 PHE cc_start: 0.9239 (m-80) cc_final: 0.9025 (m-10) REVERT: C 563 LYS cc_start: 0.9247 (tppt) cc_final: 0.8998 (ttmt) REVERT: C 587 MET cc_start: 0.8582 (mtt) cc_final: 0.8374 (mtt) REVERT: C 593 ASP cc_start: 0.8791 (t70) cc_final: 0.8307 (t0) REVERT: C 662 MET cc_start: 0.5335 (mtp) cc_final: 0.4287 (ttp) REVERT: D 180 ASN cc_start: 0.9351 (t0) cc_final: 0.8948 (t0) REVERT: D 195 ASP cc_start: 0.8154 (t70) cc_final: 0.7914 (t0) REVERT: D 212 GLU cc_start: 0.8901 (tt0) cc_final: 0.8697 (tt0) REVERT: D 227 SER cc_start: 0.8968 (OUTLIER) cc_final: 0.8731 (p) REVERT: D 248 SER cc_start: 0.9708 (m) cc_final: 0.9153 (t) REVERT: D 274 ASN cc_start: 0.9258 (t0) cc_final: 0.8942 (t0) REVERT: D 344 ARG cc_start: 0.8057 (ttp-170) cc_final: 0.7612 (ttp-170) REVERT: D 356 ASP cc_start: 0.8778 (t70) cc_final: 0.8503 (t70) REVERT: D 387 LYS cc_start: 0.9386 (tptp) cc_final: 0.9137 (tppp) REVERT: D 401 LEU cc_start: 0.9184 (tt) cc_final: 0.8924 (tt) REVERT: D 499 ASN cc_start: 0.8633 (m-40) cc_final: 0.8207 (m-40) REVERT: D 549 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8587 (mt-10) REVERT: D 559 SER cc_start: 0.8800 (t) cc_final: 0.8498 (p) REVERT: D 593 ASP cc_start: 0.8363 (t0) cc_final: 0.7974 (t0) REVERT: D 596 PHE cc_start: 0.8703 (m-80) cc_final: 0.8133 (m-80) REVERT: D 637 LYS cc_start: 0.8932 (ttpp) cc_final: 0.8671 (ttpp) REVERT: E 180 ASN cc_start: 0.9479 (t0) cc_final: 0.9053 (t0) REVERT: E 184 PRO cc_start: 0.9085 (Cg_exo) cc_final: 0.8782 (Cg_endo) REVERT: E 200 ARG cc_start: 0.7131 (mpp80) cc_final: 0.6796 (mpp80) REVERT: E 202 PHE cc_start: 0.8204 (m-10) cc_final: 0.7858 (m-10) REVERT: E 217 THR cc_start: 0.8956 (m) cc_final: 0.8642 (p) REVERT: E 218 LYS cc_start: 0.9249 (ttpt) cc_final: 0.8987 (ttmt) REVERT: E 219 TYR cc_start: 0.9033 (m-10) cc_final: 0.8327 (m-10) REVERT: E 287 ARG cc_start: 0.8404 (mtt90) cc_final: 0.7890 (mtt90) REVERT: E 289 ILE cc_start: 0.8942 (mt) cc_final: 0.8731 (mt) REVERT: E 366 TYR cc_start: 0.8793 (m-10) cc_final: 0.8250 (m-10) REVERT: E 393 THR cc_start: 0.9345 (OUTLIER) cc_final: 0.9085 (p) REVERT: E 422 ASN cc_start: 0.9113 (p0) cc_final: 0.8802 (p0) REVERT: E 447 GLN cc_start: 0.8967 (mt0) cc_final: 0.8497 (mm110) REVERT: E 462 TYR cc_start: 0.8790 (t80) cc_final: 0.8490 (t80) REVERT: E 486 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7921 (mm-30) REVERT: E 494 ASN cc_start: 0.9233 (p0) cc_final: 0.8749 (p0) REVERT: E 496 LYS cc_start: 0.8525 (tppt) cc_final: 0.7951 (ttmm) REVERT: E 499 ASN cc_start: 0.8483 (m-40) cc_final: 0.7809 (m-40) REVERT: E 514 LEU cc_start: 0.9340 (tp) cc_final: 0.9057 (tt) REVERT: E 515 GLU cc_start: 0.8011 (tp30) cc_final: 0.6553 (tp30) REVERT: E 518 LYS cc_start: 0.8807 (mtmt) cc_final: 0.7268 (mtmt) REVERT: E 525 GLU cc_start: 0.8768 (tp30) cc_final: 0.8420 (tp30) REVERT: E 546 ASP cc_start: 0.8190 (t0) cc_final: 0.7607 (t70) REVERT: E 557 GLN cc_start: 0.9059 (mp-120) cc_final: 0.8747 (mp10) REVERT: E 563 LYS cc_start: 0.9285 (tppt) cc_final: 0.9000 (mtpt) REVERT: E 586 LYS cc_start: 0.9125 (mtpp) cc_final: 0.8365 (mtpp) REVERT: E 587 MET cc_start: 0.9017 (mtt) cc_final: 0.8756 (mtm) REVERT: E 588 ASN cc_start: 0.8846 (m-40) cc_final: 0.8424 (m-40) REVERT: E 593 ASP cc_start: 0.8740 (t0) cc_final: 0.8510 (t0) REVERT: F 180 ASN cc_start: 0.9550 (t0) cc_final: 0.9292 (t0) REVERT: F 276 ASP cc_start: 0.8391 (p0) cc_final: 0.8008 (p0) REVERT: F 283 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8190 (t70) REVERT: F 284 SER cc_start: 0.8950 (m) cc_final: 0.8529 (p) REVERT: F 344 ARG cc_start: 0.7773 (ttp-110) cc_final: 0.7336 (ttm110) REVERT: F 356 ASP cc_start: 0.8814 (t70) cc_final: 0.8478 (t70) REVERT: F 430 THR cc_start: 0.9117 (m) cc_final: 0.8541 (p) REVERT: F 451 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7314 (t0) REVERT: F 479 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8207 (mt-10) REVERT: F 486 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8228 (mm-30) REVERT: F 496 LYS cc_start: 0.9410 (tttt) cc_final: 0.8756 (tppp) REVERT: F 535 GLU cc_start: 0.8319 (pt0) cc_final: 0.8012 (pt0) REVERT: F 543 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8276 (mp10) REVERT: F 575 TYR cc_start: 0.9039 (m-10) cc_final: 0.8606 (m-10) REVERT: F 593 ASP cc_start: 0.8373 (t0) cc_final: 0.7955 (t0) REVERT: F 637 LYS cc_start: 0.9406 (ttmt) cc_final: 0.8861 (ptmt) REVERT: F 662 MET cc_start: 0.3418 (ttt) cc_final: 0.2654 (ttp) REVERT: F 703 LYS cc_start: 0.8914 (mmtp) cc_final: 0.8421 (mmtt) REVERT: G 178 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8559 (mtt180) REVERT: G 197 LYS cc_start: 0.8627 (tttt) cc_final: 0.8284 (tppt) REVERT: G 238 LYS cc_start: 0.9282 (ttmp) cc_final: 0.8755 (mtpp) REVERT: G 264 VAL cc_start: 0.9700 (t) cc_final: 0.9484 (p) REVERT: G 269 ILE cc_start: 0.9383 (mm) cc_final: 0.9105 (mm) REVERT: G 340 LEU cc_start: 0.8433 (mt) cc_final: 0.8225 (mt) REVERT: G 346 TRP cc_start: 0.8153 (t-100) cc_final: 0.7705 (m-90) REVERT: G 353 ASN cc_start: 0.8490 (t0) cc_final: 0.8085 (t0) REVERT: G 356 ASP cc_start: 0.8627 (t0) cc_final: 0.7898 (t0) REVERT: G 361 ASN cc_start: 0.8327 (t0) cc_final: 0.8090 (t0) REVERT: G 419 ILE cc_start: 0.9043 (pp) cc_final: 0.8677 (pp) REVERT: G 438 GLN cc_start: 0.8891 (mt0) cc_final: 0.8603 (mt0) REVERT: G 451 ASP cc_start: 0.8198 (m-30) cc_final: 0.7903 (m-30) REVERT: G 469 VAL cc_start: 0.9478 (t) cc_final: 0.9224 (p) REVERT: G 472 ASP cc_start: 0.7723 (t0) cc_final: 0.7033 (t0) REVERT: G 512 ASP cc_start: 0.8885 (t0) cc_final: 0.8586 (t0) REVERT: G 518 LYS cc_start: 0.9021 (mtmm) cc_final: 0.8769 (mtmm) REVERT: G 543 GLN cc_start: 0.9397 (mm-40) cc_final: 0.8603 (mm-40) REVERT: G 556 GLN cc_start: 0.9306 (tt0) cc_final: 0.9040 (tm-30) REVERT: G 560 GLN cc_start: 0.9079 (tp40) cc_final: 0.8427 (tp-100) REVERT: G 568 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8368 (mt-10) REVERT: G 573 ASN cc_start: 0.8706 (t0) cc_final: 0.8328 (t0) REVERT: G 582 LYS cc_start: 0.9193 (mmtt) cc_final: 0.8887 (mtmm) REVERT: G 657 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.7577 (m-40) outliers start: 232 outliers final: 173 residues processed: 1344 average time/residue: 0.1834 time to fit residues: 411.6065 Evaluate side-chains 1410 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 1222 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 40 MET Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain L residue 120 TYR Chi-restraints excluded: chain L residue 122 LYS Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 250 GLN Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 665 ILE Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 375 TYR Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 545 LYS Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 636 ARG Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 703 LYS Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain D residue 638 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 524 LYS Chi-restraints excluded: chain E residue 537 ASN Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 263 HIS Chi-restraints excluded: chain F residue 265 ASP Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 515 GLU Chi-restraints excluded: chain F residue 543 GLN Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 713 ASN Chi-restraints excluded: chain G residue 178 ARG Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 263 HIS Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 283 ASP Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain G residue 452 THR Chi-restraints excluded: chain G residue 458 ASN Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 620 ILE Chi-restraints excluded: chain G residue 657 ASN Chi-restraints excluded: chain G residue 665 ILE Chi-restraints excluded: chain G residue 675 PHE Chi-restraints excluded: chain G residue 724 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 337 optimal weight: 0.9980 chunk 342 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 71 optimal weight: 0.0470 chunk 165 optimal weight: 0.5980 chunk 254 optimal weight: 0.9990 chunk 368 optimal weight: 5.9990 chunk 251 optimal weight: 0.7980 chunk 207 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 281 ASN A 363 ASN ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 ASN A 556 GLN A 565 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 GLN B 561 ASN B 565 GLN ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 588 ASN ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 GLN D 556 GLN E 299 HIS E 389 GLN ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 557 GLN ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 GLN G 616 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.192350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.124491 restraints weight = 46519.782| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 3.53 r_work: 0.3299 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 33385 Z= 0.112 Angle : 0.610 11.353 45291 Z= 0.310 Chirality : 0.047 0.220 5178 Planarity : 0.003 0.080 5938 Dihedral : 5.155 59.059 4515 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.50 % Favored : 96.35 % Rotamer: Outliers : 4.61 % Allowed : 25.36 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.13), residues: 4138 helix: 0.57 (0.22), residues: 641 sheet: 1.42 (0.16), residues: 983 loop : -0.84 (0.13), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 595 TYR 0.021 0.001 TYR F 411 PHE 0.031 0.001 PHE E 439 TRP 0.028 0.002 TRP A 206 HIS 0.007 0.001 HIS E 263 Details of bonding type rmsd covalent geometry : bond 0.00250 (33385) covalent geometry : angle 0.61032 (45291) hydrogen bonds : bond 0.02749 ( 1183) hydrogen bonds : angle 5.16282 ( 3228) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1463 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 1293 time to evaluate : 1.194 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: 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 250 GLU cc_start: 0.8959 (pm20) cc_final: 0.8674 (pm20) REVERT: A 256 VAL cc_start: 0.9679 (t) cc_final: 0.9411 (p) REVERT: A 274 ASN cc_start: 0.9188 (t0) cc_final: 0.8687 (t0) REVERT: A 275 GLU cc_start: 0.8583 (tt0) cc_final: 0.8326 (tt0) REVERT: A 287 ARG cc_start: 0.7754 (mtt90) cc_final: 0.7388 (mtt90) REVERT: A 290 SER cc_start: 0.8981 (m) cc_final: 0.8639 (t) REVERT: A 296 SER cc_start: 0.9427 (m) cc_final: 0.9178 (p) REVERT: A 364 ILE cc_start: 0.9120 (pt) cc_final: 0.8612 (mp) REVERT: A 368 ASN cc_start: 0.8973 (t0) cc_final: 0.8474 (t0) REVERT: A 389 GLN cc_start: 0.8231 (tt0) cc_final: 0.7943 (tt0) REVERT: A 411 TYR cc_start: 0.8802 (t80) cc_final: 0.8456 (t80) REVERT: A 448 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8527 (tm) REVERT: A 451 ASP cc_start: 0.7583 (m-30) cc_final: 0.6998 (m-30) REVERT: A 454 GLN cc_start: 0.8714 (pt0) cc_final: 0.7777 (pt0) REVERT: A 486 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8723 (mm-30) REVERT: A 545 LYS cc_start: 0.8688 (mmmt) cc_final: 0.7391 (tptp) REVERT: A 594 LYS cc_start: 0.8974 (ttpp) cc_final: 0.8708 (ttmm) REVERT: A 597 HIS cc_start: 0.8380 (m170) cc_final: 0.7856 (m90) REVERT: A 662 MET cc_start: 0.4540 (mtp) cc_final: 0.3112 (ttp) REVERT: B 211 HIS cc_start: 0.8963 (m90) cc_final: 0.8477 (m90) REVERT: B 219 TYR cc_start: 0.8917 (m-80) cc_final: 0.8656 (m-10) REVERT: B 259 TYR cc_start: 0.9397 (p90) cc_final: 0.9039 (p90) REVERT: B 274 ASN cc_start: 0.9043 (t0) cc_final: 0.8551 (t0) REVERT: B 281 ASN cc_start: 0.8829 (t0) cc_final: 0.8612 (m-40) REVERT: B 287 ARG cc_start: 0.8209 (mtt90) cc_final: 0.7980 (mtt90) REVERT: B 291 LYS cc_start: 0.8120 (tptm) cc_final: 0.7486 (tptt) REVERT: B 361 ASN cc_start: 0.8985 (t0) cc_final: 0.8616 (t0) REVERT: B 364 ILE cc_start: 0.8985 (pt) cc_final: 0.8584 (mp) REVERT: B 375 TYR cc_start: 0.9036 (m-80) cc_final: 0.8561 (m-80) REVERT: B 388 ASN cc_start: 0.8588 (p0) cc_final: 0.8029 (p0) REVERT: B 399 ASN cc_start: 0.9458 (m-40) cc_final: 0.9226 (m-40) REVERT: B 403 GLN cc_start: 0.8967 (mt0) cc_final: 0.8190 (mt0) REVERT: B 425 ASP cc_start: 0.8453 (m-30) cc_final: 0.7634 (m-30) REVERT: B 430 THR cc_start: 0.9092 (m) cc_final: 0.8781 (m) REVERT: B 450 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8117 (mm) REVERT: B 486 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8776 (mm-30) REVERT: B 525 GLU cc_start: 0.8989 (tp30) cc_final: 0.8012 (tp30) REVERT: B 529 ILE cc_start: 0.9243 (pt) cc_final: 0.8354 (pt) REVERT: B 546 ASP cc_start: 0.8683 (t0) cc_final: 0.8120 (t0) REVERT: B 548 THR cc_start: 0.9253 (p) cc_final: 0.8499 (p) REVERT: B 586 LYS cc_start: 0.9188 (ttmm) cc_final: 0.8618 (ttmm) REVERT: B 587 MET cc_start: 0.8828 (mtt) cc_final: 0.8419 (mtt) REVERT: B 662 MET cc_start: 0.8294 (ttm) cc_final: 0.7655 (ttt) REVERT: C 185 ASP cc_start: 0.8892 (p0) cc_final: 0.8585 (p0) REVERT: C 200 ARG cc_start: 0.8186 (mpp80) cc_final: 0.7931 (mpp-170) REVERT: C 202 PHE cc_start: 0.8268 (m-10) cc_final: 0.8025 (m-10) REVERT: C 274 ASN cc_start: 0.8993 (t0) cc_final: 0.8371 (t0) REVERT: C 348 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7455 (mt-10) REVERT: C 356 ASP cc_start: 0.8236 (t0) cc_final: 0.7505 (t0) REVERT: C 438 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8531 (mt0) REVERT: C 443 GLU cc_start: 0.8456 (tt0) cc_final: 0.8201 (tt0) REVERT: C 515 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8603 (mp0) REVERT: C 545 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8452 (ttpt) REVERT: C 546 ASP cc_start: 0.8757 (t0) cc_final: 0.8437 (t0) REVERT: C 549 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8385 (mt-10) REVERT: C 550 PHE cc_start: 0.9181 (m-80) cc_final: 0.8951 (m-10) REVERT: C 563 LYS cc_start: 0.9237 (tppt) cc_final: 0.8952 (ttmt) REVERT: C 586 LYS cc_start: 0.8847 (mtpp) cc_final: 0.8606 (mttp) REVERT: C 593 ASP cc_start: 0.8623 (t70) cc_final: 0.8194 (t0) REVERT: C 662 MET cc_start: 0.5356 (mtp) cc_final: 0.4324 (ttp) REVERT: D 180 ASN cc_start: 0.9382 (t0) cc_final: 0.8949 (t0) REVERT: D 195 ASP cc_start: 0.8103 (t70) cc_final: 0.7857 (t0) REVERT: D 200 ARG cc_start: 0.8197 (mpp80) cc_final: 0.7813 (mpp-170) REVERT: D 240 THR cc_start: 0.9420 (m) cc_final: 0.9191 (t) REVERT: D 274 ASN cc_start: 0.9216 (t0) cc_final: 0.8859 (t0) REVERT: D 297 ARG cc_start: 0.8161 (tpp80) cc_final: 0.7520 (tpp80) REVERT: D 344 ARG cc_start: 0.8087 (ttp-170) cc_final: 0.7640 (ttp-170) REVERT: D 356 ASP cc_start: 0.8853 (t70) cc_final: 0.8456 (t70) REVERT: D 387 LYS cc_start: 0.9383 (tptp) cc_final: 0.8988 (tppp) REVERT: D 401 LEU cc_start: 0.9048 (tt) cc_final: 0.8789 (tt) REVERT: D 411 TYR cc_start: 0.8823 (t80) cc_final: 0.8560 (t80) REVERT: D 476 ASN cc_start: 0.9126 (p0) cc_final: 0.8509 (p0) REVERT: D 499 ASN cc_start: 0.8574 (m-40) cc_final: 0.8149 (m-40) REVERT: D 593 ASP cc_start: 0.8122 (t0) cc_final: 0.7735 (t0) REVERT: D 596 PHE cc_start: 0.8586 (m-80) cc_final: 0.7949 (m-80) REVERT: D 614 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8479 (mp0) REVERT: D 637 LYS cc_start: 0.8910 (ttpp) cc_final: 0.8665 (ttpp) REVERT: E 180 ASN cc_start: 0.9493 (t0) cc_final: 0.9045 (t0) REVERT: E 184 PRO cc_start: 0.9125 (Cg_exo) cc_final: 0.8859 (Cg_endo) REVERT: E 200 ARG cc_start: 0.6977 (mpp80) cc_final: 0.6685 (mpp80) REVERT: E 202 PHE cc_start: 0.8155 (m-10) cc_final: 0.7784 (m-10) REVERT: E 217 THR cc_start: 0.8915 (m) cc_final: 0.8495 (p) REVERT: E 218 LYS cc_start: 0.9307 (ttpt) cc_final: 0.8958 (ttmm) REVERT: E 219 TYR cc_start: 0.8625 (m-10) cc_final: 0.7976 (m-10) REVERT: E 236 PHE cc_start: 0.9127 (t80) cc_final: 0.8895 (t80) REVERT: E 238 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8859 (ttmp) REVERT: E 287 ARG cc_start: 0.8358 (mtt90) cc_final: 0.7789 (mtt90) REVERT: E 339 SER cc_start: 0.9366 (m) cc_final: 0.8881 (p) REVERT: E 366 TYR cc_start: 0.8700 (m-10) cc_final: 0.8160 (m-10) REVERT: E 393 THR cc_start: 0.9331 (OUTLIER) cc_final: 0.9104 (p) REVERT: E 422 ASN cc_start: 0.9126 (p0) cc_final: 0.8818 (p0) REVERT: E 447 GLN cc_start: 0.8964 (mt0) cc_final: 0.8551 (mm110) REVERT: E 462 TYR cc_start: 0.8731 (t80) cc_final: 0.8463 (t80) REVERT: E 476 ASN cc_start: 0.9000 (p0) cc_final: 0.8518 (p0) REVERT: E 486 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8045 (mm-30) REVERT: E 494 ASN cc_start: 0.9149 (p0) cc_final: 0.8736 (p0) REVERT: E 499 ASN cc_start: 0.8382 (m-40) cc_final: 0.7731 (m-40) REVERT: E 515 GLU cc_start: 0.8000 (tp30) cc_final: 0.6494 (tp30) REVERT: E 518 LYS cc_start: 0.8836 (mtmt) cc_final: 0.7834 (ptpp) REVERT: E 525 GLU cc_start: 0.8568 (tp30) cc_final: 0.8129 (tp30) REVERT: E 541 GLN cc_start: 0.8917 (tt0) cc_final: 0.8273 (tp40) REVERT: E 546 ASP cc_start: 0.8206 (t0) cc_final: 0.7908 (t70) REVERT: E 563 LYS cc_start: 0.9261 (tppt) cc_final: 0.8977 (mtpt) REVERT: E 586 LYS cc_start: 0.9139 (mtpp) cc_final: 0.8520 (mtpp) REVERT: E 587 MET cc_start: 0.8997 (mtt) cc_final: 0.8717 (mtm) REVERT: E 588 ASN cc_start: 0.8828 (m-40) cc_final: 0.8375 (m-40) REVERT: E 593 ASP cc_start: 0.8712 (t0) cc_final: 0.8247 (t0) REVERT: F 180 ASN cc_start: 0.9561 (t0) cc_final: 0.9277 (t0) REVERT: F 276 ASP cc_start: 0.8477 (p0) cc_final: 0.8061 (p0) REVERT: F 282 THR cc_start: 0.9006 (m) cc_final: 0.8349 (p) REVERT: F 283 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8111 (t70) REVERT: F 284 SER cc_start: 0.9007 (m) cc_final: 0.8555 (p) REVERT: F 344 ARG cc_start: 0.7738 (ttp-110) cc_final: 0.7325 (ttm110) REVERT: F 430 THR cc_start: 0.9077 (m) cc_final: 0.8471 (p) REVERT: F 434 MET cc_start: 0.7729 (mtm) cc_final: 0.7328 (ttm) REVERT: F 450 LEU cc_start: 0.9184 (tp) cc_final: 0.8938 (tt) REVERT: F 451 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7270 (t0) REVERT: F 486 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8060 (mm-30) REVERT: F 496 LYS cc_start: 0.9387 (tttt) cc_final: 0.8761 (tppp) REVERT: F 535 GLU cc_start: 0.8323 (pt0) cc_final: 0.8034 (pt0) REVERT: F 575 TYR cc_start: 0.9041 (m-10) cc_final: 0.8529 (m-10) REVERT: F 593 ASP cc_start: 0.8271 (t0) cc_final: 0.7663 (t70) REVERT: F 637 LYS cc_start: 0.9371 (ttmt) cc_final: 0.8731 (ptmt) REVERT: F 662 MET cc_start: 0.3340 (ttt) cc_final: 0.2623 (ttp) REVERT: F 703 LYS cc_start: 0.8902 (mmtp) cc_final: 0.8474 (mmtm) REVERT: G 178 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8566 (mtt90) REVERT: G 264 VAL cc_start: 0.9703 (t) cc_final: 0.9422 (p) REVERT: G 281 ASN cc_start: 0.8252 (t0) cc_final: 0.8046 (m-40) REVERT: G 346 TRP cc_start: 0.8142 (t-100) cc_final: 0.7404 (m-90) REVERT: G 353 ASN cc_start: 0.8461 (t0) cc_final: 0.8088 (t0) REVERT: G 356 ASP cc_start: 0.8571 (t0) cc_final: 0.7845 (t0) REVERT: G 361 ASN cc_start: 0.8326 (t0) cc_final: 0.8046 (t0) REVERT: G 419 ILE cc_start: 0.8953 (pp) cc_final: 0.8542 (pp) REVERT: G 472 ASP cc_start: 0.7768 (t0) cc_final: 0.6986 (t0) REVERT: G 512 ASP cc_start: 0.8845 (t0) cc_final: 0.8102 (t0) REVERT: G 515 GLU cc_start: 0.9410 (OUTLIER) cc_final: 0.8416 (mp0) REVERT: G 518 LYS cc_start: 0.9104 (mtmm) cc_final: 0.8883 (mtmm) REVERT: G 556 GLN cc_start: 0.9299 (tt0) cc_final: 0.9028 (tm-30) REVERT: G 560 GLN cc_start: 0.9048 (tp40) cc_final: 0.8407 (tp-100) REVERT: G 568 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8321 (mt-10) REVERT: G 573 ASN cc_start: 0.8656 (t0) cc_final: 0.8241 (t0) REVERT: G 582 LYS cc_start: 0.9184 (mmtt) cc_final: 0.8860 (mtmm) REVERT: G 600 ARG cc_start: 0.8313 (ttp80) cc_final: 0.7917 (ttp80) REVERT: G 657 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.7536 (m-40) outliers start: 170 outliers final: 132 residues processed: 1357 average time/residue: 0.1839 time to fit residues: 418.0188 Evaluate side-chains 1402 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 1258 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 40 MET Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain L residue 120 TYR Chi-restraints excluded: chain L residue 122 LYS Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 250 GLN Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 545 LYS Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 636 ARG Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 703 LYS Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 374 ILE Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 537 ASN Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 263 HIS Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 451 ASP Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 515 GLU Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 713 ASN Chi-restraints excluded: chain G residue 178 ARG Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain G residue 452 THR Chi-restraints excluded: chain G residue 458 ASN Chi-restraints excluded: chain G residue 515 GLU Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 569 LEU Chi-restraints excluded: chain G residue 620 ILE Chi-restraints excluded: chain G residue 657 ASN Chi-restraints excluded: chain G residue 665 ILE Chi-restraints excluded: chain G residue 675 PHE Chi-restraints excluded: chain G residue 724 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 236 optimal weight: 8.9990 chunk 352 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 248 optimal weight: 6.9990 chunk 289 optimal weight: 1.9990 chunk 204 optimal weight: 40.0000 chunk 16 optimal weight: 0.0470 chunk 203 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 202 optimal weight: 10.0000 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 281 ASN ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 ASN ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 ASN A 556 GLN B 541 GLN ** B 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 ASN B 565 GLN C 211 HIS ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 539 ASN ** D 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 HIS E 299 HIS E 389 GLN ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 ASN F 584 ASN ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 403 GLN G 494 ASN G 541 GLN G 553 ASN G 616 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.185599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.117738 restraints weight = 46759.003| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.42 r_work: 0.3218 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 33385 Z= 0.288 Angle : 0.697 10.571 45291 Z= 0.365 Chirality : 0.050 0.267 5178 Planarity : 0.004 0.080 5938 Dihedral : 5.331 50.223 4509 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.05 % Favored : 94.80 % Rotamer: Outliers : 5.47 % Allowed : 25.01 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.13), residues: 4138 helix: 0.41 (0.22), residues: 634 sheet: 0.99 (0.15), residues: 1066 loop : -0.91 (0.13), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 595 TYR 0.046 0.002 TYR D 411 PHE 0.038 0.002 PHE E 439 TRP 0.034 0.002 TRP A 206 HIS 0.006 0.001 HIS D 263 Details of bonding type rmsd covalent geometry : bond 0.00627 (33385) covalent geometry : angle 0.69742 (45291) hydrogen bonds : bond 0.03561 ( 1183) hydrogen bonds : angle 5.43663 ( 3228) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1463 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 1261 time to evaluate : 1.208 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: 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 246 ASN cc_start: 0.9109 (m110) cc_final: 0.8749 (m110) REVERT: A 250 GLU cc_start: 0.8947 (pm20) cc_final: 0.8731 (pm20) REVERT: A 256 VAL cc_start: 0.9705 (t) cc_final: 0.9469 (p) REVERT: A 263 HIS cc_start: 0.9003 (OUTLIER) cc_final: 0.8474 (p-80) REVERT: A 274 ASN cc_start: 0.9218 (t0) cc_final: 0.8755 (t0) REVERT: A 275 GLU cc_start: 0.8619 (tt0) cc_final: 0.8363 (tt0) REVERT: A 287 ARG cc_start: 0.8014 (mtt90) cc_final: 0.7736 (mtt90) REVERT: A 368 ASN cc_start: 0.9050 (t0) cc_final: 0.8454 (t0) REVERT: A 411 TYR cc_start: 0.8977 (t80) cc_final: 0.8397 (t80) REVERT: A 448 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8648 (tm) REVERT: A 451 ASP cc_start: 0.7566 (m-30) cc_final: 0.7045 (m-30) REVERT: A 486 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8888 (mm-30) REVERT: A 587 MET cc_start: 0.9037 (mtp) cc_final: 0.8240 (mtm) REVERT: A 597 HIS cc_start: 0.7978 (m170) cc_final: 0.7395 (m90) REVERT: A 662 MET cc_start: 0.4760 (mtp) cc_final: 0.3453 (ttp) REVERT: B 200 ARG cc_start: 0.9006 (mtm180) cc_final: 0.8391 (mtm180) REVERT: B 211 HIS cc_start: 0.9067 (m90) cc_final: 0.8496 (m90) REVERT: B 219 TYR cc_start: 0.8913 (m-80) cc_final: 0.8649 (m-10) REVERT: B 226 TRP cc_start: 0.9243 (t60) cc_final: 0.8961 (t60) REVERT: B 252 ARG cc_start: 0.9054 (mmt90) cc_final: 0.8750 (mmt-90) REVERT: B 259 TYR cc_start: 0.9321 (p90) cc_final: 0.8626 (p90) REVERT: B 274 ASN cc_start: 0.9026 (t0) cc_final: 0.8595 (t0) REVERT: B 291 LYS cc_start: 0.8423 (tptm) cc_final: 0.7780 (tptt) REVERT: B 375 TYR cc_start: 0.9205 (m-80) cc_final: 0.8911 (m-80) REVERT: B 388 ASN cc_start: 0.8684 (p0) cc_final: 0.8066 (p0) REVERT: B 403 GLN cc_start: 0.9039 (mt0) cc_final: 0.8189 (mt0) REVERT: B 425 ASP cc_start: 0.8520 (m-30) cc_final: 0.7809 (m-30) REVERT: B 430 THR cc_start: 0.8940 (m) cc_final: 0.8610 (m) REVERT: B 450 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8230 (mm) REVERT: B 486 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8973 (mm-30) REVERT: B 525 GLU cc_start: 0.9090 (tp30) cc_final: 0.8187 (tp30) REVERT: B 529 ILE cc_start: 0.9403 (pt) cc_final: 0.8555 (pt) REVERT: B 546 ASP cc_start: 0.8767 (t0) cc_final: 0.8514 (t0) REVERT: B 586 LYS cc_start: 0.9158 (ttmm) cc_final: 0.8590 (mtpp) REVERT: B 662 MET cc_start: 0.8456 (ttm) cc_final: 0.8065 (ttm) REVERT: B 689 ILE cc_start: 0.6577 (OUTLIER) cc_final: 0.6324 (mp) REVERT: C 274 ASN cc_start: 0.9006 (t0) cc_final: 0.8572 (t0) REVERT: C 281 ASN cc_start: 0.8311 (m-40) cc_final: 0.7448 (p0) REVERT: C 346 TRP cc_start: 0.7288 (t-100) cc_final: 0.6494 (t-100) REVERT: C 348 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7359 (mt-10) REVERT: C 356 ASP cc_start: 0.8333 (t0) cc_final: 0.7667 (t0) REVERT: C 436 TYR cc_start: 0.8871 (t80) cc_final: 0.8394 (t80) REVERT: C 443 GLU cc_start: 0.8492 (tt0) cc_final: 0.8234 (tt0) REVERT: C 515 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8692 (mp0) REVERT: C 525 GLU cc_start: 0.9141 (tp30) cc_final: 0.8033 (tp30) REVERT: C 546 ASP cc_start: 0.8787 (t0) cc_final: 0.8536 (t0) REVERT: C 549 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8735 (mt-10) REVERT: C 550 PHE cc_start: 0.9252 (m-80) cc_final: 0.8990 (m-10) REVERT: C 563 LYS cc_start: 0.9247 (tppt) cc_final: 0.8978 (ttmt) REVERT: C 587 MET cc_start: 0.8815 (mtt) cc_final: 0.8607 (mtt) REVERT: C 593 ASP cc_start: 0.8737 (t70) cc_final: 0.8271 (t0) REVERT: C 596 PHE cc_start: 0.9242 (m-10) cc_final: 0.8657 (m-10) REVERT: D 180 ASN cc_start: 0.9353 (t0) cc_final: 0.8982 (t0) REVERT: D 195 ASP cc_start: 0.8168 (t70) cc_final: 0.7942 (t0) REVERT: D 212 GLU cc_start: 0.8843 (tt0) cc_final: 0.8320 (tt0) REVERT: D 248 SER cc_start: 0.9652 (m) cc_final: 0.9212 (t) REVERT: D 250 GLU cc_start: 0.8929 (pm20) cc_final: 0.8501 (pm20) REVERT: D 274 ASN cc_start: 0.9299 (t0) cc_final: 0.8471 (t0) REVERT: D 297 ARG cc_start: 0.8296 (tpp80) cc_final: 0.7603 (tpp80) REVERT: D 356 ASP cc_start: 0.8881 (t70) cc_final: 0.8540 (t70) REVERT: D 387 LYS cc_start: 0.9436 (tptp) cc_final: 0.9058 (tppp) REVERT: D 466 ASN cc_start: 0.9460 (p0) cc_final: 0.9086 (p0) REVERT: D 499 ASN cc_start: 0.8597 (m-40) cc_final: 0.8212 (m-40) REVERT: D 549 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8630 (mt-10) REVERT: D 559 SER cc_start: 0.8880 (t) cc_final: 0.8583 (p) REVERT: D 593 ASP cc_start: 0.8380 (t0) cc_final: 0.8086 (t0) REVERT: D 596 PHE cc_start: 0.8823 (m-80) cc_final: 0.8414 (m-80) REVERT: D 613 LYS cc_start: 0.6401 (pttp) cc_final: 0.6120 (ttmt) REVERT: D 614 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8533 (mp0) REVERT: D 637 LYS cc_start: 0.8919 (ttpp) cc_final: 0.8646 (ttpp) REVERT: E 180 ASN cc_start: 0.9454 (t0) cc_final: 0.9033 (t0) REVERT: E 184 PRO cc_start: 0.9170 (Cg_exo) cc_final: 0.8892 (Cg_endo) REVERT: E 200 ARG cc_start: 0.7249 (mpp80) cc_final: 0.6855 (mpp80) REVERT: E 202 PHE cc_start: 0.8167 (m-10) cc_final: 0.7734 (m-10) REVERT: E 217 THR cc_start: 0.8927 (m) cc_final: 0.8416 (p) REVERT: E 218 LYS cc_start: 0.9237 (ttpt) cc_final: 0.8958 (ttmt) REVERT: E 219 TYR cc_start: 0.8815 (m-10) cc_final: 0.8206 (m-10) REVERT: E 287 ARG cc_start: 0.8450 (mtt90) cc_final: 0.8078 (mtt90) REVERT: E 339 SER cc_start: 0.9421 (OUTLIER) cc_final: 0.8971 (p) REVERT: E 344 ARG cc_start: 0.7897 (ttp-110) cc_final: 0.7380 (ttp-170) REVERT: E 366 TYR cc_start: 0.8950 (m-10) cc_final: 0.8236 (m-10) REVERT: E 393 THR cc_start: 0.9265 (OUTLIER) cc_final: 0.9014 (p) REVERT: E 416 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8741 (mt) REVERT: E 422 ASN cc_start: 0.9148 (p0) cc_final: 0.8880 (p0) REVERT: E 447 GLN cc_start: 0.8916 (mt0) cc_final: 0.8509 (mm110) REVERT: E 462 TYR cc_start: 0.8786 (t80) cc_final: 0.8404 (t80) REVERT: E 486 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8091 (mm-30) REVERT: E 496 LYS cc_start: 0.8775 (tppt) cc_final: 0.8127 (ttmm) REVERT: E 499 ASN cc_start: 0.8589 (m-40) cc_final: 0.7936 (m-40) REVERT: E 515 GLU cc_start: 0.8257 (tp30) cc_final: 0.6380 (tp30) REVERT: E 518 LYS cc_start: 0.8779 (mtmt) cc_final: 0.7258 (mtmt) REVERT: E 525 GLU cc_start: 0.8888 (tp30) cc_final: 0.8461 (tp30) REVERT: E 531 PHE cc_start: 0.9303 (m-80) cc_final: 0.9073 (m-80) REVERT: E 546 ASP cc_start: 0.8256 (t0) cc_final: 0.7756 (t70) REVERT: E 563 LYS cc_start: 0.9328 (tppt) cc_final: 0.9010 (mtpt) REVERT: E 586 LYS cc_start: 0.9224 (mtpp) cc_final: 0.8508 (mtpp) REVERT: E 587 MET cc_start: 0.8991 (mtt) cc_final: 0.8693 (mtm) REVERT: E 588 ASN cc_start: 0.8927 (m-40) cc_final: 0.8472 (m-40) REVERT: F 180 ASN cc_start: 0.9566 (t0) cc_final: 0.9319 (t0) REVERT: F 276 ASP cc_start: 0.8428 (p0) cc_final: 0.8085 (p0) REVERT: F 283 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8218 (m-30) REVERT: F 284 SER cc_start: 0.9054 (m) cc_final: 0.8735 (p) REVERT: F 344 ARG cc_start: 0.7917 (ttp-110) cc_final: 0.7439 (ttm110) REVERT: F 356 ASP cc_start: 0.8943 (t70) cc_final: 0.8649 (t70) REVERT: F 359 ARG cc_start: 0.8973 (mtt180) cc_final: 0.8461 (mtp85) REVERT: F 430 THR cc_start: 0.9089 (m) cc_final: 0.8564 (p) REVERT: F 486 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8203 (mm-30) REVERT: F 496 LYS cc_start: 0.9447 (tttt) cc_final: 0.9147 (tptm) REVERT: F 535 GLU cc_start: 0.8316 (pt0) cc_final: 0.8012 (pt0) REVERT: F 556 GLN cc_start: 0.9013 (mt0) cc_final: 0.8391 (tp-100) REVERT: F 583 LEU cc_start: 0.9586 (mm) cc_final: 0.9313 (mm) REVERT: F 584 ASN cc_start: 0.9295 (OUTLIER) cc_final: 0.8516 (m-40) REVERT: F 587 MET cc_start: 0.8901 (mtt) cc_final: 0.8412 (mtp) REVERT: F 593 ASP cc_start: 0.8490 (t0) cc_final: 0.8006 (t70) REVERT: F 637 LYS cc_start: 0.9423 (ttmt) cc_final: 0.8979 (ptmt) REVERT: F 662 MET cc_start: 0.3257 (ttt) cc_final: 0.2570 (ttp) REVERT: F 703 LYS cc_start: 0.8958 (mmtp) cc_final: 0.8514 (mmtp) REVERT: G 178 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8560 (mtt90) REVERT: G 197 LYS cc_start: 0.8703 (tttt) cc_final: 0.8473 (tppt) REVERT: G 238 LYS cc_start: 0.9403 (ttmp) cc_final: 0.8995 (mtpp) REVERT: G 287 ARG cc_start: 0.7832 (mtt90) cc_final: 0.7291 (mtt180) REVERT: G 292 ASN cc_start: 0.8206 (t0) cc_final: 0.7932 (t0) REVERT: G 346 TRP cc_start: 0.8148 (t-100) cc_final: 0.7705 (m-90) REVERT: G 356 ASP cc_start: 0.8601 (t0) cc_final: 0.7938 (t0) REVERT: G 361 ASN cc_start: 0.8427 (t0) cc_final: 0.8137 (t0) REVERT: G 419 ILE cc_start: 0.9017 (pp) cc_final: 0.8676 (pp) REVERT: G 472 ASP cc_start: 0.7991 (t0) cc_final: 0.7294 (t0) REVERT: G 512 ASP cc_start: 0.8838 (t0) cc_final: 0.8240 (t0) REVERT: G 515 GLU cc_start: 0.9482 (OUTLIER) cc_final: 0.8556 (mp0) REVERT: G 518 LYS cc_start: 0.9118 (mtmm) cc_final: 0.8901 (mtmm) REVERT: G 556 GLN cc_start: 0.9340 (tt0) cc_final: 0.9103 (tm-30) REVERT: G 568 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8447 (mt-10) REVERT: G 573 ASN cc_start: 0.8937 (t0) cc_final: 0.8570 (t0) REVERT: G 582 LYS cc_start: 0.9210 (mmtt) cc_final: 0.8949 (mmmm) REVERT: G 600 ARG cc_start: 0.8365 (ttp80) cc_final: 0.7941 (ttp80) REVERT: G 657 ASN cc_start: 0.8416 (OUTLIER) cc_final: 0.7635 (m-40) outliers start: 202 outliers final: 165 residues processed: 1344 average time/residue: 0.1837 time to fit residues: 413.4884 Evaluate side-chains 1404 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 1226 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 40 MET Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain L residue 120 TYR Chi-restraints excluded: chain L residue 122 LYS Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 250 GLN Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 665 ILE Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 375 TYR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 703 LYS Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 465 GLU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 587 MET Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain E residue 374 ILE Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 537 ASN Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 589 ILE Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 263 HIS Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 497 ASP Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 584 ASN Chi-restraints excluded: chain F residue 713 ASN Chi-restraints excluded: chain G residue 178 ARG Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 263 HIS Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 403 GLN Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain G residue 452 THR Chi-restraints excluded: chain G residue 458 ASN Chi-restraints excluded: chain G residue 515 GLU Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 620 ILE Chi-restraints excluded: chain G residue 657 ASN Chi-restraints excluded: chain G residue 665 ILE Chi-restraints excluded: chain G residue 675 PHE Chi-restraints excluded: chain G residue 724 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 3 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 163 optimal weight: 0.7980 chunk 276 optimal weight: 1.9990 chunk 358 optimal weight: 0.5980 chunk 274 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 395 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 368 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 281 ASN ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 GLN B 541 GLN ** B 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 ASN ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 539 ASN ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 556 GLN E 299 HIS E 389 GLN ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 553 ASN G 403 GLN G 494 ASN G 616 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.189279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.122240 restraints weight = 46500.329| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.47 r_work: 0.3264 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.5769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 33385 Z= 0.135 Angle : 0.655 10.517 45291 Z= 0.333 Chirality : 0.048 0.280 5178 Planarity : 0.004 0.080 5938 Dihedral : 5.186 51.977 4505 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.94 % Favored : 95.92 % Rotamer: Outliers : 4.42 % Allowed : 26.82 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.13), residues: 4138 helix: 0.51 (0.22), residues: 628 sheet: 1.05 (0.16), residues: 1065 loop : -0.84 (0.13), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 595 TYR 0.031 0.001 TYR B 462 PHE 0.029 0.002 PHE E 439 TRP 0.027 0.002 TRP A 206 HIS 0.006 0.001 HIS F 263 Details of bonding type rmsd covalent geometry : bond 0.00298 (33385) covalent geometry : angle 0.65508 (45291) hydrogen bonds : bond 0.02946 ( 1183) hydrogen bonds : angle 5.25916 ( 3228) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1453 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 1290 time to evaluate : 0.897 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: 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: symmetry clash REVERT: A 246 ASN cc_start: 0.9106 (m110) cc_final: 0.8736 (m110) REVERT: A 250 GLU cc_start: 0.8945 (pm20) cc_final: 0.8687 (pm20) REVERT: A 256 VAL cc_start: 0.9721 (t) cc_final: 0.9471 (p) REVERT: A 263 HIS cc_start: 0.8830 (OUTLIER) cc_final: 0.8224 (p-80) REVERT: A 274 ASN cc_start: 0.9296 (t0) cc_final: 0.8711 (t0) REVERT: A 275 GLU cc_start: 0.8576 (tt0) cc_final: 0.8373 (tt0) REVERT: A 286 THR cc_start: 0.8581 (m) cc_final: 0.8075 (p) REVERT: A 287 ARG cc_start: 0.7901 (mtt90) cc_final: 0.7602 (mtt90) REVERT: A 368 ASN cc_start: 0.8998 (t0) cc_final: 0.8505 (t0) REVERT: A 411 TYR cc_start: 0.8844 (t80) cc_final: 0.8480 (t80) REVERT: A 448 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8540 (tm) REVERT: A 451 ASP cc_start: 0.7615 (m-30) cc_final: 0.7071 (m-30) REVERT: A 486 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8608 (mm-30) REVERT: A 541 GLN cc_start: 0.7774 (tt0) cc_final: 0.7407 (tp40) REVERT: A 586 LYS cc_start: 0.9247 (mtpt) cc_final: 0.8696 (mtpt) REVERT: A 594 LYS cc_start: 0.8999 (ttpp) cc_final: 0.8781 (ttmm) REVERT: A 597 HIS cc_start: 0.8004 (m170) cc_final: 0.7382 (m90) REVERT: A 662 MET cc_start: 0.4660 (mtp) cc_final: 0.3281 (ttp) REVERT: B 200 ARG cc_start: 0.8964 (mtm180) cc_final: 0.8348 (mtm180) REVERT: B 211 HIS cc_start: 0.9037 (m90) cc_final: 0.8514 (m90) REVERT: B 219 TYR cc_start: 0.8944 (m-80) cc_final: 0.8698 (m-10) REVERT: B 226 TRP cc_start: 0.9223 (t60) cc_final: 0.8957 (t60) REVERT: B 259 TYR cc_start: 0.9380 (p90) cc_final: 0.8933 (p90) REVERT: B 274 ASN cc_start: 0.9032 (t0) cc_final: 0.8757 (t0) REVERT: B 291 LYS cc_start: 0.8322 (tptm) cc_final: 0.7677 (tptt) REVERT: B 348 GLU cc_start: 0.8659 (tt0) cc_final: 0.7645 (tt0) REVERT: B 359 ARG cc_start: 0.9138 (mtt180) cc_final: 0.8858 (ttm170) REVERT: B 375 TYR cc_start: 0.9158 (m-80) cc_final: 0.8741 (m-80) REVERT: B 388 ASN cc_start: 0.8564 (p0) cc_final: 0.8047 (p0) REVERT: B 403 GLN cc_start: 0.8973 (mt0) cc_final: 0.8334 (mt0) REVERT: B 425 ASP cc_start: 0.8498 (m-30) cc_final: 0.7701 (m-30) REVERT: B 430 THR cc_start: 0.8743 (m) cc_final: 0.8149 (m) REVERT: B 440 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9285 (mm) REVERT: B 525 GLU cc_start: 0.8976 (tp30) cc_final: 0.8060 (tp30) REVERT: B 529 ILE cc_start: 0.9356 (pt) cc_final: 0.8472 (pt) REVERT: B 541 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8149 (tp-100) REVERT: B 586 LYS cc_start: 0.9178 (ttmm) cc_final: 0.8618 (mtpp) REVERT: B 662 MET cc_start: 0.8408 (ttm) cc_final: 0.7649 (ttt) REVERT: C 185 ASP cc_start: 0.8747 (p0) cc_final: 0.8516 (p0) REVERT: C 202 PHE cc_start: 0.8407 (m-10) cc_final: 0.8202 (m-10) REVERT: C 274 ASN cc_start: 0.8978 (t0) cc_final: 0.8518 (t0) REVERT: C 281 ASN cc_start: 0.8343 (m-40) cc_final: 0.7061 (p0) REVERT: C 346 TRP cc_start: 0.7291 (t-100) cc_final: 0.6496 (t-100) REVERT: C 348 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7294 (mt-10) REVERT: C 356 ASP cc_start: 0.8279 (t0) cc_final: 0.7610 (t0) REVERT: C 438 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8598 (mt0) REVERT: C 443 GLU cc_start: 0.8483 (tt0) cc_final: 0.8222 (tt0) REVERT: C 492 ILE cc_start: 0.9223 (mp) cc_final: 0.8841 (mp) REVERT: C 515 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8635 (mp0) REVERT: C 525 GLU cc_start: 0.9063 (tp30) cc_final: 0.7902 (tp30) REVERT: C 546 ASP cc_start: 0.8731 (t0) cc_final: 0.8528 (t0) REVERT: C 549 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8721 (mt-10) REVERT: C 550 PHE cc_start: 0.9157 (m-80) cc_final: 0.8947 (m-10) REVERT: C 563 LYS cc_start: 0.9203 (tppt) cc_final: 0.8918 (ttmt) REVERT: C 593 ASP cc_start: 0.8576 (t70) cc_final: 0.8057 (t0) REVERT: C 596 PHE cc_start: 0.9197 (m-10) cc_final: 0.8577 (m-10) REVERT: D 180 ASN cc_start: 0.9372 (t0) cc_final: 0.8978 (t0) REVERT: D 195 ASP cc_start: 0.8118 (t70) cc_final: 0.7882 (t0) REVERT: D 200 ARG cc_start: 0.8280 (mpp80) cc_final: 0.8010 (mtm180) REVERT: D 212 GLU cc_start: 0.8762 (tt0) cc_final: 0.8232 (tt0) REVERT: D 274 ASN cc_start: 0.9243 (t0) cc_final: 0.8431 (t0) REVERT: D 344 ARG cc_start: 0.8010 (ttp-170) cc_final: 0.7681 (ttp-170) REVERT: D 356 ASP cc_start: 0.8840 (t70) cc_final: 0.8464 (t70) REVERT: D 387 LYS cc_start: 0.9411 (tptp) cc_final: 0.9048 (tppp) REVERT: D 499 ASN cc_start: 0.8514 (m-40) cc_final: 0.8071 (m-40) REVERT: D 549 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8560 (mt-10) REVERT: D 593 ASP cc_start: 0.8301 (t0) cc_final: 0.7961 (t0) REVERT: D 595 ARG cc_start: 0.8464 (mtm110) cc_final: 0.8237 (ptm160) REVERT: D 596 PHE cc_start: 0.8770 (m-80) cc_final: 0.8146 (m-80) REVERT: D 614 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8591 (mp0) REVERT: D 637 LYS cc_start: 0.8853 (ttpp) cc_final: 0.8615 (ttpp) REVERT: E 180 ASN cc_start: 0.9521 (t0) cc_final: 0.9039 (t0) REVERT: E 184 PRO cc_start: 0.9184 (Cg_exo) cc_final: 0.8931 (Cg_endo) REVERT: E 200 ARG cc_start: 0.7109 (mpp80) cc_final: 0.6767 (mpp80) REVERT: E 202 PHE cc_start: 0.8122 (m-10) cc_final: 0.7878 (m-10) REVERT: E 217 THR cc_start: 0.8901 (m) cc_final: 0.8446 (p) REVERT: E 218 LYS cc_start: 0.9254 (ttpt) cc_final: 0.8941 (ttmt) REVERT: E 219 TYR cc_start: 0.8680 (m-10) cc_final: 0.7994 (m-10) REVERT: E 236 PHE cc_start: 0.9155 (t80) cc_final: 0.8919 (t80) REVERT: E 238 LYS cc_start: 0.9330 (ttmp) cc_final: 0.8993 (ttmp) REVERT: E 287 ARG cc_start: 0.8404 (mtt90) cc_final: 0.7804 (mtt90) REVERT: E 339 SER cc_start: 0.9390 (m) cc_final: 0.8924 (p) REVERT: E 344 ARG cc_start: 0.7873 (ttp-110) cc_final: 0.7340 (ttp-110) REVERT: E 366 TYR cc_start: 0.8824 (m-10) cc_final: 0.8220 (m-10) REVERT: E 422 ASN cc_start: 0.9074 (p0) cc_final: 0.8777 (p0) REVERT: E 447 GLN cc_start: 0.8846 (mt0) cc_final: 0.8458 (mm110) REVERT: E 462 TYR cc_start: 0.8778 (t80) cc_final: 0.8491 (t80) REVERT: E 486 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8013 (mm-30) REVERT: E 494 ASN cc_start: 0.9352 (p0) cc_final: 0.8892 (p0) REVERT: E 499 ASN cc_start: 0.8479 (m-40) cc_final: 0.7841 (m-40) REVERT: E 515 GLU cc_start: 0.8000 (tp30) cc_final: 0.6422 (tp30) REVERT: E 518 LYS cc_start: 0.8746 (mtmt) cc_final: 0.7237 (mtmt) REVERT: E 525 GLU cc_start: 0.8745 (tp30) cc_final: 0.8292 (tp30) REVERT: E 531 PHE cc_start: 0.9240 (m-80) cc_final: 0.8971 (m-80) REVERT: E 541 GLN cc_start: 0.8957 (tt0) cc_final: 0.8548 (tp40) REVERT: E 542 TYR cc_start: 0.9027 (t80) cc_final: 0.8821 (t80) REVERT: E 546 ASP cc_start: 0.8190 (t0) cc_final: 0.7909 (t70) REVERT: E 563 LYS cc_start: 0.9278 (tppt) cc_final: 0.8988 (mtpt) REVERT: E 586 LYS cc_start: 0.9194 (mtpp) cc_final: 0.8488 (mtpp) REVERT: E 587 MET cc_start: 0.8938 (mtt) cc_final: 0.8661 (mtm) REVERT: E 588 ASN cc_start: 0.8813 (m-40) cc_final: 0.8351 (m-40) REVERT: F 180 ASN cc_start: 0.9567 (t0) cc_final: 0.9298 (t0) REVERT: F 276 ASP cc_start: 0.8363 (p0) cc_final: 0.8012 (p0) REVERT: F 283 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8202 (m-30) REVERT: F 284 SER cc_start: 0.9137 (m) cc_final: 0.8761 (p) REVERT: F 344 ARG cc_start: 0.7817 (ttp-110) cc_final: 0.7312 (ttm110) REVERT: F 385 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8947 (tp) REVERT: F 430 THR cc_start: 0.9058 (m) cc_final: 0.8487 (p) REVERT: F 451 ASP cc_start: 0.7612 (t0) cc_final: 0.7342 (t0) REVERT: F 486 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8128 (mm-30) REVERT: F 496 LYS cc_start: 0.9412 (tttt) cc_final: 0.8762 (tppp) REVERT: F 535 GLU cc_start: 0.8331 (pt0) cc_final: 0.8017 (pt0) REVERT: F 556 GLN cc_start: 0.8911 (mt0) cc_final: 0.8280 (tp-100) REVERT: F 575 TYR cc_start: 0.8986 (m-10) cc_final: 0.8411 (m-10) REVERT: F 587 MET cc_start: 0.8954 (mtt) cc_final: 0.8224 (mtt) REVERT: F 593 ASP cc_start: 0.8392 (t0) cc_final: 0.7874 (t70) REVERT: F 637 LYS cc_start: 0.9330 (ttmt) cc_final: 0.8816 (ptmt) REVERT: F 662 MET cc_start: 0.3258 (ttt) cc_final: 0.2204 (ttp) REVERT: F 703 LYS cc_start: 0.8934 (mmtp) cc_final: 0.8334 (mmtt) REVERT: G 178 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8629 (mtt90) REVERT: G 238 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.9116 (mtpp) REVERT: G 292 ASN cc_start: 0.8162 (t0) cc_final: 0.7896 (t0) REVERT: G 346 TRP cc_start: 0.8198 (t-100) cc_final: 0.7739 (m-90) REVERT: G 356 ASP cc_start: 0.8580 (t0) cc_final: 0.7931 (t0) REVERT: G 361 ASN cc_start: 0.8379 (t0) cc_final: 0.8053 (t0) REVERT: G 419 ILE cc_start: 0.8963 (pp) cc_final: 0.8657 (pp) REVERT: G 472 ASP cc_start: 0.7882 (t0) cc_final: 0.7111 (t0) REVERT: G 512 ASP cc_start: 0.8780 (t0) cc_final: 0.8146 (t0) REVERT: G 515 GLU cc_start: 0.9451 (OUTLIER) cc_final: 0.8442 (mp0) REVERT: G 518 LYS cc_start: 0.9077 (mtmm) cc_final: 0.8868 (mtmm) REVERT: G 546 ASP cc_start: 0.7835 (t70) cc_final: 0.7579 (t70) REVERT: G 556 GLN cc_start: 0.9351 (tt0) cc_final: 0.9096 (tm-30) REVERT: G 560 GLN cc_start: 0.9075 (tp40) cc_final: 0.8088 (tp-100) REVERT: G 568 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8365 (mt-10) REVERT: G 573 ASN cc_start: 0.8887 (t0) cc_final: 0.8511 (t0) REVERT: G 582 LYS cc_start: 0.9183 (mmtt) cc_final: 0.8858 (mtmm) REVERT: G 657 ASN cc_start: 0.8355 (OUTLIER) cc_final: 0.7589 (m-40) outliers start: 163 outliers final: 135 residues processed: 1354 average time/residue: 0.1849 time to fit residues: 419.8560 Evaluate side-chains 1421 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1274 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 40 MET Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain L residue 120 TYR Chi-restraints excluded: chain L residue 122 LYS Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 250 GLN Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 665 ILE Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 375 TYR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 703 LYS Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 465 GLU Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 556 GLN Chi-restraints excluded: chain D residue 587 MET Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 374 ILE Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 537 ASN Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 704 GLU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 263 HIS Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 713 ASN Chi-restraints excluded: chain G residue 178 ARG Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 263 HIS Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain G residue 452 THR Chi-restraints excluded: chain G residue 458 ASN Chi-restraints excluded: chain G residue 515 GLU Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 620 ILE Chi-restraints excluded: chain G residue 657 ASN Chi-restraints excluded: chain G residue 665 ILE Chi-restraints excluded: chain G residue 675 PHE Chi-restraints excluded: chain G residue 724 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 116 optimal weight: 1.9990 chunk 373 optimal weight: 30.0000 chunk 138 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 292 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 151 optimal weight: 8.9990 chunk 217 optimal weight: 1.9990 chunk 263 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 402 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 281 ASN ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 ASN A 556 GLN B 363 ASN ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 GLN ** B 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 ASN B 565 GLN ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 588 ASN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 GLN D 424 GLN D 557 GLN E 299 HIS ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 556 GLN G 424 GLN ** G 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 GLN G 570 ASN G 616 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.187222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.119623 restraints weight = 46754.866| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 3.45 r_work: 0.3247 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.5890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 33385 Z= 0.202 Angle : 0.673 15.253 45291 Z= 0.346 Chirality : 0.049 0.261 5178 Planarity : 0.004 0.080 5938 Dihedral : 5.209 52.069 4505 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.69 % Favored : 95.19 % Rotamer: Outliers : 4.61 % Allowed : 27.28 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.13), residues: 4138 helix: 0.45 (0.22), residues: 633 sheet: 1.00 (0.16), residues: 1065 loop : -0.89 (0.13), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 595 TYR 0.032 0.002 TYR D 411 PHE 0.028 0.002 PHE E 439 TRP 0.034 0.002 TRP A 206 HIS 0.008 0.001 HIS E 263 Details of bonding type rmsd covalent geometry : bond 0.00447 (33385) covalent geometry : angle 0.67255 (45291) hydrogen bonds : bond 0.03201 ( 1183) hydrogen bonds : angle 5.29552 ( 3228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12161.71 seconds wall clock time: 207 minutes 26.08 seconds (12446.08 seconds total)