Starting phenix.real_space_refine on Sat Jul 4 03:09:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zv4_74855/07_2026/9zv4_74855.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zv4_74855/07_2026/9zv4_74855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zv4_74855/07_2026/9zv4_74855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zv4_74855/07_2026/9zv4_74855.map" model { file = "/net/cci-nas-00/data/ceres_data/9zv4_74855/07_2026/9zv4_74855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zv4_74855/07_2026/9zv4_74855.cif" } resolution = 3.15 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= -0.000 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 10973 2.51 5 N 2958 2.21 5 O 3456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17483 Number of models: 1 Model: "" Number of chains: 15 Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 3926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3926 Classifications: {'peptide': 491} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 20, 'TRANS': 470} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3927 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 20, 'TRANS': 470} Chain breaks: 1 Chain: "C" Number of atoms: 3927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3927 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 20, 'TRANS': 470} Chain breaks: 1 Chain: "I" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "K" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "G" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "E" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 1, 'NAG': 3, 'SIA': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 1, 'NAG': 3, 'SIA': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 7 Chain: "J" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 1, 'NAG': 3, 'SIA': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.94, per 1000 atoms: 0.23 Number of scatterers: 17483 At special positions: 0 Unit cell: (122.1, 122.925, 147.675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 3456 8.00 N 2958 7.00 C 10973 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 471 " distance=2.05 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.02 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 482 " distance=2.09 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 479 " distance=2.04 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 286 " distance=2.03 Simple disulfide: pdb=" SG CYS B 59 " - pdb=" SG CYS B 71 " distance=2.02 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 314 " distance=2.02 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 490 " distance=2.03 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS C 479 " distance=2.06 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 286 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 314 " distance=2.02 Simple disulfide: pdb=" SG CYS C 486 " - pdb=" SG CYS C 490 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " " BMA J 3 " - " MAN J 4 " BETA1-2 " MAN E 4 " - " NAG E 5 " " MAN F 4 " - " NAG F 5 " " MAN J 4 " - " NAG J 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG E 5 " - " GAL E 6 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG F 5 " - " GAL F 6 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG J 5 " - " GAL J 6 " BETA2-3 " GAL E 6 " - " SIA E 7 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL F 6 " - " SIA F 7 " " GAL J 6 " - " SIA J 7 " NAG-ASN " NAG A 601 " - " ASN A 27 " " NAG A 602 " - " ASN A 290 " " NAG A 603 " - " ASN A 14 " " NAG A 604 " - " ASN A 488 " " NAG B 601 " - " ASN B 27 " " NAG B 602 " - " ASN B 298 " " NAG B 603 " - " ASN B 15 " " NAG B 604 " - " ASN B 496 " " NAG C 601 " - " ASN C 27 " " NAG C 602 " - " ASN C 298 " " NAG C 603 " - " ASN C 14 " " NAG C 604 " - " ASN C 496 " Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 717.2 milliseconds 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3958 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 46 sheets defined 19.2% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.624A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.884A pdb=" N ILE A 75 " --> pdb=" O ASP A 72 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG A 76 " --> pdb=" O GLU A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 76' Processing helix chain 'A' and resid 101 through 110 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.972A pdb=" N TRP A 126 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 371 through 393 removed outlier: 3.961A pdb=" N THR A 375 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 461 removed outlier: 3.647A pdb=" N GLU A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG A 440 " --> pdb=" O MET A 436 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 452 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS A 455 " --> pdb=" O ASN A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 505 removed outlier: 3.573A pdb=" N ARG A 504 " --> pdb=" O ARG A 501 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU A 505 " --> pdb=" O LEU A 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 501 through 505' Processing helix chain 'B' and resid 60 through 67 Processing helix chain 'B' and resid 72 through 77 removed outlier: 4.030A pdb=" N ILE B 75 " --> pdb=" O ASP B 72 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG B 76 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL B 77 " --> pdb=" O PHE B 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 72 through 77' Processing helix chain 'B' and resid 101 through 110 Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.957A pdb=" N TRP B 126 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 379 through 401 Processing helix chain 'B' and resid 416 through 468 removed outlier: 3.700A pdb=" N GLU B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG B 448 " --> pdb=" O MET B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 497 removed outlier: 3.522A pdb=" N SER B 493 " --> pdb=" O GLU B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 503 No H-bonds generated for 'chain 'B' and resid 501 through 503' Processing helix chain 'B' and resid 504 through 512 removed outlier: 3.821A pdb=" N LEU B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS B 511 " --> pdb=" O GLU B 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 67 Processing helix chain 'C' and resid 72 through 76 removed outlier: 3.874A pdb=" N ILE C 75 " --> pdb=" O ASP C 72 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ARG C 76 " --> pdb=" O GLU C 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 72 through 76' Processing helix chain 'C' and resid 101 through 110 Processing helix chain 'C' and resid 122 through 126 removed outlier: 4.024A pdb=" N TRP C 126 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'C' and resid 379 through 401 removed outlier: 3.523A pdb=" N THR C 383 " --> pdb=" O ASP C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 466 removed outlier: 3.677A pdb=" N GLU C 447 " --> pdb=" O LEU C 443 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG C 448 " --> pdb=" O MET C 444 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 497 Processing helix chain 'C' and resid 504 through 513 removed outlier: 3.786A pdb=" N LEU C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS C 511 " --> pdb=" O GLU C 507 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU C 513 " --> pdb=" O ARG C 509 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 31 Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.640A pdb=" N THR I 87 " --> pdb=" O ALA I 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 31 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.614A pdb=" N THR D 87 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.576A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 56 through 59 removed outlier: 3.642A pdb=" N SER H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR H 58 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.134A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.640A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 6 through 8 removed outlier: 3.666A pdb=" N ILE A 7 " --> pdb=" O PHE A 472 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE A 472 " --> pdb=" O ILE A 7 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA7, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA8, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA9, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.605A pdb=" N LEU A 54 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE A 83 " --> pdb=" O MET A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.615A pdb=" N SER A 98 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N TRP A 234 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS A 114 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LYS A 263 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE A 112 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.615A pdb=" N SER A 98 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N TRP A 234 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AB4, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.597A pdb=" N ALA A 138 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 10.430A pdb=" N ALA A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 164 through 166 Processing sheet with id=AB6, first strand: chain 'A' and resid 288 through 289 removed outlier: 4.281A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 374 through 378 Processing sheet with id=AB8, first strand: chain 'B' and resid 19 through 20 Processing sheet with id=AB9, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AC1, first strand: chain 'B' and resid 37 through 38 Processing sheet with id=AC2, first strand: chain 'B' and resid 54 through 55 removed outlier: 6.656A pdb=" N LEU B 54 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE B 83 " --> pdb=" O MET B 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 97 through 99 removed outlier: 6.484A pdb=" N SER B 98 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N TRP B 234 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU B 179 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TYR B 264 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 269 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N HIS B 114 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS B 271 " --> pdb=" O ILE B 112 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE B 112 " --> pdb=" O LYS B 271 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 97 through 99 removed outlier: 6.484A pdb=" N SER B 98 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N TRP B 234 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU B 179 " --> pdb=" O PRO B 262 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 129 through 130 Processing sheet with id=AC6, first strand: chain 'B' and resid 136 through 141 removed outlier: 4.666A pdb=" N CYS B 139 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AC8, first strand: chain 'B' and resid 295 through 297 removed outlier: 4.183A pdb=" N CYS B 290 " --> pdb=" O ILE B 297 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 6 through 8 removed outlier: 3.605A pdb=" N ILE C 7 " --> pdb=" O PHE C 480 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE C 480 " --> pdb=" O ILE C 7 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 10 through 11 removed outlier: 3.634A pdb=" N GLY C 365 " --> pdb=" O GLY C 10 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AD3, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AD4, first strand: chain 'C' and resid 37 through 38 Processing sheet with id=AD5, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.646A pdb=" N LEU C 54 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE C 83 " --> pdb=" O MET C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 97 through 99 removed outlier: 6.537A pdb=" N SER C 98 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N TRP C 234 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU C 179 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N TYR C 264 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 269 " --> pdb=" O HIS C 114 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS C 114 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS C 271 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE C 112 " --> pdb=" O LYS C 271 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 97 through 99 removed outlier: 6.537A pdb=" N SER C 98 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N TRP C 234 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU C 179 " --> pdb=" O PRO C 262 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AD9, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.717A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 164 through 166 Processing sheet with id=AE2, first strand: chain 'C' and resid 295 through 297 removed outlier: 4.329A pdb=" N CYS C 290 " --> pdb=" O ILE C 297 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 3 through 5 removed outlier: 3.592A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 56 through 59 removed outlier: 3.715A pdb=" N SER I 56 " --> pdb=" O SER I 52 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR I 58 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.518A pdb=" N ARG K 24 " --> pdb=" O THR K 5 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.634A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.571A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 56 through 59 removed outlier: 3.693A pdb=" N SER D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR D 58 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.587A pdb=" N ARG G 24 " --> pdb=" O THR G 5 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE G 71 " --> pdb=" O CYS G 23 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.651A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) 633 hydrogen bonds defined for protein. 1683 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: 3.64 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.34: 5584 1.34 - 1.50: 5151 1.50 - 1.66: 6994 1.66 - 1.82: 137 1.82 - 1.98: 7 Bond restraints: 17873 Sorted by residual: bond pdb=" CB CYS A 482 " pdb=" SG CYS A 482 " ideal model delta sigma weight residual 1.808 1.979 -0.171 3.30e-02 9.18e+02 2.70e+01 bond pdb=" CB CYS A 478 " pdb=" SG CYS A 478 " ideal model delta sigma weight residual 1.808 1.938 -0.130 3.30e-02 9.18e+02 1.54e+01 bond pdb=" C MET A 483 " pdb=" O MET A 483 " ideal model delta sigma weight residual 1.233 1.179 0.054 1.49e-02 4.50e+03 1.31e+01 bond pdb=" C ASP A 479 " pdb=" N ASN A 480 " ideal model delta sigma weight residual 1.332 1.381 -0.049 1.40e-02 5.10e+03 1.21e+01 bond pdb=" CA ASN A 480 " pdb=" C ASN A 480 " ideal model delta sigma weight residual 1.523 1.565 -0.041 1.34e-02 5.57e+03 9.58e+00 ... (remaining 17868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 23969 3.41 - 6.81: 202 6.81 - 10.22: 27 10.22 - 13.63: 8 13.63 - 17.03: 2 Bond angle restraints: 24208 Sorted by residual: angle pdb=" CA CYS A 478 " pdb=" CB CYS A 478 " pdb=" SG CYS A 478 " ideal model delta sigma weight residual 114.40 131.43 -17.03 2.30e+00 1.89e-01 5.49e+01 angle pdb=" C GLN G 90 " pdb=" N HIS G 91 " pdb=" CA HIS G 91 " ideal model delta sigma weight residual 121.54 134.36 -12.82 1.91e+00 2.74e-01 4.51e+01 angle pdb=" C GLN L 90 " pdb=" N HIS L 91 " pdb=" CA HIS L 91 " ideal model delta sigma weight residual 121.54 134.34 -12.80 1.91e+00 2.74e-01 4.49e+01 angle pdb=" CA CYS A 482 " pdb=" CB CYS A 482 " pdb=" SG CYS A 482 " ideal model delta sigma weight residual 114.40 129.57 -15.17 2.30e+00 1.89e-01 4.35e+01 angle pdb=" C GLN K 90 " pdb=" N HIS K 91 " pdb=" CA HIS K 91 " ideal model delta sigma weight residual 121.54 134.10 -12.56 1.91e+00 2.74e-01 4.33e+01 ... (remaining 24203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.15: 9489 18.15 - 36.30: 1195 36.30 - 54.45: 335 54.45 - 72.60: 68 72.60 - 90.75: 20 Dihedral angle restraints: 11107 sinusoidal: 4896 harmonic: 6211 Sorted by residual: dihedral pdb=" CA CYS A 482 " pdb=" C CYS A 482 " pdb=" N MET A 483 " pdb=" CA MET A 483 " ideal model delta harmonic sigma weight residual 180.00 107.48 72.52 0 5.00e+00 4.00e-02 2.10e+02 dihedral pdb=" CB CYS B 46 " pdb=" SG CYS B 46 " pdb=" SG CYS B 286 " pdb=" CB CYS B 286 " ideal model delta sinusoidal sigma weight residual -86.00 -14.13 -71.87 1 1.00e+01 1.00e-02 6.61e+01 dihedral pdb=" CB CYS B 486 " pdb=" SG CYS B 486 " pdb=" SG CYS B 490 " pdb=" CB CYS B 490 " ideal model delta sinusoidal sigma weight residual 93.00 163.07 -70.07 1 1.00e+01 1.00e-02 6.33e+01 ... (remaining 11104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.215: 2669 0.215 - 0.430: 15 0.430 - 0.646: 2 0.646 - 0.861: 0 0.861 - 1.076: 1 Chirality restraints: 2687 Sorted by residual: chirality pdb=" C2 SIA J 7 " pdb=" O3 GAL J 6 " pdb=" C1 SIA J 7 " pdb=" O6 SIA J 7 " both_signs ideal model delta sigma weight residual False -2.50 -2.84 0.34 2.00e-02 2.50e+03 2.86e+02 chirality pdb=" C2 SIA E 7 " pdb=" O3 GAL E 6 " pdb=" C1 SIA E 7 " pdb=" O6 SIA E 7 " both_signs ideal model delta sigma weight residual False -2.50 -2.82 0.32 2.00e-02 2.50e+03 2.51e+02 chirality pdb=" C2 SIA F 7 " pdb=" O3 GAL F 6 " pdb=" C1 SIA F 7 " pdb=" O6 SIA F 7 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.31 2.00e-02 2.50e+03 2.41e+02 ... (remaining 2684 not shown) Planarity restraints: 3111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 14 " 0.045 2.00e-02 2.50e+03 4.55e-02 2.59e+01 pdb=" CG ASN A 14 " -0.063 2.00e-02 2.50e+03 pdb=" OD1 ASN A 14 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN A 14 " -0.046 2.00e-02 2.50e+03 pdb=" C1 NAG A 603 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE K 94 " 0.060 5.00e-02 4.00e+02 9.15e-02 1.34e+01 pdb=" N PRO K 95 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO K 95 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO K 95 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE G 94 " 0.060 5.00e-02 4.00e+02 9.08e-02 1.32e+01 pdb=" N PRO G 95 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO G 95 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO G 95 " 0.048 5.00e-02 4.00e+02 ... (remaining 3108 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 8307 2.99 - 3.47: 16122 3.47 - 3.95: 30036 3.95 - 4.42: 35692 4.42 - 4.90: 58391 Nonbonded interactions: 148548 Sorted by model distance: nonbonded pdb=" O5 NAG C 604 " pdb=" O6 NAG C 604 " model vdw 2.517 2.432 nonbonded pdb=" C4 NAG F 1 " pdb=" O5 NAG F 2 " model vdw 2.531 2.776 nonbonded pdb=" N ASP A 353 " pdb=" O ASP A 353 " model vdw 2.587 2.496 nonbonded pdb=" N ASP C 92 " pdb=" O ASP C 92 " model vdw 2.588 2.496 nonbonded pdb=" O5 NAG J 1 " pdb=" O6 NAG J 1 " model vdw 2.591 2.432 ... (remaining 148543 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' and (resid 5 through 241 or (resid 242 and (name N or name CA or name \ C or name O )) or resid 243 through 604)) selection = (chain 'C' and (resid 5 through 241 or (resid 242 and (name N or name CA or name \ C or name O )) or resid 243 through 604)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'L' } 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: 5.410 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 16.310 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.010 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5651 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.171 17924 Z= 0.217 Angle : 0.919 17.717 24340 Z= 0.467 Chirality : 0.060 1.076 2687 Planarity : 0.007 0.091 3099 Dihedral : 17.270 90.751 7086 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.91 % Favored : 93.62 % Rotamer: Outliers : 3.26 % Allowed : 24.77 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.17), residues: 2133 helix: 0.32 (0.27), residues: 364 sheet: -1.15 (0.22), residues: 551 loop : -1.65 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 111 TYR 0.019 0.002 TYR A 491 PHE 0.040 0.002 PHE D 99 TRP 0.021 0.001 TRP A 153 HIS 0.009 0.001 HIS G 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.22 (17873) covalent geometry : angle 0.85085 / 0.45 (24208) SS BOND : bond 0.01485 / 0.89 ( 21) SS BOND : angle 3.84764 / 3.02 ( 42) hydrogen bonds : bond 0.18796 / 12.90 ( 603) hydrogen bonds : angle 8.43340 / 5.68 ( 1683) link_ALPHA1-3 : bond 0.00740 / 0.37 ( 3) link_ALPHA1-3 : angle 1.36246 / 0.70 ( 9) link_BETA1-2 : bond 0.00089 / 0.04 ( 3) link_BETA1-2 : angle 1.33937 / 0.66 ( 9) link_BETA1-4 : bond 0.00631 / 0.39 ( 9) link_BETA1-4 : angle 3.51577 / 2.11 ( 27) link_BETA2-3 : bond 0.00117 / 0.06 ( 3) link_BETA2-3 : angle 6.10634 / 3.09 ( 9) link_NAG-ASN : bond 0.00993 / 0.56 ( 12) link_NAG-ASN : angle 6.89396 / 4.85 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 234 time to evaluate : 0.691 Fit side-chains REVERT: L 70 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.6407 (tt0) REVERT: A 18 GLU cc_start: 0.6617 (mm-30) cc_final: 0.6092 (mt-10) REVERT: A 139 CYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6138 (m) REVERT: A 165 LYS cc_start: 0.7268 (mtmt) cc_final: 0.6675 (mttm) REVERT: A 175 ASP cc_start: 0.7191 (m-30) cc_final: 0.6521 (m-30) REVERT: A 187 ASN cc_start: 0.6662 (OUTLIER) cc_final: 0.5975 (p0) REVERT: A 262 LYS cc_start: 0.7112 (OUTLIER) cc_final: 0.5856 (tttt) REVERT: A 305 GLU cc_start: 0.6441 (mt-10) cc_final: 0.6024 (mm-30) REVERT: A 311 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7068 (mtmm) REVERT: A 345 GLU cc_start: 0.6472 (mp0) cc_final: 0.5831 (pt0) REVERT: A 356 TYR cc_start: 0.6504 (OUTLIER) cc_final: 0.4437 (p90) REVERT: A 384 ASN cc_start: 0.6547 (m-40) cc_final: 0.6251 (m-40) REVERT: A 440 ARG cc_start: 0.6324 (mtm180) cc_final: 0.5676 (mtp85) REVERT: B 18 GLU cc_start: 0.6416 (mm-30) cc_final: 0.5868 (mt-10) REVERT: B 111 ARG cc_start: 0.6186 (OUTLIER) cc_final: 0.5051 (mtt90) REVERT: B 139 CYS cc_start: 0.6956 (OUTLIER) cc_final: 0.6212 (m) REVERT: B 165 LYS cc_start: 0.7267 (mttt) cc_final: 0.5966 (mmmt) REVERT: B 175 ASP cc_start: 0.7244 (m-30) cc_final: 0.6449 (m-30) REVERT: B 193 ASN cc_start: 0.6411 (m-40) cc_final: 0.6048 (m110) REVERT: B 231 ASP cc_start: 0.5758 (OUTLIER) cc_final: 0.5205 (m-30) REVERT: B 270 LYS cc_start: 0.6656 (tttt) cc_final: 0.6096 (tttp) REVERT: B 271 LYS cc_start: 0.7638 (mtmt) cc_final: 0.6412 (mtpt) REVERT: B 289 LYS cc_start: 0.6990 (mttt) cc_final: 0.6371 (mmtm) REVERT: B 313 GLU cc_start: 0.6263 (mt-10) cc_final: 0.5991 (mm-30) REVERT: B 381 GLU cc_start: 0.6251 (tt0) cc_final: 0.5945 (tt0) REVERT: B 385 LYS cc_start: 0.6155 (OUTLIER) cc_final: 0.5474 (mtmt) REVERT: B 392 ASN cc_start: 0.6567 (m-40) cc_final: 0.6328 (m-40) REVERT: B 424 LYS cc_start: 0.6530 (tttt) cc_final: 0.6011 (ttpp) REVERT: B 448 ARG cc_start: 0.6553 (mtm-85) cc_final: 0.5780 (mtp85) REVERT: B 473 LYS cc_start: 0.6884 (ttmt) cc_final: 0.6422 (tttm) REVERT: B 481 GLU cc_start: 0.7309 (tt0) cc_final: 0.7004 (tt0) REVERT: C 18 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.6010 (mt-10) REVERT: C 57 LYS cc_start: 0.7166 (mttm) cc_final: 0.6751 (mtpt) REVERT: C 111 ARG cc_start: 0.6747 (mtt90) cc_final: 0.6100 (mpt90) REVERT: C 165 LYS cc_start: 0.7385 (mttt) cc_final: 0.7003 (mttm) REVERT: C 175 ASP cc_start: 0.7598 (m-30) cc_final: 0.6830 (m-30) REVERT: C 231 ASP cc_start: 0.6102 (OUTLIER) cc_final: 0.5579 (m-30) REVERT: C 271 LYS cc_start: 0.7380 (mtmt) cc_final: 0.6361 (mtpt) REVERT: C 319 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7077 (mtmm) REVERT: C 353 GLU cc_start: 0.6503 (mp0) cc_final: 0.5673 (mm-30) REVERT: C 385 LYS cc_start: 0.6045 (OUTLIER) cc_final: 0.5379 (mtmt) REVERT: C 424 LYS cc_start: 0.6903 (tttt) cc_final: 0.6544 (tttm) REVERT: C 491 MET cc_start: 0.7211 (mmt) cc_final: 0.6912 (mmt) REVERT: C 493 SER cc_start: 0.7142 (m) cc_final: 0.6810 (p) REVERT: C 500 ASP cc_start: 0.7163 (OUTLIER) cc_final: 0.6698 (t70) REVERT: K 70 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6631 (tt0) REVERT: K 95 MET cc_start: 0.7786 (mtm) cc_final: 0.7480 (mtm) REVERT: G 70 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6449 (tt0) outliers start: 61 outliers final: 35 residues processed: 285 average time/residue: 0.1302 time to fit residues: 55.6640 Evaluate side-chains 282 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 230 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 500 ASP Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 70 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 ASN C 169 ASN C 367 HIS ** C 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.150006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.110200 restraints weight = 169724.233| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 7.05 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 17924 Z= 0.211 Angle : 0.764 15.406 24340 Z= 0.378 Chirality : 0.051 0.669 2687 Planarity : 0.006 0.090 3099 Dihedral : 10.049 79.555 3159 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.70 % Allowed : 4.97 % Favored : 94.33 % Rotamer: Outliers : 5.19 % Allowed : 22.31 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.42 (0.17), residues: 2133 helix: 0.87 (0.27), residues: 378 sheet: -0.96 (0.22), residues: 548 loop : -1.55 (0.16), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 111 TYR 0.018 0.002 TYR A 491 PHE 0.023 0.002 PHE D 99 TRP 0.010 0.002 TRP B 153 HIS 0.009 0.001 HIS K 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 (17873) covalent geometry : angle 0.70546 / 0.36 (24208) SS BOND : bond 0.00909 / 0.50 ( 21) SS BOND : angle 2.79604 / 2.10 ( 42) hydrogen bonds : bond 0.04302 / 2.98 ( 603) hydrogen bonds : angle 6.00579 / 4.08 ( 1683) link_ALPHA1-3 : bond 0.00538 / 0.27 ( 3) link_ALPHA1-3 : angle 1.58475 / 0.80 ( 9) link_BETA1-2 : bond 0.00061 / 0.03 ( 3) link_BETA1-2 : angle 1.40948 / 0.70 ( 9) link_BETA1-4 : bond 0.00395 / 0.23 ( 9) link_BETA1-4 : angle 3.49834 / 2.08 ( 27) link_BETA2-3 : bond 0.00676 / 0.34 ( 3) link_BETA2-3 : angle 4.78579 / 2.46 ( 9) link_NAG-ASN : bond 0.00825 / 0.49 ( 12) link_NAG-ASN : angle 5.92035 / 4.14 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 232 time to evaluate : 0.607 Fit side-chains REVERT: H 31 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7701 (m110) REVERT: A 187 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.7688 (p0) REVERT: A 293 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8207 (mmm) REVERT: A 345 GLU cc_start: 0.7725 (mp0) cc_final: 0.7302 (pt0) REVERT: A 356 TYR cc_start: 0.7961 (OUTLIER) cc_final: 0.6219 (p90) REVERT: A 373 GLU cc_start: 0.8045 (tt0) cc_final: 0.7706 (tt0) REVERT: A 398 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7082 (mt-10) REVERT: B 76 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.5676 (tpt170) REVERT: B 271 LYS cc_start: 0.8534 (mtmt) cc_final: 0.8062 (mtpt) REVERT: B 301 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.7344 (mmt) REVERT: B 353 GLU cc_start: 0.7556 (mp0) cc_final: 0.7248 (pt0) REVERT: B 379 ASP cc_start: 0.7758 (t70) cc_final: 0.7513 (t70) REVERT: B 385 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8031 (mtmt) REVERT: B 406 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: B 424 LYS cc_start: 0.8254 (tttt) cc_final: 0.7919 (ttpp) REVERT: B 473 LYS cc_start: 0.7878 (ttmt) cc_final: 0.7217 (tttm) REVERT: C 57 LYS cc_start: 0.8381 (mttm) cc_final: 0.8074 (mtpt) REVERT: C 133 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8845 (mp) REVERT: C 173 ARG cc_start: 0.6255 (mmp-170) cc_final: 0.5855 (mmp-170) REVERT: C 174 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7433 (mt-10) REVERT: C 271 LYS cc_start: 0.8587 (mtmt) cc_final: 0.8276 (mtpt) REVERT: C 301 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.7784 (mmt) REVERT: C 353 GLU cc_start: 0.7547 (mp0) cc_final: 0.7047 (mm-30) REVERT: C 385 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8003 (mtmt) REVERT: C 469 ARG cc_start: 0.5831 (OUTLIER) cc_final: 0.5313 (ptm160) REVERT: C 473 LYS cc_start: 0.7231 (tttt) cc_final: 0.6882 (tmtt) REVERT: C 500 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7317 (t70) REVERT: I 71 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.6069 (ptp-170) REVERT: K 95 MET cc_start: 0.8217 (mtm) cc_final: 0.7726 (mtm) REVERT: D 31 ASN cc_start: 0.8476 (m-40) cc_final: 0.8071 (m-40) REVERT: D 91 TYR cc_start: 0.8150 (m-80) cc_final: 0.7768 (m-80) REVERT: G 95 MET cc_start: 0.8206 (mtm) cc_final: 0.7803 (mtm) outliers start: 97 outliers final: 49 residues processed: 315 average time/residue: 0.1198 time to fit residues: 56.5822 Evaluate side-chains 282 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 217 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 94 PHE Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain C residue 500 ASP Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 94 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 55 optimal weight: 0.0470 chunk 129 optimal weight: 0.1980 chunk 35 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 158 optimal weight: 0.6980 chunk 204 optimal weight: 6.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.149839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.110496 restraints weight = 168242.570| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 7.03 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 17924 Z= 0.176 Angle : 0.736 14.872 24340 Z= 0.360 Chirality : 0.050 0.662 2687 Planarity : 0.005 0.089 3099 Dihedral : 9.441 77.110 3103 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.06 % Favored : 94.28 % Rotamer: Outliers : 5.08 % Allowed : 21.51 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.19 (0.17), residues: 2133 helix: 1.18 (0.27), residues: 378 sheet: -0.69 (0.22), residues: 543 loop : -1.52 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 229 TYR 0.016 0.002 TYR A 491 PHE 0.024 0.002 PHE D 99 TRP 0.009 0.001 TRP B 153 HIS 0.009 0.001 HIS G 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (17873) covalent geometry : angle 0.67318 / 0.34 (24208) SS BOND : bond 0.00902 / 0.49 ( 21) SS BOND : angle 2.74135 / 2.08 ( 42) hydrogen bonds : bond 0.03985 / 2.77 ( 603) hydrogen bonds : angle 5.67401 / 3.86 ( 1683) link_ALPHA1-3 : bond 0.00596 / 0.30 ( 3) link_ALPHA1-3 : angle 1.44885 / 0.73 ( 9) link_BETA1-2 : bond 0.00082 / 0.04 ( 3) link_BETA1-2 : angle 1.30362 / 0.64 ( 9) link_BETA1-4 : bond 0.00410 / 0.26 ( 9) link_BETA1-4 : angle 3.40225 / 2.02 ( 27) link_BETA2-3 : bond 0.00725 / 0.36 ( 3) link_BETA2-3 : angle 4.79791 / 2.47 ( 9) link_NAG-ASN : bond 0.00940 / 0.52 ( 12) link_NAG-ASN : angle 6.09960 / 4.36 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 219 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 187 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.7925 (p0) REVERT: A 193 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7895 (m110) REVERT: A 293 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.7655 (mmt) REVERT: A 345 GLU cc_start: 0.7642 (mp0) cc_final: 0.7265 (pt0) REVERT: A 356 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.6093 (p90) REVERT: A 373 GLU cc_start: 0.8025 (tt0) cc_final: 0.7680 (tt0) REVERT: A 398 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7093 (mt-10) REVERT: A 406 ASN cc_start: 0.8709 (t0) cc_final: 0.8355 (t0) REVERT: A 473 GLU cc_start: 0.7217 (tt0) cc_final: 0.6889 (mt-10) REVERT: B 76 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.5626 (tpt170) REVERT: B 271 LYS cc_start: 0.8585 (mtmt) cc_final: 0.8126 (mtpt) REVERT: B 301 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.7511 (mmt) REVERT: B 353 GLU cc_start: 0.7403 (mp0) cc_final: 0.7146 (pt0) REVERT: B 385 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7845 (mtmt) REVERT: B 406 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7297 (mt-10) REVERT: B 424 LYS cc_start: 0.8421 (tttt) cc_final: 0.8129 (ttpp) REVERT: B 473 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7264 (tttm) REVERT: C 57 LYS cc_start: 0.8414 (mttm) cc_final: 0.8136 (mtpt) REVERT: C 133 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8804 (mp) REVERT: C 173 ARG cc_start: 0.6355 (mmp-170) cc_final: 0.6112 (mmp-170) REVERT: C 213 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8549 (mt) REVERT: C 271 LYS cc_start: 0.8574 (mtmt) cc_final: 0.8245 (mtpt) REVERT: C 301 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.7663 (mmt) REVERT: C 353 GLU cc_start: 0.7442 (mp0) cc_final: 0.6961 (mm-30) REVERT: C 385 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7821 (mtmt) REVERT: C 469 ARG cc_start: 0.5887 (OUTLIER) cc_final: 0.5228 (ptm160) REVERT: C 473 LYS cc_start: 0.7358 (tttt) cc_final: 0.7147 (tttt) REVERT: I 71 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.6137 (ptp-170) REVERT: K 95 MET cc_start: 0.8322 (mtm) cc_final: 0.7816 (mtm) REVERT: D 31 ASN cc_start: 0.8398 (m-40) cc_final: 0.7920 (m-40) REVERT: D 46 GLU cc_start: 0.8242 (tt0) cc_final: 0.7910 (tt0) REVERT: G 95 MET cc_start: 0.8268 (mtm) cc_final: 0.7830 (mtm) outliers start: 95 outliers final: 61 residues processed: 295 average time/residue: 0.1198 time to fit residues: 53.4686 Evaluate side-chains 288 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 212 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 94 PHE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 448 ARG Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 94 PHE Chi-restraints excluded: chain G residue 103 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 64 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 chunk 207 optimal weight: 0.0670 chunk 154 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 175 optimal weight: 0.7980 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 193 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.150983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.111883 restraints weight = 172359.020| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 7.07 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 17924 Z= 0.153 Angle : 0.702 15.455 24340 Z= 0.345 Chirality : 0.050 0.745 2687 Planarity : 0.005 0.088 3099 Dihedral : 9.151 75.175 3098 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.06 % Favored : 94.28 % Rotamer: Outliers : 5.03 % Allowed : 21.51 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.98 (0.18), residues: 2133 helix: 1.42 (0.27), residues: 378 sheet: -0.53 (0.22), residues: 543 loop : -1.42 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 111 TYR 0.014 0.001 TYR A 491 PHE 0.014 0.002 PHE C 351 TRP 0.011 0.001 TRP B 153 HIS 0.009 0.001 HIS G 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (17873) covalent geometry : angle 0.64061 / 0.33 (24208) SS BOND : bond 0.00975 / 0.55 ( 21) SS BOND : angle 2.74236 / 2.07 ( 42) hydrogen bonds : bond 0.03682 / 2.56 ( 603) hydrogen bonds : angle 5.37876 / 3.66 ( 1683) link_ALPHA1-3 : bond 0.00621 / 0.31 ( 3) link_ALPHA1-3 : angle 1.37625 / 0.69 ( 9) link_BETA1-2 : bond 0.00088 / 0.04 ( 3) link_BETA1-2 : angle 1.21021 / 0.59 ( 9) link_BETA1-4 : bond 0.00421 / 0.27 ( 9) link_BETA1-4 : angle 3.28792 / 1.95 ( 27) link_BETA2-3 : bond 0.00648 / 0.32 ( 3) link_BETA2-3 : angle 4.60598 / 2.37 ( 9) link_NAG-ASN : bond 0.00996 / 0.54 ( 12) link_NAG-ASN : angle 5.85276 / 4.10 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 219 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 139 CYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8394 (m) REVERT: A 187 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7765 (p0) REVERT: A 293 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.7624 (mmt) REVERT: A 345 GLU cc_start: 0.7657 (mp0) cc_final: 0.7280 (pt0) REVERT: A 356 TYR cc_start: 0.7781 (OUTLIER) cc_final: 0.5904 (p90) REVERT: A 373 GLU cc_start: 0.7947 (tt0) cc_final: 0.7589 (tt0) REVERT: A 398 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.7028 (mt-10) REVERT: A 406 ASN cc_start: 0.8687 (t0) cc_final: 0.8335 (t0) REVERT: A 473 GLU cc_start: 0.7028 (tt0) cc_final: 0.6705 (mt-10) REVERT: B 76 ARG cc_start: 0.6728 (OUTLIER) cc_final: 0.5628 (tpt170) REVERT: B 213 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8451 (mt) REVERT: B 271 LYS cc_start: 0.8651 (mtmt) cc_final: 0.8163 (mtpt) REVERT: B 385 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.7819 (mtmt) REVERT: B 406 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7304 (mt-10) REVERT: B 424 LYS cc_start: 0.8361 (tttt) cc_final: 0.8050 (ttpp) REVERT: B 473 LYS cc_start: 0.7854 (ttmt) cc_final: 0.7117 (tttm) REVERT: C 57 LYS cc_start: 0.8410 (mttm) cc_final: 0.8122 (mtpt) REVERT: C 133 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8864 (mp) REVERT: C 174 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7695 (mt-10) REVERT: C 187 ASN cc_start: 0.8115 (OUTLIER) cc_final: 0.7696 (p0) REVERT: C 213 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8578 (mt) REVERT: C 271 LYS cc_start: 0.8623 (mtmt) cc_final: 0.8275 (mtpt) REVERT: C 301 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.7378 (mmt) REVERT: C 353 GLU cc_start: 0.7428 (mp0) cc_final: 0.6982 (mm-30) REVERT: C 371 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6684 (pm20) REVERT: C 385 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7841 (mtmt) REVERT: C 469 ARG cc_start: 0.5937 (OUTLIER) cc_final: 0.5261 (ptm160) REVERT: C 473 LYS cc_start: 0.7400 (tttt) cc_final: 0.7092 (tttt) REVERT: I 71 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.6131 (ptp-170) REVERT: K 95 MET cc_start: 0.8178 (mtm) cc_final: 0.7689 (mtm) REVERT: D 31 ASN cc_start: 0.8348 (m-40) cc_final: 0.8015 (m-40) REVERT: G 95 MET cc_start: 0.8191 (mtm) cc_final: 0.7717 (mtm) outliers start: 94 outliers final: 60 residues processed: 297 average time/residue: 0.1182 time to fit residues: 53.6886 Evaluate side-chains 288 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 210 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 94 PHE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 448 ARG Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 94 PHE Chi-restraints excluded: chain G residue 103 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 84 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 143 optimal weight: 0.0870 chunk 25 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.149835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.110891 restraints weight = 170425.059| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 6.97 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 17924 Z= 0.168 Angle : 0.716 16.181 24340 Z= 0.354 Chirality : 0.051 0.995 2687 Planarity : 0.005 0.088 3099 Dihedral : 9.061 74.570 3093 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.16 % Favored : 94.19 % Rotamer: Outliers : 4.98 % Allowed : 21.46 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.94 (0.18), residues: 2133 helix: 1.45 (0.27), residues: 378 sheet: -0.54 (0.22), residues: 570 loop : -1.38 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 229 TYR 0.015 0.002 TYR A 491 PHE 0.016 0.002 PHE C 480 TRP 0.012 0.001 TRP B 153 HIS 0.008 0.001 HIS G 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (17873) covalent geometry : angle 0.65582 / 0.34 (24208) SS BOND : bond 0.01034 / 0.62 ( 21) SS BOND : angle 2.76382 / 2.06 ( 42) hydrogen bonds : bond 0.03778 / 2.62 ( 603) hydrogen bonds : angle 5.33405 / 3.63 ( 1683) link_ALPHA1-3 : bond 0.00566 / 0.28 ( 3) link_ALPHA1-3 : angle 1.41098 / 0.71 ( 9) link_BETA1-2 : bond 0.00093 / 0.04 ( 3) link_BETA1-2 : angle 1.18565 / 0.58 ( 9) link_BETA1-4 : bond 0.00411 / 0.26 ( 9) link_BETA1-4 : angle 3.27100 / 1.95 ( 27) link_BETA2-3 : bond 0.00684 / 0.34 ( 3) link_BETA2-3 : angle 4.70360 / 2.42 ( 9) link_NAG-ASN : bond 0.00850 / 0.47 ( 12) link_NAG-ASN : angle 5.84252 / 4.08 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 218 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: A 139 CYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8554 (m) REVERT: A 187 ASN cc_start: 0.8256 (OUTLIER) cc_final: 0.7848 (p0) REVERT: A 193 ASN cc_start: 0.8291 (OUTLIER) cc_final: 0.7944 (m110) REVERT: A 293 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.7739 (mmt) REVERT: A 345 GLU cc_start: 0.7676 (mp0) cc_final: 0.7303 (pt0) REVERT: A 356 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.5937 (p90) REVERT: A 373 GLU cc_start: 0.7973 (tt0) cc_final: 0.7629 (tt0) REVERT: A 398 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7175 (mt-10) REVERT: A 406 ASN cc_start: 0.8687 (t0) cc_final: 0.8300 (t0) REVERT: A 473 GLU cc_start: 0.7261 (tt0) cc_final: 0.6928 (mt-10) REVERT: B 76 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.5515 (tpt170) REVERT: B 213 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8458 (mt) REVERT: B 271 LYS cc_start: 0.8643 (mtmt) cc_final: 0.8178 (mtpt) REVERT: B 301 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.7395 (mmt) REVERT: B 385 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7859 (mtmt) REVERT: B 406 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7435 (mt-10) REVERT: B 424 LYS cc_start: 0.8397 (tttt) cc_final: 0.8073 (ttpp) REVERT: B 473 LYS cc_start: 0.7915 (ttmt) cc_final: 0.7187 (tttm) REVERT: C 57 LYS cc_start: 0.8300 (mttm) cc_final: 0.7995 (mtpt) REVERT: C 133 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8795 (mp) REVERT: C 174 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7777 (mt-10) REVERT: C 187 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7745 (p0) REVERT: C 213 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8522 (mt) REVERT: C 271 LYS cc_start: 0.8565 (mtmt) cc_final: 0.8257 (mtpt) REVERT: C 301 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.7526 (mmt) REVERT: C 353 GLU cc_start: 0.7423 (mp0) cc_final: 0.7032 (mm-30) REVERT: C 371 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6539 (pm20) REVERT: C 385 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7897 (mtmt) REVERT: C 469 ARG cc_start: 0.6027 (OUTLIER) cc_final: 0.5363 (ptm160) REVERT: C 473 LYS cc_start: 0.7577 (tttt) cc_final: 0.7297 (tttt) REVERT: I 71 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.6124 (ptp-170) REVERT: K 95 MET cc_start: 0.8125 (mtm) cc_final: 0.7581 (mtm) REVERT: D 31 ASN cc_start: 0.8401 (m-40) cc_final: 0.8035 (m-40) REVERT: D 91 TYR cc_start: 0.8120 (m-80) cc_final: 0.7848 (m-80) REVERT: G 95 MET cc_start: 0.8011 (mtm) cc_final: 0.7545 (mtm) outliers start: 93 outliers final: 64 residues processed: 292 average time/residue: 0.1437 time to fit residues: 63.4825 Evaluate side-chains 297 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 213 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 94 PHE Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 448 ARG Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain G residue 94 PHE Chi-restraints excluded: chain G residue 103 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 122 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 140 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 193 ASN B 467 GLN C 193 ASN C 414 ASN ** C 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.145799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.106772 restraints weight = 173434.496| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 6.93 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 17924 Z= 0.303 Angle : 0.858 15.545 24340 Z= 0.424 Chirality : 0.058 1.078 2687 Planarity : 0.006 0.087 3099 Dihedral : 9.531 77.598 3088 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.70 % Allowed : 6.24 % Favored : 93.06 % Rotamer: Outliers : 5.24 % Allowed : 22.15 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.26 (0.17), residues: 2133 helix: 0.88 (0.27), residues: 387 sheet: -0.74 (0.22), residues: 555 loop : -1.50 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 229 TYR 0.018 0.002 TYR A 491 PHE 0.019 0.003 PHE C 148 TRP 0.017 0.002 TRP B 153 HIS 0.012 0.002 HIS K 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00729 / 0.30 (17873) covalent geometry : angle 0.79542 / 0.41 (24208) SS BOND : bond 0.01099 / 0.69 ( 21) SS BOND : angle 3.01632 / 2.16 ( 42) hydrogen bonds : bond 0.04601 / 3.19 ( 603) hydrogen bonds : angle 5.71520 / 3.89 ( 1683) link_ALPHA1-3 : bond 0.00363 / 0.18 ( 3) link_ALPHA1-3 : angle 1.69764 / 0.86 ( 9) link_BETA1-2 : bond 0.00097 / 0.05 ( 3) link_BETA1-2 : angle 1.40694 / 0.69 ( 9) link_BETA1-4 : bond 0.00420 / 0.23 ( 9) link_BETA1-4 : angle 3.56669 / 2.15 ( 27) link_BETA2-3 : bond 0.00857 / 0.43 ( 3) link_BETA2-3 : angle 5.29774 / 2.72 ( 9) link_NAG-ASN : bond 0.01013 / 0.59 ( 12) link_NAG-ASN : angle 6.62883 / 4.70 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 217 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: A 187 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.8019 (p0) REVERT: A 193 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.8090 (m110) REVERT: A 345 GLU cc_start: 0.7522 (mp0) cc_final: 0.7192 (pt0) REVERT: A 373 GLU cc_start: 0.7989 (tt0) cc_final: 0.7632 (tt0) REVERT: A 398 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7114 (mt-10) REVERT: A 419 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.7885 (mt-10) REVERT: B 55 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8677 (mp) REVERT: B 76 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6054 (tpt170) REVERT: B 213 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8566 (mt) REVERT: B 271 LYS cc_start: 0.8624 (mtmt) cc_final: 0.8329 (mtpt) REVERT: B 301 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.7305 (mmt) REVERT: B 385 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.7929 (mtmt) REVERT: B 406 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7357 (mt-10) REVERT: B 424 LYS cc_start: 0.8524 (tttt) cc_final: 0.8167 (ttpp) REVERT: B 473 LYS cc_start: 0.7929 (ttmt) cc_final: 0.7257 (tttm) REVERT: C 57 LYS cc_start: 0.8422 (mttm) cc_final: 0.8036 (mtpt) REVERT: C 133 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8920 (mp) REVERT: C 174 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7881 (mt-10) REVERT: C 213 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8457 (mt) REVERT: C 271 LYS cc_start: 0.8568 (mtmt) cc_final: 0.8336 (mtpp) REVERT: C 353 GLU cc_start: 0.7447 (mp0) cc_final: 0.6845 (tp30) REVERT: C 371 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6733 (pm20) REVERT: C 385 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.7962 (mtmt) REVERT: C 469 ARG cc_start: 0.5990 (OUTLIER) cc_final: 0.5305 (ptm160) REVERT: K 95 MET cc_start: 0.8203 (mtm) cc_final: 0.7649 (mtm) REVERT: D 31 ASN cc_start: 0.8517 (m-40) cc_final: 0.8090 (m-40) REVERT: D 46 GLU cc_start: 0.8401 (tt0) cc_final: 0.8102 (tt0) REVERT: G 95 MET cc_start: 0.8103 (mtm) cc_final: 0.7626 (mtm) outliers start: 98 outliers final: 60 residues processed: 298 average time/residue: 0.1204 time to fit residues: 54.8600 Evaluate side-chains 287 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 211 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain G residue 103 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 181 optimal weight: 8.9990 chunk 211 optimal weight: 4.9990 chunk 200 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 186 optimal weight: 8.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 467 GLN C 414 ASN ** C 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.149728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.110925 restraints weight = 169204.442| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 6.96 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 17924 Z= 0.158 Angle : 0.727 20.415 24340 Z= 0.357 Chirality : 0.050 0.869 2687 Planarity : 0.005 0.086 3099 Dihedral : 9.054 76.038 3086 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.25 % Favored : 94.09 % Rotamer: Outliers : 4.28 % Allowed : 23.01 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.96 (0.18), residues: 2133 helix: 1.44 (0.28), residues: 376 sheet: -0.52 (0.22), residues: 570 loop : -1.41 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 111 TYR 0.014 0.001 TYR A 491 PHE 0.015 0.002 PHE C 351 TRP 0.013 0.001 TRP B 153 HIS 0.009 0.001 HIS G 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (17873) covalent geometry : angle 0.65815 / 0.34 (24208) SS BOND : bond 0.01085 / 0.61 ( 21) SS BOND : angle 2.73310 / 2.07 ( 42) hydrogen bonds : bond 0.03769 / 2.59 ( 603) hydrogen bonds : angle 5.35807 / 3.65 ( 1683) link_ALPHA1-3 : bond 0.00593 / 0.30 ( 3) link_ALPHA1-3 : angle 1.35696 / 0.68 ( 9) link_BETA1-2 : bond 0.00083 / 0.04 ( 3) link_BETA1-2 : angle 1.17882 / 0.57 ( 9) link_BETA1-4 : bond 0.00419 / 0.27 ( 9) link_BETA1-4 : angle 3.25977 / 1.93 ( 27) link_BETA2-3 : bond 0.00708 / 0.36 ( 3) link_BETA2-3 : angle 4.67231 / 2.40 ( 9) link_NAG-ASN : bond 0.00692 / 0.39 ( 12) link_NAG-ASN : angle 6.55233 / 4.47 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 214 time to evaluate : 0.692 Fit side-chains REVERT: A 187 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.7922 (p0) REVERT: A 293 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.7635 (mmt) REVERT: A 345 GLU cc_start: 0.7656 (mp0) cc_final: 0.7281 (pt0) REVERT: A 356 TYR cc_start: 0.7983 (OUTLIER) cc_final: 0.6131 (p90) REVERT: A 373 GLU cc_start: 0.8022 (tt0) cc_final: 0.7682 (tt0) REVERT: A 398 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.7025 (mt-10) REVERT: A 406 ASN cc_start: 0.8676 (t0) cc_final: 0.8282 (t0) REVERT: B 76 ARG cc_start: 0.6742 (OUTLIER) cc_final: 0.5191 (tpt170) REVERT: B 213 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8417 (mt) REVERT: B 271 LYS cc_start: 0.8641 (mtmt) cc_final: 0.8157 (mtpt) REVERT: B 301 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.7447 (mmt) REVERT: B 385 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.7948 (mtmt) REVERT: B 406 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7418 (mt-10) REVERT: B 424 LYS cc_start: 0.8509 (tttt) cc_final: 0.8196 (ttpp) REVERT: B 473 LYS cc_start: 0.7904 (ttmt) cc_final: 0.7252 (tttm) REVERT: C 57 LYS cc_start: 0.8390 (mttm) cc_final: 0.8094 (mtpt) REVERT: C 133 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8858 (mp) REVERT: C 213 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8524 (mt) REVERT: C 271 LYS cc_start: 0.8499 (mtmt) cc_final: 0.8172 (mtpt) REVERT: C 301 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.7503 (mmt) REVERT: C 371 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6531 (pm20) REVERT: C 385 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7921 (mtmt) REVERT: C 414 ASN cc_start: 0.8707 (t0) cc_final: 0.8507 (t0) REVERT: C 469 ARG cc_start: 0.6001 (OUTLIER) cc_final: 0.5361 (ptm160) REVERT: K 95 MET cc_start: 0.8124 (mtm) cc_final: 0.7567 (mtm) REVERT: D 31 ASN cc_start: 0.8303 (m-40) cc_final: 0.7943 (m-40) REVERT: D 46 GLU cc_start: 0.8283 (tt0) cc_final: 0.8000 (tt0) REVERT: G 95 MET cc_start: 0.8111 (mtm) cc_final: 0.7633 (mtm) outliers start: 80 outliers final: 57 residues processed: 277 average time/residue: 0.1414 time to fit residues: 59.3953 Evaluate side-chains 282 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 210 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 94 PHE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 448 ARG Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain G residue 94 PHE Chi-restraints excluded: chain G residue 103 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 83 optimal weight: 4.9990 chunk 180 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 61 optimal weight: 0.4980 chunk 205 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 467 GLN C 193 ASN ** C 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.148038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.109335 restraints weight = 170601.535| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 7.06 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 17924 Z= 0.202 Angle : 0.758 19.503 24340 Z= 0.374 Chirality : 0.052 0.863 2687 Planarity : 0.005 0.086 3099 Dihedral : 9.028 76.201 3084 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.70 % Allowed : 5.86 % Favored : 93.44 % Rotamer: Outliers : 4.65 % Allowed : 22.79 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.18), residues: 2133 helix: 1.33 (0.27), residues: 378 sheet: -0.53 (0.22), residues: 570 loop : -1.41 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 229 TYR 0.016 0.002 TYR A 491 PHE 0.016 0.002 PHE A 343 TRP 0.012 0.001 TRP B 153 HIS 0.009 0.001 HIS G 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (17873) covalent geometry : angle 0.69418 / 0.36 (24208) SS BOND : bond 0.01032 / 0.60 ( 21) SS BOND : angle 2.76551 / 2.09 ( 42) hydrogen bonds : bond 0.04024 / 2.78 ( 603) hydrogen bonds : angle 5.42291 / 3.70 ( 1683) link_ALPHA1-3 : bond 0.00503 / 0.25 ( 3) link_ALPHA1-3 : angle 1.48435 / 0.75 ( 9) link_BETA1-2 : bond 0.00084 / 0.04 ( 3) link_BETA1-2 : angle 1.22797 / 0.59 ( 9) link_BETA1-4 : bond 0.00420 / 0.25 ( 9) link_BETA1-4 : angle 3.33412 / 1.99 ( 27) link_BETA2-3 : bond 0.00729 / 0.37 ( 3) link_BETA2-3 : angle 4.81869 / 2.47 ( 9) link_NAG-ASN : bond 0.00781 / 0.45 ( 12) link_NAG-ASN : angle 6.36365 / 4.36 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 220 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 187 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.7895 (p0) REVERT: A 193 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8027 (m110) REVERT: A 293 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.7906 (mmt) REVERT: A 345 GLU cc_start: 0.7640 (mp0) cc_final: 0.7200 (pt0) REVERT: A 373 GLU cc_start: 0.8098 (tt0) cc_final: 0.7783 (tt0) REVERT: A 398 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7148 (mt-10) REVERT: A 406 ASN cc_start: 0.8672 (t0) cc_final: 0.8243 (t0) REVERT: A 419 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7805 (mt-10) REVERT: B 76 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.5429 (tpt170) REVERT: B 213 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8453 (mt) REVERT: B 271 LYS cc_start: 0.8629 (mtmt) cc_final: 0.8126 (mtpt) REVERT: B 301 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.7512 (mmt) REVERT: B 385 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8039 (mtpt) REVERT: B 406 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: B 424 LYS cc_start: 0.8499 (tttt) cc_final: 0.8144 (ttpp) REVERT: B 473 LYS cc_start: 0.7904 (ttmt) cc_final: 0.7184 (tttm) REVERT: C 57 LYS cc_start: 0.8377 (mttm) cc_final: 0.8052 (mtpt) REVERT: C 133 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8850 (mp) REVERT: C 187 ASN cc_start: 0.8213 (OUTLIER) cc_final: 0.7747 (p0) REVERT: C 213 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8555 (mt) REVERT: C 271 LYS cc_start: 0.8558 (mtmt) cc_final: 0.8260 (mtpt) REVERT: C 301 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.7606 (mmt) REVERT: C 371 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6624 (pm20) REVERT: C 385 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7907 (mtmt) REVERT: C 469 ARG cc_start: 0.5995 (OUTLIER) cc_final: 0.5394 (ptm160) REVERT: C 500 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7320 (t70) REVERT: K 95 MET cc_start: 0.8018 (mtm) cc_final: 0.7493 (mtm) REVERT: D 31 ASN cc_start: 0.8338 (m-40) cc_final: 0.7924 (m-40) REVERT: D 46 GLU cc_start: 0.8331 (tt0) cc_final: 0.8033 (tt0) REVERT: G 95 MET cc_start: 0.8090 (mtm) cc_final: 0.7582 (mtm) outliers start: 87 outliers final: 61 residues processed: 291 average time/residue: 0.1277 time to fit residues: 56.7510 Evaluate side-chains 296 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 217 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 94 PHE Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain C residue 500 ASP Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain G residue 94 PHE Chi-restraints excluded: chain G residue 103 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 23 optimal weight: 0.0870 chunk 20 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 141 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 180 optimal weight: 0.0060 chunk 31 optimal weight: 0.5980 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN B 467 GLN C 193 ASN C 414 ASN ** K 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.152811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.114130 restraints weight = 170679.430| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 6.84 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 17924 Z= 0.129 Angle : 0.665 14.410 24340 Z= 0.331 Chirality : 0.048 0.702 2687 Planarity : 0.005 0.088 3099 Dihedral : 8.494 73.730 3084 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.16 % Favored : 94.23 % Rotamer: Outliers : 3.91 % Allowed : 23.54 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.18), residues: 2133 helix: 1.69 (0.28), residues: 376 sheet: -0.37 (0.22), residues: 565 loop : -1.29 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 487 TYR 0.010 0.001 TYR A 491 PHE 0.016 0.001 PHE A 343 TRP 0.013 0.001 TRP B 153 HIS 0.009 0.001 HIS G 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (17873) covalent geometry : angle 0.60818 / 0.32 (24208) SS BOND : bond 0.00948 / 0.57 ( 21) SS BOND : angle 2.53522 / 2.00 ( 42) hydrogen bonds : bond 0.03443 / 2.35 ( 603) hydrogen bonds : angle 5.09753 / 3.48 ( 1683) link_ALPHA1-3 : bond 0.00628 / 0.31 ( 3) link_ALPHA1-3 : angle 1.29324 / 0.65 ( 9) link_BETA1-2 : bond 0.00081 / 0.04 ( 3) link_BETA1-2 : angle 1.06910 / 0.52 ( 9) link_BETA1-4 : bond 0.00414 / 0.28 ( 9) link_BETA1-4 : angle 3.09268 / 1.83 ( 27) link_BETA2-3 : bond 0.00560 / 0.28 ( 3) link_BETA2-3 : angle 4.31354 / 2.21 ( 9) link_NAG-ASN : bond 0.00748 / 0.41 ( 12) link_NAG-ASN : angle 5.46944 / 3.85 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 214 time to evaluate : 0.682 Fit side-chains REVERT: A 34 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: A 345 GLU cc_start: 0.7768 (mp0) cc_final: 0.6980 (mm-30) REVERT: A 356 TYR cc_start: 0.7536 (OUTLIER) cc_final: 0.5687 (p90) REVERT: A 398 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7127 (mt-10) REVERT: B 213 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8552 (mt) REVERT: B 271 LYS cc_start: 0.8540 (mtmt) cc_final: 0.8047 (mtpt) REVERT: B 301 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.7307 (mmt) REVERT: B 385 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7868 (mtmt) REVERT: B 406 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7379 (mt-10) REVERT: B 424 LYS cc_start: 0.8348 (tttt) cc_final: 0.8021 (ttpp) REVERT: B 473 LYS cc_start: 0.7836 (ttmt) cc_final: 0.7211 (tttm) REVERT: C 57 LYS cc_start: 0.8408 (mttm) cc_final: 0.8085 (mtpt) REVERT: C 111 ARG cc_start: 0.8187 (mtt90) cc_final: 0.7886 (mpt90) REVERT: C 174 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7546 (mt-10) REVERT: C 187 ASN cc_start: 0.7952 (OUTLIER) cc_final: 0.7576 (p0) REVERT: C 213 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8583 (mt) REVERT: C 271 LYS cc_start: 0.8429 (mtmt) cc_final: 0.8114 (mtpt) REVERT: C 301 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.7207 (mmt) REVERT: C 371 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6609 (pm20) REVERT: C 385 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7946 (mtmt) REVERT: C 414 ASN cc_start: 0.8751 (t0) cc_final: 0.8526 (t0) REVERT: C 469 ARG cc_start: 0.6253 (OUTLIER) cc_final: 0.5639 (ptm160) REVERT: C 500 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7449 (t70) REVERT: I 71 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.6492 (ptp-170) REVERT: K 95 MET cc_start: 0.8264 (mtm) cc_final: 0.7819 (mtm) REVERT: D 31 ASN cc_start: 0.8241 (m-40) cc_final: 0.7933 (m-40) REVERT: G 95 MET cc_start: 0.8127 (mtm) cc_final: 0.7731 (mtm) outliers start: 73 outliers final: 47 residues processed: 277 average time/residue: 0.1215 time to fit residues: 51.1852 Evaluate side-chains 272 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 209 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 94 PHE Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 448 ARG Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain C residue 500 ASP Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 94 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 140 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 208 optimal weight: 9.9990 chunk 138 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 204 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 GLN C 193 ASN C 321 ASN ** C 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.149459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.110471 restraints weight = 170088.618| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 7.12 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 17924 Z= 0.179 Angle : 0.729 15.163 24340 Z= 0.363 Chirality : 0.050 0.765 2687 Planarity : 0.005 0.088 3099 Dihedral : 8.521 74.775 3076 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.70 % Allowed : 5.30 % Favored : 94.00 % Rotamer: Outliers : 3.37 % Allowed : 23.81 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.76 (0.18), residues: 2133 helix: 1.56 (0.27), residues: 376 sheet: -0.32 (0.22), residues: 570 loop : -1.32 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 229 TYR 0.012 0.002 TYR A 491 PHE 0.016 0.002 PHE A 343 TRP 0.015 0.001 TRP B 153 HIS 0.009 0.001 HIS G 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (17873) covalent geometry : angle 0.67229 / 0.35 (24208) SS BOND : bond 0.01012 / 0.61 ( 21) SS BOND : angle 2.96160 / 2.20 ( 42) hydrogen bonds : bond 0.03832 / 2.63 ( 603) hydrogen bonds : angle 5.21116 / 3.56 ( 1683) link_ALPHA1-3 : bond 0.00526 / 0.26 ( 3) link_ALPHA1-3 : angle 1.41837 / 0.71 ( 9) link_BETA1-2 : bond 0.00101 / 0.05 ( 3) link_BETA1-2 : angle 1.08464 / 0.52 ( 9) link_BETA1-4 : bond 0.00400 / 0.26 ( 9) link_BETA1-4 : angle 3.18758 / 1.90 ( 27) link_BETA2-3 : bond 0.00626 / 0.31 ( 3) link_BETA2-3 : angle 4.59154 / 2.36 ( 9) link_NAG-ASN : bond 0.00779 / 0.44 ( 12) link_NAG-ASN : angle 5.63291 / 3.96 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 211 time to evaluate : 0.665 Fit side-chains REVERT: A 345 GLU cc_start: 0.7688 (mp0) cc_final: 0.6875 (mm-30) REVERT: A 356 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.5972 (p90) REVERT: A 373 GLU cc_start: 0.8083 (tt0) cc_final: 0.7717 (tt0) REVERT: A 398 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7165 (mt-10) REVERT: A 419 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7720 (mt-10) REVERT: B 193 ASN cc_start: 0.8387 (m-40) cc_final: 0.8043 (m110) REVERT: B 213 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8459 (mt) REVERT: B 271 LYS cc_start: 0.8548 (mtmt) cc_final: 0.8004 (mtpt) REVERT: B 301 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.7402 (mmt) REVERT: B 385 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.7990 (mtpt) REVERT: B 406 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7433 (mt-10) REVERT: B 424 LYS cc_start: 0.8492 (tttt) cc_final: 0.8121 (ttpp) REVERT: B 473 LYS cc_start: 0.7920 (ttmt) cc_final: 0.7213 (tttm) REVERT: C 57 LYS cc_start: 0.8419 (mttm) cc_final: 0.8087 (mtpt) REVERT: C 174 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: C 187 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7781 (p0) REVERT: C 213 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8611 (mt) REVERT: C 271 LYS cc_start: 0.8575 (mtmt) cc_final: 0.8182 (mtpt) REVERT: C 301 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.7385 (mmt) REVERT: C 371 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6505 (pm20) REVERT: C 385 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.7965 (mtmt) REVERT: C 469 ARG cc_start: 0.6207 (OUTLIER) cc_final: 0.5474 (ptm160) REVERT: C 500 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7533 (t70) REVERT: I 71 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.6355 (ptp-170) REVERT: K 95 MET cc_start: 0.8104 (mtm) cc_final: 0.7485 (mtm) REVERT: D 31 ASN cc_start: 0.8412 (m-40) cc_final: 0.7982 (m-40) REVERT: G 95 MET cc_start: 0.8112 (mtm) cc_final: 0.7692 (mtm) outliers start: 63 outliers final: 46 residues processed: 266 average time/residue: 0.1389 time to fit residues: 56.2369 Evaluate side-chains 273 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 211 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 94 PHE Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 385 LYS Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 364 TYR Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain C residue 500 ASP Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 94 PHE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 94 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 152 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 48 optimal weight: 0.0060 chunk 210 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 GLN C 193 ASN C 321 ASN C 414 ASN ** C 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.149445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.110901 restraints weight = 170347.851| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 6.85 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 17924 Z= 0.172 Angle : 0.721 14.332 24340 Z= 0.359 Chirality : 0.049 0.732 2687 Planarity : 0.005 0.087 3099 Dihedral : 8.499 75.280 3076 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.70 % Allowed : 5.53 % Favored : 93.76 % Rotamer: Outliers : 3.64 % Allowed : 23.65 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.78 (0.18), residues: 2133 helix: 1.53 (0.27), residues: 376 sheet: -0.34 (0.22), residues: 570 loop : -1.32 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 229 TYR 0.011 0.002 TYR A 491 PHE 0.016 0.002 PHE A 343 TRP 0.015 0.001 TRP B 153 HIS 0.009 0.001 HIS G 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (17873) covalent geometry : angle 0.66454 / 0.34 (24208) SS BOND : bond 0.00978 / 0.58 ( 21) SS BOND : angle 2.95563 / 2.15 ( 42) hydrogen bonds : bond 0.03790 / 2.61 ( 603) hydrogen bonds : angle 5.21795 / 3.56 ( 1683) link_ALPHA1-3 : bond 0.00547 / 0.27 ( 3) link_ALPHA1-3 : angle 1.38633 / 0.70 ( 9) link_BETA1-2 : bond 0.00094 / 0.05 ( 3) link_BETA1-2 : angle 1.05459 / 0.51 ( 9) link_BETA1-4 : bond 0.00410 / 0.26 ( 9) link_BETA1-4 : angle 3.16497 / 1.89 ( 27) link_BETA2-3 : bond 0.00693 / 0.35 ( 3) link_BETA2-3 : angle 4.61492 / 2.37 ( 9) link_NAG-ASN : bond 0.00753 / 0.42 ( 12) link_NAG-ASN : angle 5.55344 / 3.93 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3042.21 seconds wall clock time: 53 minutes 35.01 seconds (3215.01 seconds total)