Starting phenix.real_space_refine on Thu Dec 26 11:29:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jon_36461/12_2024/8jon_36461.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jon_36461/12_2024/8jon_36461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jon_36461/12_2024/8jon_36461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jon_36461/12_2024/8jon_36461.map" model { file = "/net/cci-nas-00/data/ceres_data/8jon_36461/12_2024/8jon_36461.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jon_36461/12_2024/8jon_36461.cif" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.130 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: 7 Type Number sf(0) Gaussians P 30 5.49 5 Mg 12 5.21 5 S 78 5.16 5 C 14556 2.51 5 N 4050 2.21 5 O 4500 1.98 5 H 22716 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 45942 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7597 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 14, 'TRANS': 470} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 23.30, per 1000 atoms: 0.51 Number of scatterers: 45942 At special positions: 0 Unit cell: (115.73, 121.41, 116.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 78 16.00 P 30 15.00 Mg 12 11.99 O 4500 8.00 N 4050 7.00 C 14556 6.00 H 22716 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.52 Conformation dependent library (CDL) restraints added in 3.7 seconds 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5304 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 30 sheets defined 41.4% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.68 Creating SS restraints... Processing helix chain 'A' and resid 31 through 36 Processing helix chain 'A' and resid 55 through 72 Processing helix chain 'A' and resid 83 through 92 removed outlier: 3.597A pdb=" N ARG A 92 " --> pdb=" O ILE A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 97 through 104 removed outlier: 3.503A pdb=" N LEU A 101 " --> pdb=" O ASN A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 142 removed outlier: 3.592A pdb=" N LEU A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 156 removed outlier: 3.821A pdb=" N VAL A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 179 Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.502A pdb=" N VAL A 204 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.600A pdb=" N MET A 256 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 297 through 312 Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'A' and resid 338 through 345 Processing helix chain 'A' and resid 354 through 358 removed outlier: 3.790A pdb=" N ALA A 358 " --> pdb=" O PRO A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 375 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.620A pdb=" N LEU A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 410 Processing helix chain 'A' and resid 433 through 437 removed outlier: 3.794A pdb=" N THR A 436 " --> pdb=" O HIS A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 55 through 72 Processing helix chain 'B' and resid 83 through 92 removed outlier: 3.596A pdb=" N ARG B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 97 through 104 removed outlier: 3.503A pdb=" N LEU B 101 " --> pdb=" O ASN B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 142 removed outlier: 3.593A pdb=" N LEU B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 156 removed outlier: 3.820A pdb=" N VAL B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 179 Processing helix chain 'B' and resid 200 through 205 removed outlier: 3.502A pdb=" N VAL B 204 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.598A pdb=" N MET B 256 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 278 Processing helix chain 'B' and resid 297 through 312 Processing helix chain 'B' and resid 324 through 335 Processing helix chain 'B' and resid 338 through 345 Processing helix chain 'B' and resid 354 through 358 removed outlier: 3.790A pdb=" N ALA B 358 " --> pdb=" O PRO B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 375 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.620A pdb=" N LEU B 387 " --> pdb=" O SER B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 410 Processing helix chain 'B' and resid 433 through 437 removed outlier: 3.794A pdb=" N THR B 436 " --> pdb=" O HIS B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 496 Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 55 through 72 Processing helix chain 'C' and resid 83 through 92 removed outlier: 3.597A pdb=" N ARG C 92 " --> pdb=" O ILE C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 97 through 104 removed outlier: 3.502A pdb=" N LEU C 101 " --> pdb=" O ASN C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 142 removed outlier: 3.592A pdb=" N LEU C 130 " --> pdb=" O ASP C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 156 removed outlier: 3.821A pdb=" N VAL C 154 " --> pdb=" O SER C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 179 Processing helix chain 'C' and resid 200 through 205 removed outlier: 3.503A pdb=" N VAL C 204 " --> pdb=" O VAL C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.599A pdb=" N MET C 256 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'C' and resid 297 through 312 Processing helix chain 'C' and resid 324 through 335 Processing helix chain 'C' and resid 338 through 345 Processing helix chain 'C' and resid 354 through 358 removed outlier: 3.790A pdb=" N ALA C 358 " --> pdb=" O PRO C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 375 Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.621A pdb=" N LEU C 387 " --> pdb=" O SER C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 410 Processing helix chain 'C' and resid 433 through 437 removed outlier: 3.794A pdb=" N THR C 436 " --> pdb=" O HIS C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 496 Processing helix chain 'D' and resid 31 through 36 Processing helix chain 'D' and resid 55 through 72 Processing helix chain 'D' and resid 83 through 92 removed outlier: 3.597A pdb=" N ARG D 92 " --> pdb=" O ILE D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 95 No H-bonds generated for 'chain 'D' and resid 93 through 95' Processing helix chain 'D' and resid 97 through 104 removed outlier: 3.503A pdb=" N LEU D 101 " --> pdb=" O ASN D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 142 removed outlier: 3.592A pdb=" N LEU D 130 " --> pdb=" O ASP D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 156 removed outlier: 3.822A pdb=" N VAL D 154 " --> pdb=" O SER D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 179 Processing helix chain 'D' and resid 200 through 205 removed outlier: 3.502A pdb=" N VAL D 204 " --> pdb=" O VAL D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.599A pdb=" N MET D 256 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 278 Processing helix chain 'D' and resid 297 through 312 Processing helix chain 'D' and resid 324 through 335 Processing helix chain 'D' and resid 338 through 345 Processing helix chain 'D' and resid 354 through 358 removed outlier: 3.791A pdb=" N ALA D 358 " --> pdb=" O PRO D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 375 Processing helix chain 'D' and resid 383 through 388 removed outlier: 3.620A pdb=" N LEU D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 410 Processing helix chain 'D' and resid 433 through 437 removed outlier: 3.794A pdb=" N THR D 436 " --> pdb=" O HIS D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 496 Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 55 through 72 Processing helix chain 'E' and resid 83 through 92 removed outlier: 3.597A pdb=" N ARG E 92 " --> pdb=" O ILE E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 97 through 104 removed outlier: 3.503A pdb=" N LEU E 101 " --> pdb=" O ASN E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 142 removed outlier: 3.592A pdb=" N LEU E 130 " --> pdb=" O ASP E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 156 removed outlier: 3.821A pdb=" N VAL E 154 " --> pdb=" O SER E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 179 Processing helix chain 'E' and resid 200 through 205 removed outlier: 3.502A pdb=" N VAL E 204 " --> pdb=" O VAL E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 256 removed outlier: 3.598A pdb=" N MET E 256 " --> pdb=" O LEU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 278 Processing helix chain 'E' and resid 297 through 312 Processing helix chain 'E' and resid 324 through 335 Processing helix chain 'E' and resid 338 through 345 Processing helix chain 'E' and resid 354 through 358 removed outlier: 3.791A pdb=" N ALA E 358 " --> pdb=" O PRO E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 375 Processing helix chain 'E' and resid 383 through 388 removed outlier: 3.621A pdb=" N LEU E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 410 Processing helix chain 'E' and resid 433 through 437 removed outlier: 3.793A pdb=" N THR E 436 " --> pdb=" O HIS E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 496 Processing helix chain 'F' and resid 31 through 36 Processing helix chain 'F' and resid 55 through 72 Processing helix chain 'F' and resid 83 through 92 removed outlier: 3.597A pdb=" N ARG F 92 " --> pdb=" O ILE F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 95 No H-bonds generated for 'chain 'F' and resid 93 through 95' Processing helix chain 'F' and resid 97 through 104 removed outlier: 3.503A pdb=" N LEU F 101 " --> pdb=" O ASN F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 142 removed outlier: 3.593A pdb=" N LEU F 130 " --> pdb=" O ASP F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 156 removed outlier: 3.821A pdb=" N VAL F 154 " --> pdb=" O SER F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 179 Processing helix chain 'F' and resid 200 through 205 removed outlier: 3.501A pdb=" N VAL F 204 " --> pdb=" O VAL F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 256 removed outlier: 3.599A pdb=" N MET F 256 " --> pdb=" O LEU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 278 Processing helix chain 'F' and resid 297 through 312 Processing helix chain 'F' and resid 324 through 335 Processing helix chain 'F' and resid 338 through 345 Processing helix chain 'F' and resid 354 through 358 removed outlier: 3.790A pdb=" N ALA F 358 " --> pdb=" O PRO F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 375 Processing helix chain 'F' and resid 383 through 388 removed outlier: 3.620A pdb=" N LEU F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 410 Processing helix chain 'F' and resid 433 through 437 removed outlier: 3.794A pdb=" N THR F 436 " --> pdb=" O HIS F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 496 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 25 Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 111 removed outlier: 6.796A pdb=" N GLY A 75 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEU A 110 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N PHE A 77 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 76 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASP A 149 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL A 78 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY A 50 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N SER A 45 " --> pdb=" O ASN A 207 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL A 209 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU A 47 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU A 211 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N SER A 49 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ASN A 213 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 208 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 12.648A pdb=" N ARG A 220 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N ILE A 243 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ARG A 222 " --> pdb=" O PHE A 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 266 through 267 Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 352 removed outlier: 6.533A pdb=" N ILE A 317 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE A 288 " --> pdb=" O PHE A 416 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ASN A 418 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA A 290 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE A 287 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU A 442 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU A 289 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU A 444 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR A 291 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N TYR A 446 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE A 441 " --> pdb=" O PHE A 460 " (cutoff:3.500A) removed outlier: 12.589A pdb=" N MET A 453 " --> pdb=" O ILE A 476 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N ILE A 476 " --> pdb=" O MET A 453 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG A 455 " --> pdb=" O TYR A 474 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU A 473 " --> pdb=" O LYS A 484 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 490 through 491 Processing sheet with id=AA6, first strand: chain 'B' and resid 24 through 25 Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 111 removed outlier: 6.796A pdb=" N GLY B 75 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LEU B 110 " --> pdb=" O GLY B 75 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N PHE B 77 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE B 76 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASP B 149 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL B 78 " --> pdb=" O ASP B 149 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY B 50 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N SER B 45 " --> pdb=" O ASN B 207 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL B 209 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU B 47 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU B 211 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N SER B 49 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ASN B 213 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B 208 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 12.648A pdb=" N ARG B 220 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 9.445A pdb=" N ILE B 243 " --> pdb=" O ARG B 220 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG B 222 " --> pdb=" O PHE B 241 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 266 through 267 Processing sheet with id=AA9, first strand: chain 'B' and resid 348 through 352 removed outlier: 6.533A pdb=" N ILE B 317 " --> pdb=" O ALA B 380 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE B 288 " --> pdb=" O PHE B 416 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ASN B 418 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 290 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE B 287 " --> pdb=" O THR B 440 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU B 442 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU B 289 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU B 444 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N THR B 291 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N TYR B 446 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE B 441 " --> pdb=" O PHE B 460 " (cutoff:3.500A) removed outlier: 12.588A pdb=" N MET B 453 " --> pdb=" O ILE B 476 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N ILE B 476 " --> pdb=" O MET B 453 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG B 455 " --> pdb=" O TYR B 474 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU B 473 " --> pdb=" O LYS B 484 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 490 through 491 Processing sheet with id=AB2, first strand: chain 'C' and resid 24 through 25 Processing sheet with id=AB3, first strand: chain 'C' and resid 107 through 111 removed outlier: 6.795A pdb=" N GLY C 75 " --> pdb=" O PHE C 108 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU C 110 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N PHE C 77 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE C 76 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ASP C 149 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C 78 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY C 50 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N SER C 45 " --> pdb=" O ASN C 207 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL C 209 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU C 47 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU C 211 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N SER C 49 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ASN C 213 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL C 208 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 12.648A pdb=" N ARG C 220 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 9.445A pdb=" N ILE C 243 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG C 222 " --> pdb=" O PHE C 241 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 266 through 267 Processing sheet with id=AB5, first strand: chain 'C' and resid 348 through 352 removed outlier: 6.534A pdb=" N ILE C 317 " --> pdb=" O ALA C 380 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE C 288 " --> pdb=" O PHE C 416 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ASN C 418 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA C 290 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE C 287 " --> pdb=" O THR C 440 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU C 442 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU C 289 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU C 444 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N THR C 291 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N TYR C 446 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE C 441 " --> pdb=" O PHE C 460 " (cutoff:3.500A) removed outlier: 12.590A pdb=" N MET C 453 " --> pdb=" O ILE C 476 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N ILE C 476 " --> pdb=" O MET C 453 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG C 455 " --> pdb=" O TYR C 474 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU C 473 " --> pdb=" O LYS C 484 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 490 through 491 Processing sheet with id=AB7, first strand: chain 'D' and resid 24 through 25 Processing sheet with id=AB8, first strand: chain 'D' and resid 107 through 111 removed outlier: 6.796A pdb=" N GLY D 75 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU D 110 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N PHE D 77 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE D 76 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ASP D 149 " --> pdb=" O ILE D 76 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL D 78 " --> pdb=" O ASP D 149 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY D 50 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N SER D 45 " --> pdb=" O ASN D 207 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL D 209 " --> pdb=" O SER D 45 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LEU D 47 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU D 211 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N SER D 49 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ASN D 213 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL D 208 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 12.648A pdb=" N ARG D 220 " --> pdb=" O ILE D 243 " (cutoff:3.500A) removed outlier: 9.445A pdb=" N ILE D 243 " --> pdb=" O ARG D 220 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG D 222 " --> pdb=" O PHE D 241 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 266 through 267 Processing sheet with id=AC1, first strand: chain 'D' and resid 348 through 352 removed outlier: 6.534A pdb=" N ILE D 317 " --> pdb=" O ALA D 380 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE D 288 " --> pdb=" O PHE D 416 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ASN D 418 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA D 290 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE D 287 " --> pdb=" O THR D 440 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU D 442 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU D 289 " --> pdb=" O LEU D 442 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU D 444 " --> pdb=" O LEU D 289 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N THR D 291 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N TYR D 446 " --> pdb=" O THR D 291 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE D 441 " --> pdb=" O PHE D 460 " (cutoff:3.500A) removed outlier: 12.589A pdb=" N MET D 453 " --> pdb=" O ILE D 476 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N ILE D 476 " --> pdb=" O MET D 453 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG D 455 " --> pdb=" O TYR D 474 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU D 473 " --> pdb=" O LYS D 484 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 490 through 491 Processing sheet with id=AC3, first strand: chain 'E' and resid 24 through 25 Processing sheet with id=AC4, first strand: chain 'E' and resid 107 through 111 removed outlier: 6.796A pdb=" N GLY E 75 " --> pdb=" O PHE E 108 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LEU E 110 " --> pdb=" O GLY E 75 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N PHE E 77 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE E 76 " --> pdb=" O SER E 147 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASP E 149 " --> pdb=" O ILE E 76 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL E 78 " --> pdb=" O ASP E 149 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY E 50 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER E 45 " --> pdb=" O ASN E 207 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL E 209 " --> pdb=" O SER E 45 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU E 47 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU E 211 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N SER E 49 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ASN E 213 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL E 208 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 12.648A pdb=" N ARG E 220 " --> pdb=" O ILE E 243 " (cutoff:3.500A) removed outlier: 9.445A pdb=" N ILE E 243 " --> pdb=" O ARG E 220 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG E 222 " --> pdb=" O PHE E 241 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 266 through 267 Processing sheet with id=AC6, first strand: chain 'E' and resid 348 through 352 removed outlier: 6.533A pdb=" N ILE E 317 " --> pdb=" O ALA E 380 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE E 288 " --> pdb=" O PHE E 416 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ASN E 418 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA E 290 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE E 287 " --> pdb=" O THR E 440 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU E 442 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU E 289 " --> pdb=" O LEU E 442 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU E 444 " --> pdb=" O LEU E 289 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N THR E 291 " --> pdb=" O LEU E 444 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N TYR E 446 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE E 441 " --> pdb=" O PHE E 460 " (cutoff:3.500A) removed outlier: 12.588A pdb=" N MET E 453 " --> pdb=" O ILE E 476 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N ILE E 476 " --> pdb=" O MET E 453 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG E 455 " --> pdb=" O TYR E 474 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU E 473 " --> pdb=" O LYS E 484 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 490 through 491 Processing sheet with id=AC8, first strand: chain 'F' and resid 24 through 25 Processing sheet with id=AC9, first strand: chain 'F' and resid 107 through 111 removed outlier: 6.796A pdb=" N GLY F 75 " --> pdb=" O PHE F 108 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LEU F 110 " --> pdb=" O GLY F 75 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N PHE F 77 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE F 76 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ASP F 149 " --> pdb=" O ILE F 76 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL F 78 " --> pdb=" O ASP F 149 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY F 50 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER F 45 " --> pdb=" O ASN F 207 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL F 209 " --> pdb=" O SER F 45 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LEU F 47 " --> pdb=" O VAL F 209 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU F 211 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N SER F 49 " --> pdb=" O LEU F 211 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ASN F 213 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL F 208 " --> pdb=" O LEU F 227 " (cutoff:3.500A) removed outlier: 12.648A pdb=" N ARG F 220 " --> pdb=" O ILE F 243 " (cutoff:3.500A) removed outlier: 9.444A pdb=" N ILE F 243 " --> pdb=" O ARG F 220 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG F 222 " --> pdb=" O PHE F 241 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 266 through 267 Processing sheet with id=AD2, first strand: chain 'F' and resid 348 through 352 removed outlier: 6.534A pdb=" N ILE F 317 " --> pdb=" O ALA F 380 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE F 288 " --> pdb=" O PHE F 416 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ASN F 418 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA F 290 " --> pdb=" O ASN F 418 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE F 287 " --> pdb=" O THR F 440 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU F 442 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU F 289 " --> pdb=" O LEU F 442 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU F 444 " --> pdb=" O LEU F 289 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N THR F 291 " --> pdb=" O LEU F 444 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N TYR F 446 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE F 441 " --> pdb=" O PHE F 460 " (cutoff:3.500A) removed outlier: 12.589A pdb=" N MET F 453 " --> pdb=" O ILE F 476 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N ILE F 476 " --> pdb=" O MET F 453 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG F 455 " --> pdb=" O TYR F 474 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU F 473 " --> pdb=" O LYS F 484 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 490 through 491 1032 hydrogen bonds defined for protein. 2862 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: 23.68 Time building geometry restraints manager: 15.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 22698 1.03 - 1.23: 24 1.23 - 1.42: 9852 1.42 - 1.62: 13638 1.62 - 1.81: 138 Bond restraints: 46350 Sorted by residual: bond pdb=" C ILE F 476 " pdb=" O ILE F 476 " ideal model delta sigma weight residual 1.237 1.269 -0.031 1.10e-02 8.26e+03 8.15e+00 bond pdb=" C ILE C 476 " pdb=" O ILE C 476 " ideal model delta sigma weight residual 1.237 1.269 -0.031 1.10e-02 8.26e+03 8.15e+00 bond pdb=" C ILE A 476 " pdb=" O ILE A 476 " ideal model delta sigma weight residual 1.237 1.268 -0.031 1.10e-02 8.26e+03 8.08e+00 bond pdb=" C ILE B 476 " pdb=" O ILE B 476 " ideal model delta sigma weight residual 1.237 1.268 -0.031 1.10e-02 8.26e+03 8.07e+00 bond pdb=" C ILE D 476 " pdb=" O ILE D 476 " ideal model delta sigma weight residual 1.237 1.268 -0.031 1.10e-02 8.26e+03 7.89e+00 ... (remaining 46345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 82669 1.99 - 3.97: 644 3.97 - 5.96: 81 5.96 - 7.95: 30 7.95 - 9.94: 18 Bond angle restraints: 83442 Sorted by residual: angle pdb=" CB THR F 233 " pdb=" CG2 THR F 233 " pdb="HG21 THR F 233 " ideal model delta sigma weight residual 110.00 100.06 9.94 3.00e+00 1.11e-01 1.10e+01 angle pdb=" CB THR C 233 " pdb=" CG2 THR C 233 " pdb="HG21 THR C 233 " ideal model delta sigma weight residual 110.00 100.09 9.91 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CB THR B 233 " pdb=" CG2 THR B 233 " pdb="HG21 THR B 233 " ideal model delta sigma weight residual 110.00 100.09 9.91 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CB THR D 233 " pdb=" CG2 THR D 233 " pdb="HG21 THR D 233 " ideal model delta sigma weight residual 110.00 100.11 9.89 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CB THR A 233 " pdb=" CG2 THR A 233 " pdb="HG21 THR A 233 " ideal model delta sigma weight residual 110.00 100.15 9.85 3.00e+00 1.11e-01 1.08e+01 ... (remaining 83437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.16: 20370 29.16 - 58.32: 1212 58.32 - 87.48: 168 87.48 - 116.64: 12 116.64 - 145.80: 6 Dihedral angle restraints: 21768 sinusoidal: 12126 harmonic: 9642 Sorted by residual: dihedral pdb=" C5' ADP A 603 " pdb=" O5' ADP A 603 " pdb=" PA ADP A 603 " pdb=" O2A ADP A 603 " ideal model delta sinusoidal sigma weight residual 300.00 154.20 145.80 1 2.00e+01 2.50e-03 4.39e+01 dihedral pdb=" C5' ADP F 603 " pdb=" O5' ADP F 603 " pdb=" PA ADP F 603 " pdb=" O2A ADP F 603 " ideal model delta sinusoidal sigma weight residual 300.00 154.22 145.79 1 2.00e+01 2.50e-03 4.38e+01 dihedral pdb=" C5' ADP E 603 " pdb=" O5' ADP E 603 " pdb=" PA ADP E 603 " pdb=" O2A ADP E 603 " ideal model delta sinusoidal sigma weight residual 300.00 154.23 145.78 1 2.00e+01 2.50e-03 4.38e+01 ... (remaining 21765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2919 0.053 - 0.106: 470 0.106 - 0.160: 163 0.160 - 0.213: 12 0.213 - 0.266: 6 Chirality restraints: 3570 Sorted by residual: chirality pdb=" C2' ADP E 603 " pdb=" C1' ADP E 603 " pdb=" C3' ADP E 603 " pdb=" O2' ADP E 603 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C2' ADP F 603 " pdb=" C1' ADP F 603 " pdb=" C3' ADP F 603 " pdb=" O2' ADP F 603 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C2' ADP A 603 " pdb=" C1' ADP A 603 " pdb=" C3' ADP A 603 " pdb=" O2' ADP A 603 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 3567 not shown) Planarity restraints: 6894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 476 " -0.028 2.00e-02 2.50e+03 5.64e-02 3.19e+01 pdb=" C ILE B 476 " 0.098 2.00e-02 2.50e+03 pdb=" O ILE B 476 " -0.037 2.00e-02 2.50e+03 pdb=" N THR B 477 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 476 " -0.028 2.00e-02 2.50e+03 5.64e-02 3.18e+01 pdb=" C ILE F 476 " 0.098 2.00e-02 2.50e+03 pdb=" O ILE F 476 " -0.037 2.00e-02 2.50e+03 pdb=" N THR F 477 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 476 " -0.028 2.00e-02 2.50e+03 5.63e-02 3.17e+01 pdb=" C ILE E 476 " 0.097 2.00e-02 2.50e+03 pdb=" O ILE E 476 " -0.037 2.00e-02 2.50e+03 pdb=" N THR E 477 " -0.033 2.00e-02 2.50e+03 ... (remaining 6891 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 1207 2.07 - 2.70: 77515 2.70 - 3.33: 142473 3.33 - 3.97: 188845 3.97 - 4.60: 296915 Nonbonded interactions: 706955 Sorted by model distance: nonbonded pdb=" H LYS B 56 " pdb=" O1B ATP B 601 " model vdw 1.435 2.450 nonbonded pdb=" H LYS D 56 " pdb=" O1B ATP D 601 " model vdw 1.435 2.450 nonbonded pdb=" H LYS F 56 " pdb=" O1B ATP F 601 " model vdw 1.435 2.450 nonbonded pdb=" H LYS E 56 " pdb=" O1B ATP E 601 " model vdw 1.436 2.450 nonbonded pdb=" H LYS C 56 " pdb=" O1B ATP C 601 " model vdw 1.436 2.450 ... (remaining 706950 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.790 Extract box with map and model: 1.760 Check model and map are aligned: 0.330 Set scattering table: 0.430 Process input model: 102.480 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 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 : 0.004 0.082 23634 Z= 0.275 Angle : 0.631 8.466 31950 Z= 0.317 Chirality : 0.047 0.266 3570 Planarity : 0.004 0.056 4092 Dihedral : 18.398 145.801 8958 Min Nonbonded Distance : 1.586 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.41 % Allowed : 22.69 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 2898 helix: 1.43 (0.16), residues: 1032 sheet: -0.72 (0.18), residues: 762 loop : -0.42 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 466 HIS 0.006 0.001 HIS A 427 PHE 0.023 0.002 PHE B 423 TYR 0.006 0.001 TYR B 158 ARG 0.011 0.001 ARG C 170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 706 time to evaluate : 4.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.5713 (OUTLIER) cc_final: 0.5471 (tm-30) REVERT: A 28 MET cc_start: 0.8150 (mmm) cc_final: 0.7940 (mmm) REVERT: A 30 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6007 (tp30) REVERT: A 85 GLN cc_start: 0.6791 (mm110) cc_final: 0.6459 (mp10) REVERT: A 132 GLU cc_start: 0.6727 (mm-30) cc_final: 0.6236 (mm-30) REVERT: A 142 LYS cc_start: 0.6972 (mtmt) cc_final: 0.6309 (mmtm) REVERT: A 167 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7535 (mm-30) REVERT: A 170 ARG cc_start: 0.7240 (mtp85) cc_final: 0.6926 (mtp85) REVERT: A 245 ASP cc_start: 0.7334 (m-30) cc_final: 0.6964 (m-30) REVERT: A 273 ARG cc_start: 0.7131 (tpt170) cc_final: 0.6352 (tpt-90) REVERT: A 276 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6669 (mm-30) REVERT: A 277 MET cc_start: 0.8529 (mtp) cc_final: 0.8223 (mtp) REVERT: A 284 LYS cc_start: 0.6852 (tptt) cc_final: 0.6583 (ttmp) REVERT: A 314 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6480 (mt-10) REVERT: A 349 LYS cc_start: 0.7322 (ttmm) cc_final: 0.6782 (mtpp) REVERT: A 422 GLN cc_start: 0.7211 (mp10) cc_final: 0.6696 (mm-40) REVERT: A 446 TYR cc_start: 0.8191 (m-80) cc_final: 0.7850 (m-80) REVERT: A 472 ARG cc_start: 0.7124 (mtt-85) cc_final: 0.6807 (mtp85) REVERT: A 482 GLU cc_start: 0.6639 (tt0) cc_final: 0.6006 (tp30) REVERT: A 484 LYS cc_start: 0.7476 (mmtt) cc_final: 0.7233 (mmtt) REVERT: A 492 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.6319 (mtp85) REVERT: B 21 GLU cc_start: 0.5675 (OUTLIER) cc_final: 0.5465 (tm-30) REVERT: B 28 MET cc_start: 0.8094 (mmm) cc_final: 0.7748 (mmm) REVERT: B 30 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.5938 (tp30) REVERT: B 72 ASP cc_start: 0.7466 (t0) cc_final: 0.7229 (t70) REVERT: B 85 GLN cc_start: 0.6762 (mm110) cc_final: 0.6521 (mp10) REVERT: B 113 SER cc_start: 0.8098 (p) cc_final: 0.7891 (m) REVERT: B 132 GLU cc_start: 0.6784 (mm-30) cc_final: 0.6460 (mm-30) REVERT: B 166 ARG cc_start: 0.7248 (ttm170) cc_final: 0.6961 (ttp-110) REVERT: B 167 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7509 (mm-30) REVERT: B 206 ASP cc_start: 0.8219 (m-30) cc_final: 0.7993 (m-30) REVERT: B 225 GLU cc_start: 0.8927 (tt0) cc_final: 0.8490 (tt0) REVERT: B 245 ASP cc_start: 0.7357 (m-30) cc_final: 0.6971 (m-30) REVERT: B 273 ARG cc_start: 0.7066 (tpt170) cc_final: 0.6307 (tpt-90) REVERT: B 275 ASP cc_start: 0.8182 (m-30) cc_final: 0.7817 (m-30) REVERT: B 276 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6293 (tp30) REVERT: B 284 LYS cc_start: 0.6813 (tptt) cc_final: 0.6456 (ttmt) REVERT: B 314 GLU cc_start: 0.6753 (mt-10) cc_final: 0.6404 (mt-10) REVERT: B 349 LYS cc_start: 0.7315 (ttmm) cc_final: 0.6811 (mtpp) REVERT: B 472 ARG cc_start: 0.7052 (mtt-85) cc_final: 0.6789 (mtp85) REVERT: B 482 GLU cc_start: 0.6777 (tt0) cc_final: 0.6257 (mt-10) REVERT: B 484 LYS cc_start: 0.7608 (mmtt) cc_final: 0.7347 (mmtt) REVERT: B 492 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.6308 (mtp85) REVERT: C 21 GLU cc_start: 0.5520 (OUTLIER) cc_final: 0.5285 (tm-30) REVERT: C 30 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6171 (tm-30) REVERT: C 65 TYR cc_start: 0.7998 (t80) cc_final: 0.7702 (t80) REVERT: C 85 GLN cc_start: 0.6762 (mm110) cc_final: 0.6550 (mp10) REVERT: C 144 ARG cc_start: 0.7904 (mmm160) cc_final: 0.7700 (mmp-170) REVERT: C 206 ASP cc_start: 0.8323 (m-30) cc_final: 0.7985 (m-30) REVERT: C 225 GLU cc_start: 0.8859 (tt0) cc_final: 0.8608 (tt0) REVERT: C 245 ASP cc_start: 0.7196 (m-30) cc_final: 0.6795 (m-30) REVERT: C 256 MET cc_start: 0.5412 (ptt) cc_final: 0.5205 (ttp) REVERT: C 273 ARG cc_start: 0.7155 (tpt170) cc_final: 0.6520 (tpt-90) REVERT: C 276 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6324 (tp30) REVERT: C 284 LYS cc_start: 0.6990 (tptt) cc_final: 0.6574 (ttmt) REVERT: C 314 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6502 (mt-10) REVERT: C 349 LYS cc_start: 0.7231 (ttmm) cc_final: 0.6747 (mtpp) REVERT: C 422 GLN cc_start: 0.7179 (mp10) cc_final: 0.6725 (mm-40) REVERT: C 455 ARG cc_start: 0.7307 (mtt90) cc_final: 0.6651 (mtt90) REVERT: C 468 ASP cc_start: 0.8131 (t0) cc_final: 0.7772 (t70) REVERT: C 482 GLU cc_start: 0.6647 (tt0) cc_final: 0.5985 (tp30) REVERT: C 492 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.6294 (mtp85) REVERT: D 21 GLU cc_start: 0.5694 (OUTLIER) cc_final: 0.5445 (tm-30) REVERT: D 28 MET cc_start: 0.8150 (mmm) cc_final: 0.7904 (mmm) REVERT: D 30 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.6017 (tp30) REVERT: D 72 ASP cc_start: 0.7421 (t0) cc_final: 0.7167 (t70) REVERT: D 85 GLN cc_start: 0.6784 (mm110) cc_final: 0.6398 (mp10) REVERT: D 142 LYS cc_start: 0.6986 (mtmt) cc_final: 0.6330 (mmtm) REVERT: D 167 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7562 (mm-30) REVERT: D 170 ARG cc_start: 0.7255 (mtp85) cc_final: 0.6947 (mtp85) REVERT: D 225 GLU cc_start: 0.8894 (tt0) cc_final: 0.8615 (tt0) REVERT: D 245 ASP cc_start: 0.7280 (m-30) cc_final: 0.6907 (m-30) REVERT: D 273 ARG cc_start: 0.7157 (tpt170) cc_final: 0.6376 (tpt-90) REVERT: D 276 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6676 (mm-30) REVERT: D 277 MET cc_start: 0.8548 (mtp) cc_final: 0.8205 (mtp) REVERT: D 284 LYS cc_start: 0.6882 (tptt) cc_final: 0.6619 (ttmp) REVERT: D 314 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6492 (mt-10) REVERT: D 349 LYS cc_start: 0.7287 (ttmm) cc_final: 0.6756 (mtpp) REVERT: D 422 GLN cc_start: 0.7261 (mp10) cc_final: 0.6663 (mm110) REVERT: D 446 TYR cc_start: 0.8168 (m-80) cc_final: 0.7922 (m-80) REVERT: D 468 ASP cc_start: 0.8175 (t0) cc_final: 0.7917 (t70) REVERT: D 472 ARG cc_start: 0.7080 (mtt-85) cc_final: 0.6740 (mtp85) REVERT: D 482 GLU cc_start: 0.6630 (tt0) cc_final: 0.6023 (tp30) REVERT: D 484 LYS cc_start: 0.7431 (mmtt) cc_final: 0.7198 (mmtt) REVERT: D 492 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.6353 (mtp85) REVERT: E 21 GLU cc_start: 0.5566 (OUTLIER) cc_final: 0.5347 (tm-30) REVERT: E 28 MET cc_start: 0.8150 (mmm) cc_final: 0.7836 (mmm) REVERT: E 30 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.5988 (tp30) REVERT: E 65 TYR cc_start: 0.8119 (t80) cc_final: 0.7911 (t80) REVERT: E 72 ASP cc_start: 0.7463 (t0) cc_final: 0.7212 (t70) REVERT: E 85 GLN cc_start: 0.6739 (mm110) cc_final: 0.6505 (mp10) REVERT: E 132 GLU cc_start: 0.6824 (mm-30) cc_final: 0.6495 (mm-30) REVERT: E 166 ARG cc_start: 0.7288 (ttm170) cc_final: 0.6993 (ttp-110) REVERT: E 167 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7620 (mm-30) REVERT: E 206 ASP cc_start: 0.8215 (m-30) cc_final: 0.7980 (m-30) REVERT: E 245 ASP cc_start: 0.7270 (m-30) cc_final: 0.6889 (m-30) REVERT: E 273 ARG cc_start: 0.7136 (tpt170) cc_final: 0.6378 (tpt-90) REVERT: E 276 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6299 (tp30) REVERT: E 277 MET cc_start: 0.8493 (mtp) cc_final: 0.8236 (mtp) REVERT: E 284 LYS cc_start: 0.6848 (tptt) cc_final: 0.6504 (ttmt) REVERT: E 314 GLU cc_start: 0.6763 (mt-10) cc_final: 0.6405 (mt-10) REVERT: E 349 LYS cc_start: 0.7278 (ttmm) cc_final: 0.6785 (mtpp) REVERT: E 472 ARG cc_start: 0.7037 (mtt-85) cc_final: 0.6771 (mtp85) REVERT: E 482 GLU cc_start: 0.6754 (tt0) cc_final: 0.6232 (mt-10) REVERT: E 484 LYS cc_start: 0.7587 (mmtt) cc_final: 0.7385 (mmtt) REVERT: E 492 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6303 (mtp85) REVERT: F 21 GLU cc_start: 0.5518 (OUTLIER) cc_final: 0.5287 (tm-30) REVERT: F 30 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.6166 (tm-30) REVERT: F 65 TYR cc_start: 0.8008 (t80) cc_final: 0.7719 (t80) REVERT: F 85 GLN cc_start: 0.6757 (mm110) cc_final: 0.6548 (mp10) REVERT: F 144 ARG cc_start: 0.7878 (mmm160) cc_final: 0.7677 (mmp-170) REVERT: F 206 ASP cc_start: 0.8302 (m-30) cc_final: 0.7965 (m-30) REVERT: F 225 GLU cc_start: 0.8853 (tt0) cc_final: 0.8637 (tt0) REVERT: F 245 ASP cc_start: 0.7172 (m-30) cc_final: 0.6764 (m-30) REVERT: F 273 ARG cc_start: 0.7150 (tpt170) cc_final: 0.6512 (tpt-90) REVERT: F 275 ASP cc_start: 0.8228 (m-30) cc_final: 0.8027 (m-30) REVERT: F 276 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6367 (tp30) REVERT: F 284 LYS cc_start: 0.6997 (tptt) cc_final: 0.6631 (ttmt) REVERT: F 314 GLU cc_start: 0.6783 (mt-10) cc_final: 0.6501 (mt-10) REVERT: F 349 LYS cc_start: 0.7235 (ttmm) cc_final: 0.6742 (mtpp) REVERT: F 455 ARG cc_start: 0.7347 (mtt90) cc_final: 0.6695 (mtt90) REVERT: F 482 GLU cc_start: 0.6649 (tt0) cc_final: 0.5984 (tp30) REVERT: F 492 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6290 (mtp85) outliers start: 60 outliers final: 10 residues processed: 745 average time/residue: 2.6311 time to fit residues: 2309.0426 Evaluate side-chains 587 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 559 time to evaluate : 3.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 492 ARG Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 492 ARG Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 188 ARG Chi-restraints excluded: chain E residue 492 ARG Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain F residue 188 ARG Chi-restraints excluded: chain F residue 492 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 ASN A 422 GLN A 445 GLN B 90 ASN B 207 ASN B 422 GLN B 445 GLN ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN C 422 GLN D 90 ASN D 207 ASN D 422 GLN D 445 GLN E 90 ASN E 207 ASN E 422 GLN E 445 GLN F 90 ASN F 99 GLN F 207 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 23634 Z= 0.408 Angle : 0.708 7.383 31950 Z= 0.367 Chirality : 0.047 0.180 3570 Planarity : 0.006 0.070 4092 Dihedral : 11.475 129.675 3548 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.13 % Allowed : 20.00 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 2898 helix: 1.02 (0.15), residues: 1086 sheet: -1.02 (0.18), residues: 726 loop : -0.19 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP F 466 HIS 0.008 0.002 HIS D 246 PHE 0.021 0.003 PHE E 32 TYR 0.018 0.002 TYR A 158 ARG 0.006 0.001 ARG E 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 640 time to evaluate : 4.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6597 (tp30) REVERT: A 34 ASP cc_start: 0.8113 (m-30) cc_final: 0.7839 (m-30) REVERT: A 72 ASP cc_start: 0.8025 (t0) cc_final: 0.7249 (m-30) REVERT: A 85 GLN cc_start: 0.7114 (mm110) cc_final: 0.6881 (mp10) REVERT: A 100 LYS cc_start: 0.7175 (tttt) cc_final: 0.6810 (ttpt) REVERT: A 135 ASN cc_start: 0.7894 (t0) cc_final: 0.7542 (t0) REVERT: A 139 GLN cc_start: 0.7132 (mt0) cc_final: 0.6492 (mm110) REVERT: A 142 LYS cc_start: 0.7501 (mtmt) cc_final: 0.6933 (mmtm) REVERT: A 149 ASP cc_start: 0.7823 (t0) cc_final: 0.7381 (t70) REVERT: A 190 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7511 (m-30) REVERT: A 206 ASP cc_start: 0.8406 (m-30) cc_final: 0.7983 (m-30) REVERT: A 216 GLU cc_start: 0.7353 (tp30) cc_final: 0.6901 (tm-30) REVERT: A 273 ARG cc_start: 0.7288 (tpt170) cc_final: 0.6686 (tmt170) REVERT: A 276 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7208 (mt-10) REVERT: A 284 LYS cc_start: 0.7446 (tptt) cc_final: 0.7168 (ttmp) REVERT: A 314 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6303 (mt-10) REVERT: A 349 LYS cc_start: 0.7475 (ttmm) cc_final: 0.7205 (ttmp) REVERT: A 439 ASP cc_start: 0.7774 (m-30) cc_final: 0.7485 (m-30) REVERT: A 445 GLN cc_start: 0.8263 (pt0) cc_final: 0.7874 (pt0) REVERT: A 472 ARG cc_start: 0.7586 (mtt-85) cc_final: 0.7041 (mtp85) REVERT: A 482 GLU cc_start: 0.7148 (tt0) cc_final: 0.6595 (tp30) REVERT: A 484 LYS cc_start: 0.7619 (mmtt) cc_final: 0.7367 (mmtt) REVERT: A 485 ASP cc_start: 0.6591 (m-30) cc_final: 0.6325 (t0) REVERT: B 30 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6670 (tp30) REVERT: B 34 ASP cc_start: 0.8039 (m-30) cc_final: 0.7812 (m-30) REVERT: B 85 GLN cc_start: 0.7086 (mm110) cc_final: 0.6805 (mp10) REVERT: B 100 LYS cc_start: 0.7214 (tttt) cc_final: 0.6744 (ttpt) REVERT: B 113 SER cc_start: 0.8270 (p) cc_final: 0.7766 (m) REVERT: B 135 ASN cc_start: 0.8008 (t0) cc_final: 0.7781 (t0) REVERT: B 139 GLN cc_start: 0.7098 (mt0) cc_final: 0.6459 (mm110) REVERT: B 142 LYS cc_start: 0.7752 (mttp) cc_final: 0.6964 (mmtm) REVERT: B 166 ARG cc_start: 0.7619 (ttm170) cc_final: 0.7323 (ttp-110) REVERT: B 191 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8176 (mm-30) REVERT: B 216 GLU cc_start: 0.7150 (tp30) cc_final: 0.6879 (tm-30) REVERT: B 273 ARG cc_start: 0.7365 (tpt170) cc_final: 0.6528 (tpt-90) REVERT: B 276 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7125 (mt-10) REVERT: B 314 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6465 (mt-10) REVERT: B 345 GLN cc_start: 0.7828 (mt0) cc_final: 0.7616 (mt0) REVERT: B 439 ASP cc_start: 0.7771 (m-30) cc_final: 0.7566 (m-30) REVERT: B 450 ARG cc_start: 0.7327 (mtt180) cc_final: 0.6945 (mtt-85) REVERT: B 479 LYS cc_start: 0.7987 (mmmm) cc_final: 0.7697 (mmmm) REVERT: B 482 GLU cc_start: 0.7274 (tt0) cc_final: 0.6592 (tp30) REVERT: B 485 ASP cc_start: 0.6621 (m-30) cc_final: 0.6318 (t0) REVERT: C 30 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6657 (tp30) REVERT: C 34 ASP cc_start: 0.8214 (m-30) cc_final: 0.7943 (m-30) REVERT: C 85 GLN cc_start: 0.6931 (mm110) cc_final: 0.6729 (mp10) REVERT: C 100 LYS cc_start: 0.7167 (tttt) cc_final: 0.6813 (ttpt) REVERT: C 139 GLN cc_start: 0.7038 (mt0) cc_final: 0.6484 (mm110) REVERT: C 142 LYS cc_start: 0.7727 (mttp) cc_final: 0.6867 (mmtm) REVERT: C 191 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8273 (mm-30) REVERT: C 273 ARG cc_start: 0.7333 (tpt170) cc_final: 0.6598 (tmt170) REVERT: C 284 LYS cc_start: 0.7379 (tptt) cc_final: 0.7066 (ttmt) REVERT: C 304 LYS cc_start: 0.7746 (mmmm) cc_final: 0.7379 (mmmm) REVERT: C 314 GLU cc_start: 0.6980 (mt-10) cc_final: 0.6511 (mt-10) REVERT: C 325 ARG cc_start: 0.8139 (ttt-90) cc_final: 0.7901 (ttt-90) REVERT: C 406 TYR cc_start: 0.7624 (t80) cc_final: 0.7390 (t80) REVERT: C 422 GLN cc_start: 0.7553 (mp-120) cc_final: 0.7159 (mm110) REVERT: C 452 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7508 (tp30) REVERT: C 462 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8353 (tpt) REVERT: C 482 GLU cc_start: 0.7302 (tt0) cc_final: 0.6712 (tp30) REVERT: C 485 ASP cc_start: 0.6647 (m-30) cc_final: 0.6345 (t0) REVERT: C 492 ARG cc_start: 0.6872 (mtp180) cc_final: 0.6382 (mtp85) REVERT: D 30 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6601 (tp30) REVERT: D 34 ASP cc_start: 0.8115 (m-30) cc_final: 0.7853 (m-30) REVERT: D 85 GLN cc_start: 0.7107 (mm110) cc_final: 0.6874 (mp10) REVERT: D 100 LYS cc_start: 0.7171 (tttt) cc_final: 0.6811 (ttpt) REVERT: D 135 ASN cc_start: 0.7968 (t0) cc_final: 0.7566 (t0) REVERT: D 139 GLN cc_start: 0.7120 (mt0) cc_final: 0.6478 (mm110) REVERT: D 142 LYS cc_start: 0.7508 (mtmt) cc_final: 0.6941 (mmtm) REVERT: D 149 ASP cc_start: 0.7829 (t0) cc_final: 0.7107 (t0) REVERT: D 190 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7513 (m-30) REVERT: D 206 ASP cc_start: 0.8401 (m-30) cc_final: 0.7978 (m-30) REVERT: D 216 GLU cc_start: 0.7365 (tp30) cc_final: 0.6895 (tm-30) REVERT: D 273 ARG cc_start: 0.7315 (tpt170) cc_final: 0.6700 (tmt170) REVERT: D 276 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7211 (mt-10) REVERT: D 284 LYS cc_start: 0.7461 (tptt) cc_final: 0.7182 (ttmp) REVERT: D 314 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6299 (mt-10) REVERT: D 349 LYS cc_start: 0.7487 (ttmm) cc_final: 0.7219 (ttmp) REVERT: D 445 GLN cc_start: 0.8246 (pt0) cc_final: 0.7861 (pt0) REVERT: D 482 GLU cc_start: 0.7109 (tt0) cc_final: 0.6546 (tp30) REVERT: D 485 ASP cc_start: 0.6707 (m-30) cc_final: 0.6482 (t0) REVERT: D 492 ARG cc_start: 0.6800 (mtp180) cc_final: 0.6327 (mtp85) REVERT: E 30 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6713 (tp30) REVERT: E 34 ASP cc_start: 0.8040 (m-30) cc_final: 0.7803 (m-30) REVERT: E 85 GLN cc_start: 0.7059 (mm110) cc_final: 0.6773 (mp10) REVERT: E 100 LYS cc_start: 0.7204 (tttt) cc_final: 0.6736 (ttpt) REVERT: E 135 ASN cc_start: 0.8010 (t0) cc_final: 0.7782 (t0) REVERT: E 139 GLN cc_start: 0.7082 (mt0) cc_final: 0.6459 (mm110) REVERT: E 142 LYS cc_start: 0.7764 (mttp) cc_final: 0.6972 (mmtm) REVERT: E 216 GLU cc_start: 0.7164 (tp30) cc_final: 0.6890 (tm-30) REVERT: E 273 ARG cc_start: 0.7367 (tpt170) cc_final: 0.6770 (tmt170) REVERT: E 276 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7107 (mt-10) REVERT: E 284 LYS cc_start: 0.7319 (tptt) cc_final: 0.7063 (ttmp) REVERT: E 294 THR cc_start: 0.8974 (p) cc_final: 0.8709 (t) REVERT: E 314 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6444 (mt-10) REVERT: E 345 GLN cc_start: 0.7814 (mt0) cc_final: 0.7602 (mt0) REVERT: E 439 ASP cc_start: 0.7804 (m-30) cc_final: 0.7576 (m-30) REVERT: E 450 ARG cc_start: 0.7501 (mtt180) cc_final: 0.7138 (mtt-85) REVERT: E 479 LYS cc_start: 0.7977 (mmmm) cc_final: 0.7677 (mmmm) REVERT: E 482 GLU cc_start: 0.7287 (tt0) cc_final: 0.6597 (tp30) REVERT: E 485 ASP cc_start: 0.6669 (m-30) cc_final: 0.6387 (t0) REVERT: E 492 ARG cc_start: 0.6889 (mtp180) cc_final: 0.6390 (mtp85) REVERT: F 30 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6654 (tp30) REVERT: F 34 ASP cc_start: 0.8219 (m-30) cc_final: 0.7894 (m-30) REVERT: F 85 GLN cc_start: 0.6984 (mm110) cc_final: 0.6753 (mp10) REVERT: F 100 LYS cc_start: 0.7133 (tttt) cc_final: 0.6748 (ttpt) REVERT: F 135 ASN cc_start: 0.8008 (t0) cc_final: 0.7731 (t0) REVERT: F 139 GLN cc_start: 0.7037 (mt0) cc_final: 0.6467 (mm110) REVERT: F 142 LYS cc_start: 0.7714 (mttp) cc_final: 0.6869 (mmtm) REVERT: F 273 ARG cc_start: 0.7347 (tpt170) cc_final: 0.6557 (tmt170) REVERT: F 275 ASP cc_start: 0.8239 (m-30) cc_final: 0.7919 (m-30) REVERT: F 284 LYS cc_start: 0.7372 (tptt) cc_final: 0.6990 (ttmt) REVERT: F 304 LYS cc_start: 0.7728 (mmmm) cc_final: 0.7482 (mmmt) REVERT: F 314 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6471 (mt-10) REVERT: F 325 ARG cc_start: 0.8140 (ttt-90) cc_final: 0.7864 (ttt-90) REVERT: F 345 GLN cc_start: 0.7866 (mt0) cc_final: 0.7653 (mt0) REVERT: F 406 TYR cc_start: 0.7612 (t80) cc_final: 0.7380 (t80) REVERT: F 479 LYS cc_start: 0.8020 (mmmm) cc_final: 0.7818 (mmmm) REVERT: F 482 GLU cc_start: 0.7308 (tt0) cc_final: 0.6713 (tp30) REVERT: F 485 ASP cc_start: 0.6633 (m-30) cc_final: 0.6312 (t0) REVERT: F 492 ARG cc_start: 0.6914 (mtp180) cc_final: 0.6370 (mtp85) outliers start: 78 outliers final: 32 residues processed: 681 average time/residue: 3.1551 time to fit residues: 2474.5529 Evaluate side-chains 581 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 543 time to evaluate : 3.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 188 ARG Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 188 ARG Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 267 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 262 optimal weight: 0.9980 chunk 283 optimal weight: 5.9990 chunk 233 optimal weight: 7.9990 chunk 259 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 210 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 177 GLN A 327 GLN B 177 GLN B 445 GLN C 90 ASN D 177 GLN D 327 GLN E 177 GLN E 445 GLN F 177 GLN F 327 GLN F 445 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23634 Z= 0.206 Angle : 0.563 6.959 31950 Z= 0.284 Chirality : 0.043 0.152 3570 Planarity : 0.004 0.048 4092 Dihedral : 9.997 115.557 3498 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.37 % Allowed : 19.84 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2898 helix: 1.51 (0.16), residues: 1086 sheet: -1.36 (0.18), residues: 702 loop : -0.15 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 96 HIS 0.003 0.001 HIS F 467 PHE 0.014 0.002 PHE B 32 TYR 0.017 0.001 TYR B 158 ARG 0.005 0.000 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 585 time to evaluate : 3.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.8551 (mmm) cc_final: 0.8285 (mmm) REVERT: A 30 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6620 (tp30) REVERT: A 34 ASP cc_start: 0.8075 (m-30) cc_final: 0.7792 (m-30) REVERT: A 100 LYS cc_start: 0.7220 (tttt) cc_final: 0.6905 (ttpt) REVERT: A 135 ASN cc_start: 0.8170 (t0) cc_final: 0.7772 (t0) REVERT: A 139 GLN cc_start: 0.7188 (mt0) cc_final: 0.6463 (mm110) REVERT: A 142 LYS cc_start: 0.7444 (mtmt) cc_final: 0.6897 (mmtm) REVERT: A 206 ASP cc_start: 0.8366 (m-30) cc_final: 0.7948 (m-30) REVERT: A 216 GLU cc_start: 0.7311 (tp30) cc_final: 0.6951 (tm-30) REVERT: A 273 ARG cc_start: 0.7402 (tpt170) cc_final: 0.6615 (tmt170) REVERT: A 276 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7211 (mt-10) REVERT: A 294 THR cc_start: 0.8910 (p) cc_final: 0.8662 (t) REVERT: A 314 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6467 (mt-10) REVERT: A 349 LYS cc_start: 0.7541 (ttmm) cc_final: 0.6940 (mtpp) REVERT: A 472 ARG cc_start: 0.7488 (mtt-85) cc_final: 0.7072 (mtp85) REVERT: A 482 GLU cc_start: 0.7199 (tt0) cc_final: 0.6620 (tp30) REVERT: A 485 ASP cc_start: 0.6563 (m-30) cc_final: 0.6298 (t0) REVERT: B 30 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6791 (tp30) REVERT: B 34 ASP cc_start: 0.8102 (m-30) cc_final: 0.7801 (m-30) REVERT: B 85 GLN cc_start: 0.7092 (mm110) cc_final: 0.6804 (mp10) REVERT: B 100 LYS cc_start: 0.7372 (tttt) cc_final: 0.7041 (tttt) REVERT: B 135 ASN cc_start: 0.8134 (t0) cc_final: 0.7870 (t0) REVERT: B 139 GLN cc_start: 0.7168 (mt0) cc_final: 0.6495 (mm110) REVERT: B 142 LYS cc_start: 0.7705 (mttp) cc_final: 0.6933 (mmtm) REVERT: B 256 MET cc_start: 0.5555 (OUTLIER) cc_final: 0.5295 (ptt) REVERT: B 273 ARG cc_start: 0.7400 (tpt170) cc_final: 0.6671 (tpt-90) REVERT: B 275 ASP cc_start: 0.8295 (m-30) cc_final: 0.7900 (m-30) REVERT: B 276 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7176 (mt-10) REVERT: B 284 LYS cc_start: 0.7649 (tttm) cc_final: 0.7174 (ttmt) REVERT: B 314 GLU cc_start: 0.6907 (mt-10) cc_final: 0.6591 (mt-10) REVERT: B 349 LYS cc_start: 0.7552 (ttmm) cc_final: 0.7327 (ttmp) REVERT: B 352 CYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8304 (p) REVERT: B 450 ARG cc_start: 0.7429 (mtt180) cc_final: 0.6987 (mtt-85) REVERT: B 482 GLU cc_start: 0.7320 (tt0) cc_final: 0.6673 (tp30) REVERT: B 485 ASP cc_start: 0.6714 (m-30) cc_final: 0.6370 (t0) REVERT: C 30 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6679 (tp30) REVERT: C 34 ASP cc_start: 0.8094 (m-30) cc_final: 0.7855 (m-30) REVERT: C 100 LYS cc_start: 0.7276 (tttt) cc_final: 0.6840 (tttt) REVERT: C 139 GLN cc_start: 0.7098 (mt0) cc_final: 0.6499 (mm110) REVERT: C 142 LYS cc_start: 0.7692 (mttp) cc_final: 0.6935 (mmtm) REVERT: C 206 ASP cc_start: 0.8401 (m-30) cc_final: 0.8153 (m-30) REVERT: C 273 ARG cc_start: 0.7223 (tpt170) cc_final: 0.6520 (tmt170) REVERT: C 284 LYS cc_start: 0.7344 (OUTLIER) cc_final: 0.7005 (ttmt) REVERT: C 304 LYS cc_start: 0.7703 (mmmm) cc_final: 0.7333 (mmmm) REVERT: C 314 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6524 (mt-10) REVERT: C 349 LYS cc_start: 0.7445 (ttmm) cc_final: 0.6498 (tttm) REVERT: C 352 CYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8261 (p) REVERT: C 406 TYR cc_start: 0.7476 (t80) cc_final: 0.7243 (t80) REVERT: C 422 GLN cc_start: 0.7407 (mp-120) cc_final: 0.7049 (mm110) REVERT: C 450 ARG cc_start: 0.7521 (mtt180) cc_final: 0.7064 (mtt-85) REVERT: C 452 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7405 (tp30) REVERT: C 482 GLU cc_start: 0.7219 (tt0) cc_final: 0.6681 (tp30) REVERT: C 485 ASP cc_start: 0.6735 (m-30) cc_final: 0.6454 (t0) REVERT: D 28 MET cc_start: 0.8565 (mmm) cc_final: 0.8296 (mmm) REVERT: D 30 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6626 (tp30) REVERT: D 34 ASP cc_start: 0.8072 (m-30) cc_final: 0.7791 (m-30) REVERT: D 100 LYS cc_start: 0.7225 (tttt) cc_final: 0.6902 (ttpt) REVERT: D 135 ASN cc_start: 0.8173 (t0) cc_final: 0.7805 (t0) REVERT: D 139 GLN cc_start: 0.7222 (mt0) cc_final: 0.6492 (mm110) REVERT: D 142 LYS cc_start: 0.7451 (mtmt) cc_final: 0.6904 (mmtm) REVERT: D 206 ASP cc_start: 0.8363 (m-30) cc_final: 0.7941 (m-30) REVERT: D 216 GLU cc_start: 0.7359 (tp30) cc_final: 0.6920 (tm-30) REVERT: D 273 ARG cc_start: 0.7255 (tpt170) cc_final: 0.6589 (tmt170) REVERT: D 276 GLU cc_start: 0.7389 (mt-10) cc_final: 0.7029 (mt-10) REVERT: D 294 THR cc_start: 0.8914 (p) cc_final: 0.8655 (t) REVERT: D 314 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6390 (mt-10) REVERT: D 349 LYS cc_start: 0.7579 (ttmm) cc_final: 0.7266 (ttmp) REVERT: D 482 GLU cc_start: 0.7182 (tt0) cc_final: 0.6635 (tp30) REVERT: D 485 ASP cc_start: 0.6733 (m-30) cc_final: 0.6515 (t0) REVERT: E 30 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6821 (tp30) REVERT: E 34 ASP cc_start: 0.8077 (m-30) cc_final: 0.7735 (m-30) REVERT: E 85 GLN cc_start: 0.7084 (mm110) cc_final: 0.6802 (mp10) REVERT: E 100 LYS cc_start: 0.7369 (tttt) cc_final: 0.7034 (tttt) REVERT: E 135 ASN cc_start: 0.8107 (t0) cc_final: 0.7850 (t0) REVERT: E 139 GLN cc_start: 0.7154 (mt0) cc_final: 0.6520 (mm110) REVERT: E 142 LYS cc_start: 0.7703 (mttp) cc_final: 0.6939 (mmtm) REVERT: E 166 ARG cc_start: 0.7802 (ttp-110) cc_final: 0.7508 (ttp-110) REVERT: E 273 ARG cc_start: 0.7239 (tpt170) cc_final: 0.6642 (tpt-90) REVERT: E 276 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7084 (mt-10) REVERT: E 284 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6961 (ttmt) REVERT: E 294 THR cc_start: 0.8875 (p) cc_final: 0.8658 (t) REVERT: E 314 GLU cc_start: 0.6827 (mt-10) cc_final: 0.6510 (mt-10) REVERT: E 352 CYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8404 (p) REVERT: E 450 ARG cc_start: 0.7556 (mtt180) cc_final: 0.7150 (mtt-85) REVERT: E 482 GLU cc_start: 0.7318 (tt0) cc_final: 0.6680 (tp30) REVERT: E 485 ASP cc_start: 0.6680 (m-30) cc_final: 0.6459 (t0) REVERT: F 30 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6676 (tp30) REVERT: F 34 ASP cc_start: 0.8094 (m-30) cc_final: 0.7872 (m-30) REVERT: F 100 LYS cc_start: 0.7302 (tttt) cc_final: 0.6907 (tttt) REVERT: F 139 GLN cc_start: 0.7097 (mt0) cc_final: 0.6526 (mm110) REVERT: F 142 LYS cc_start: 0.7687 (mttp) cc_final: 0.6933 (mmtm) REVERT: F 206 ASP cc_start: 0.8402 (m-30) cc_final: 0.8159 (m-30) REVERT: F 273 ARG cc_start: 0.7149 (tpt170) cc_final: 0.6464 (tmt170) REVERT: F 275 ASP cc_start: 0.8160 (m-30) cc_final: 0.7777 (m-30) REVERT: F 284 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.7039 (ttmt) REVERT: F 304 LYS cc_start: 0.7715 (mmmm) cc_final: 0.7343 (mmmm) REVERT: F 314 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6581 (mt-10) REVERT: F 349 LYS cc_start: 0.7452 (ttmm) cc_final: 0.6509 (tttm) REVERT: F 352 CYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8262 (p) REVERT: F 406 TYR cc_start: 0.7480 (t80) cc_final: 0.7196 (t80) REVERT: F 422 GLN cc_start: 0.7690 (mp10) cc_final: 0.7077 (mm110) REVERT: F 450 ARG cc_start: 0.7651 (mtt180) cc_final: 0.7202 (mtt-85) REVERT: F 482 GLU cc_start: 0.7215 (tt0) cc_final: 0.6689 (tp30) REVERT: F 485 ASP cc_start: 0.6732 (m-30) cc_final: 0.6454 (t0) outliers start: 84 outliers final: 40 residues processed: 631 average time/residue: 3.0219 time to fit residues: 2203.8705 Evaluate side-chains 588 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 539 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 188 ARG Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 284 LYS Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain E residue 486 SER Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 188 ARG Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 284 LYS Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 352 CYS Chi-restraints excluded: chain F residue 486 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 262 optimal weight: 4.9990 chunk 278 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 249 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN C 327 GLN D 99 GLN E 327 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.071 23634 Z= 0.635 Angle : 0.757 8.311 31950 Z= 0.394 Chirality : 0.050 0.156 3570 Planarity : 0.007 0.093 4092 Dihedral : 12.616 134.887 3498 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.86 % Allowed : 19.48 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 2898 helix: 0.76 (0.15), residues: 1122 sheet: -1.26 (0.19), residues: 696 loop : 0.01 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP F 96 HIS 0.010 0.002 HIS D 246 PHE 0.022 0.003 PHE D 32 TYR 0.023 0.003 TYR D 239 ARG 0.008 0.001 ARG C 325 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 550 time to evaluate : 3.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6792 (tp30) REVERT: A 34 ASP cc_start: 0.8153 (m-30) cc_final: 0.7823 (m-30) REVERT: A 70 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7229 (mt-10) REVERT: A 100 LYS cc_start: 0.7346 (tttt) cc_final: 0.6903 (ttpt) REVERT: A 139 GLN cc_start: 0.7530 (mt0) cc_final: 0.6815 (mm-40) REVERT: A 142 LYS cc_start: 0.7603 (mtmt) cc_final: 0.7131 (mmtm) REVERT: A 206 ASP cc_start: 0.8591 (m-30) cc_final: 0.8358 (m-30) REVERT: A 216 GLU cc_start: 0.7516 (tp30) cc_final: 0.7204 (tm-30) REVERT: A 273 ARG cc_start: 0.7366 (tpt170) cc_final: 0.6741 (tmt170) REVERT: A 294 THR cc_start: 0.8981 (p) cc_final: 0.8717 (t) REVERT: A 314 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6505 (mt-10) REVERT: A 352 CYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8491 (p) REVERT: A 364 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7422 (tp) REVERT: A 445 GLN cc_start: 0.8269 (pt0) cc_final: 0.7987 (pt0) REVERT: A 448 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: A 472 ARG cc_start: 0.7713 (mtt-85) cc_final: 0.7369 (mtp85) REVERT: A 482 GLU cc_start: 0.7351 (tt0) cc_final: 0.6841 (tp30) REVERT: A 485 ASP cc_start: 0.6778 (m-30) cc_final: 0.6424 (t0) REVERT: B 30 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6940 (tp30) REVERT: B 85 GLN cc_start: 0.7255 (mm110) cc_final: 0.6945 (mp10) REVERT: B 100 LYS cc_start: 0.7334 (tttt) cc_final: 0.7063 (ttpt) REVERT: B 139 GLN cc_start: 0.7585 (mt0) cc_final: 0.6900 (mm-40) REVERT: B 142 LYS cc_start: 0.7837 (mttp) cc_final: 0.7050 (mmtm) REVERT: B 206 ASP cc_start: 0.8641 (m-30) cc_final: 0.8410 (m-30) REVERT: B 273 ARG cc_start: 0.7004 (tpt170) cc_final: 0.6538 (tpt-90) REVERT: B 275 ASP cc_start: 0.8291 (m-30) cc_final: 0.7908 (m-30) REVERT: B 294 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8706 (t) REVERT: B 311 GLN cc_start: 0.7985 (mt0) cc_final: 0.7516 (mt0) REVERT: B 314 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6585 (mt-10) REVERT: B 450 ARG cc_start: 0.7786 (mtt180) cc_final: 0.7398 (mtt-85) REVERT: B 482 GLU cc_start: 0.7520 (tt0) cc_final: 0.6887 (tp30) REVERT: B 485 ASP cc_start: 0.6734 (m-30) cc_final: 0.6369 (t0) REVERT: C 30 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6778 (tp30) REVERT: C 100 LYS cc_start: 0.7335 (tttt) cc_final: 0.6976 (ttpt) REVERT: C 139 GLN cc_start: 0.7654 (mt0) cc_final: 0.6980 (mm-40) REVERT: C 142 LYS cc_start: 0.7897 (mttp) cc_final: 0.7134 (mmtm) REVERT: C 191 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.7669 (mp0) REVERT: C 273 ARG cc_start: 0.7077 (tpt170) cc_final: 0.6295 (tmt170) REVERT: C 284 LYS cc_start: 0.7399 (tptt) cc_final: 0.7040 (ttmt) REVERT: C 314 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6894 (mt-10) REVERT: C 352 CYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8390 (p) REVERT: C 364 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7384 (tp) REVERT: C 452 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7667 (tp30) REVERT: C 472 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.5715 (mtm180) REVERT: C 482 GLU cc_start: 0.7427 (tt0) cc_final: 0.6861 (tp30) REVERT: C 485 ASP cc_start: 0.6888 (m-30) cc_final: 0.6455 (t0) REVERT: C 492 ARG cc_start: 0.6897 (mtp180) cc_final: 0.6353 (mtp85) REVERT: D 30 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6815 (tp30) REVERT: D 34 ASP cc_start: 0.8149 (m-30) cc_final: 0.7820 (m-30) REVERT: D 70 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7207 (mt-10) REVERT: D 100 LYS cc_start: 0.7299 (tttt) cc_final: 0.6857 (ttpt) REVERT: D 139 GLN cc_start: 0.7532 (mt0) cc_final: 0.6820 (mm-40) REVERT: D 142 LYS cc_start: 0.7590 (mtmt) cc_final: 0.7125 (mmtm) REVERT: D 197 ARG cc_start: 0.8045 (mtp85) cc_final: 0.7537 (mtp85) REVERT: D 206 ASP cc_start: 0.8588 (m-30) cc_final: 0.8355 (m-30) REVERT: D 216 GLU cc_start: 0.7519 (tp30) cc_final: 0.7208 (tm-30) REVERT: D 273 ARG cc_start: 0.7165 (tpt170) cc_final: 0.6517 (tpt-90) REVERT: D 294 THR cc_start: 0.8981 (p) cc_final: 0.8715 (t) REVERT: D 314 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6545 (mt-10) REVERT: D 364 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7421 (tp) REVERT: D 445 GLN cc_start: 0.8247 (pt0) cc_final: 0.7956 (pt0) REVERT: D 448 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: D 482 GLU cc_start: 0.7329 (tt0) cc_final: 0.6846 (tp30) REVERT: D 485 ASP cc_start: 0.6947 (m-30) cc_final: 0.6531 (t0) REVERT: D 492 ARG cc_start: 0.7006 (mtp180) cc_final: 0.6469 (mtp85) REVERT: E 30 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6912 (tp30) REVERT: E 85 GLN cc_start: 0.7263 (mm110) cc_final: 0.6970 (mp10) REVERT: E 100 LYS cc_start: 0.7352 (tttt) cc_final: 0.7070 (ttpt) REVERT: E 139 GLN cc_start: 0.7587 (mt0) cc_final: 0.6915 (mm-40) REVERT: E 142 LYS cc_start: 0.7837 (mttp) cc_final: 0.7054 (mmtm) REVERT: E 273 ARG cc_start: 0.7164 (tpt170) cc_final: 0.6595 (tpt-90) REVERT: E 276 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7128 (mt-10) REVERT: E 294 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8713 (t) REVERT: E 311 GLN cc_start: 0.7945 (mt0) cc_final: 0.7471 (mt0) REVERT: E 314 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6565 (mt-10) REVERT: E 352 CYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8397 (p) REVERT: E 450 ARG cc_start: 0.7813 (mtt180) cc_final: 0.7437 (mtt-85) REVERT: E 482 GLU cc_start: 0.7481 (tt0) cc_final: 0.6952 (tp30) REVERT: E 485 ASP cc_start: 0.6895 (m-30) cc_final: 0.6486 (t0) REVERT: E 492 ARG cc_start: 0.7016 (mtp180) cc_final: 0.6413 (mtp85) REVERT: F 30 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6762 (tp30) REVERT: F 100 LYS cc_start: 0.7324 (tttt) cc_final: 0.6937 (ttpt) REVERT: F 139 GLN cc_start: 0.7654 (mt0) cc_final: 0.6979 (mm-40) REVERT: F 142 LYS cc_start: 0.7909 (mttp) cc_final: 0.7148 (mmtm) REVERT: F 273 ARG cc_start: 0.7100 (tpt170) cc_final: 0.6334 (tmt170) REVERT: F 275 ASP cc_start: 0.8120 (m-30) cc_final: 0.7731 (m-30) REVERT: F 284 LYS cc_start: 0.7401 (tptt) cc_final: 0.7039 (ttmt) REVERT: F 314 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6911 (mt-10) REVERT: F 352 CYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8391 (p) REVERT: F 364 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7387 (tp) REVERT: F 472 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.5699 (mtm180) REVERT: F 482 GLU cc_start: 0.7427 (tt0) cc_final: 0.6862 (tp30) REVERT: F 485 ASP cc_start: 0.6879 (m-30) cc_final: 0.6451 (t0) REVERT: F 492 ARG cc_start: 0.6892 (mtp180) cc_final: 0.6293 (mtp85) outliers start: 96 outliers final: 39 residues processed: 594 average time/residue: 3.1675 time to fit residues: 2163.5272 Evaluate side-chains 583 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 527 time to evaluate : 3.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 448 GLU Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 486 SER Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 352 CYS Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain F residue 472 ARG Chi-restraints excluded: chain F residue 486 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 2.9990 chunk 158 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 237 optimal weight: 0.6980 chunk 192 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 249 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN B 409 GLN C 327 GLN C 393 ASN C 445 GLN D 409 GLN E 393 ASN F 393 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23634 Z= 0.216 Angle : 0.578 6.705 31950 Z= 0.293 Chirality : 0.043 0.148 3570 Planarity : 0.004 0.056 4092 Dihedral : 10.258 118.814 3474 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.93 % Allowed : 21.33 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.16), residues: 2898 helix: 1.32 (0.16), residues: 1092 sheet: -1.55 (0.19), residues: 684 loop : -0.18 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 335 HIS 0.003 0.001 HIS C 433 PHE 0.020 0.002 PHE D 423 TYR 0.012 0.001 TYR E 198 ARG 0.008 0.001 ARG F 325 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 541 time to evaluate : 3.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6772 (tp30) REVERT: A 34 ASP cc_start: 0.8126 (m-30) cc_final: 0.7826 (m-30) REVERT: A 70 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7280 (mt-10) REVERT: A 100 LYS cc_start: 0.7344 (tttt) cc_final: 0.6956 (ttpt) REVERT: A 139 GLN cc_start: 0.7527 (mt0) cc_final: 0.6851 (mm110) REVERT: A 142 LYS cc_start: 0.7577 (mtmt) cc_final: 0.7109 (mmtm) REVERT: A 197 ARG cc_start: 0.7731 (mtp85) cc_final: 0.7441 (mtp85) REVERT: A 206 ASP cc_start: 0.8473 (m-30) cc_final: 0.8227 (m-30) REVERT: A 216 GLU cc_start: 0.7381 (tp30) cc_final: 0.7121 (tm-30) REVERT: A 256 MET cc_start: 0.5482 (tmm) cc_final: 0.5196 (ptt) REVERT: A 273 ARG cc_start: 0.7414 (tpt170) cc_final: 0.6717 (tmt170) REVERT: A 314 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6361 (mt-10) REVERT: A 349 LYS cc_start: 0.7557 (ttmm) cc_final: 0.7316 (ttmp) REVERT: A 364 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7305 (tp) REVERT: A 445 GLN cc_start: 0.8200 (pt0) cc_final: 0.7833 (pt0) REVERT: A 450 ARG cc_start: 0.7768 (mtt180) cc_final: 0.7320 (mtt-85) REVERT: A 472 ARG cc_start: 0.7573 (mtt-85) cc_final: 0.7153 (mtp85) REVERT: A 482 GLU cc_start: 0.7338 (tt0) cc_final: 0.6794 (tp30) REVERT: A 485 ASP cc_start: 0.6772 (m-30) cc_final: 0.6430 (t0) REVERT: B 30 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6875 (tp30) REVERT: B 85 GLN cc_start: 0.7155 (mm110) cc_final: 0.6929 (mp10) REVERT: B 100 LYS cc_start: 0.7372 (tttt) cc_final: 0.7117 (ttpt) REVERT: B 139 GLN cc_start: 0.7518 (mt0) cc_final: 0.6868 (mm-40) REVERT: B 142 LYS cc_start: 0.7761 (mttp) cc_final: 0.7021 (mmtm) REVERT: B 256 MET cc_start: 0.5444 (OUTLIER) cc_final: 0.5107 (ptt) REVERT: B 273 ARG cc_start: 0.7139 (tpt170) cc_final: 0.6552 (tpt-90) REVERT: B 275 ASP cc_start: 0.8285 (m-30) cc_final: 0.7871 (m-30) REVERT: B 284 LYS cc_start: 0.7776 (tttm) cc_final: 0.7276 (ttmp) REVERT: B 311 GLN cc_start: 0.7884 (mt0) cc_final: 0.7452 (mt0) REVERT: B 314 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6703 (mt-10) REVERT: B 450 ARG cc_start: 0.7677 (mtt180) cc_final: 0.7291 (mtt-85) REVERT: B 462 MET cc_start: 0.8899 (tpt) cc_final: 0.8500 (tpt) REVERT: B 482 GLU cc_start: 0.7491 (tt0) cc_final: 0.6861 (tp30) REVERT: B 485 ASP cc_start: 0.6774 (m-30) cc_final: 0.6414 (t0) REVERT: B 501 ILE cc_start: 0.6783 (pt) cc_final: 0.6477 (pp) REVERT: C 30 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6728 (tp30) REVERT: C 70 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7244 (mt-10) REVERT: C 100 LYS cc_start: 0.7359 (tttt) cc_final: 0.7046 (ttpt) REVERT: C 139 GLN cc_start: 0.7535 (mt0) cc_final: 0.6875 (mm-40) REVERT: C 142 LYS cc_start: 0.7862 (mttp) cc_final: 0.7122 (mmtm) REVERT: C 256 MET cc_start: 0.5409 (OUTLIER) cc_final: 0.5085 (ptt) REVERT: C 273 ARG cc_start: 0.7174 (tpt170) cc_final: 0.6331 (tmt170) REVERT: C 284 LYS cc_start: 0.7416 (tptt) cc_final: 0.7060 (ttmt) REVERT: C 294 THR cc_start: 0.8887 (p) cc_final: 0.8663 (t) REVERT: C 314 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6831 (mt-10) REVERT: C 341 GLU cc_start: 0.6467 (tp30) cc_final: 0.6249 (tp30) REVERT: C 422 GLN cc_start: 0.7509 (mp-120) cc_final: 0.6999 (mm110) REVERT: C 450 ARG cc_start: 0.7826 (mtt90) cc_final: 0.7560 (mtt-85) REVERT: C 452 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7546 (tp30) REVERT: C 462 MET cc_start: 0.8819 (tpt) cc_final: 0.8361 (tpt) REVERT: C 472 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.5649 (mtm180) REVERT: C 482 GLU cc_start: 0.7417 (tt0) cc_final: 0.6877 (tp30) REVERT: C 492 ARG cc_start: 0.6791 (mtp180) cc_final: 0.6234 (mtp85) REVERT: D 30 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6771 (tp30) REVERT: D 34 ASP cc_start: 0.8127 (m-30) cc_final: 0.7818 (m-30) REVERT: D 70 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7216 (mt-10) REVERT: D 100 LYS cc_start: 0.7327 (tttt) cc_final: 0.6943 (ttpt) REVERT: D 139 GLN cc_start: 0.7512 (mt0) cc_final: 0.6834 (mm110) REVERT: D 142 LYS cc_start: 0.7577 (mtmt) cc_final: 0.7108 (mmtm) REVERT: D 197 ARG cc_start: 0.7748 (mtp85) cc_final: 0.7432 (mtp85) REVERT: D 206 ASP cc_start: 0.8454 (m-30) cc_final: 0.8206 (m-30) REVERT: D 216 GLU cc_start: 0.7440 (tp30) cc_final: 0.7103 (tm-30) REVERT: D 256 MET cc_start: 0.5667 (OUTLIER) cc_final: 0.5288 (ptt) REVERT: D 273 ARG cc_start: 0.7223 (tpt170) cc_final: 0.6508 (tmt170) REVERT: D 314 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6399 (mt-10) REVERT: D 349 LYS cc_start: 0.7551 (ttmm) cc_final: 0.7203 (ttmp) REVERT: D 364 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7329 (tp) REVERT: D 445 GLN cc_start: 0.8211 (pt0) cc_final: 0.7899 (pt0) REVERT: D 450 ARG cc_start: 0.7787 (mtt180) cc_final: 0.7338 (mtt-85) REVERT: D 482 GLU cc_start: 0.7287 (tt0) cc_final: 0.6775 (tp30) REVERT: D 485 ASP cc_start: 0.6941 (m-30) cc_final: 0.6573 (t0) REVERT: D 492 ARG cc_start: 0.6797 (mtp180) cc_final: 0.6298 (mtp85) REVERT: E 30 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6869 (tp30) REVERT: E 70 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7184 (mt-10) REVERT: E 85 GLN cc_start: 0.7161 (mm110) cc_final: 0.6933 (mp10) REVERT: E 100 LYS cc_start: 0.7401 (tttt) cc_final: 0.7114 (ttpt) REVERT: E 139 GLN cc_start: 0.7496 (mt0) cc_final: 0.6861 (mm-40) REVERT: E 142 LYS cc_start: 0.7717 (mttp) cc_final: 0.7000 (mmtm) REVERT: E 256 MET cc_start: 0.5380 (tmm) cc_final: 0.5092 (ptt) REVERT: E 273 ARG cc_start: 0.7251 (tpt170) cc_final: 0.6487 (tmt170) REVERT: E 277 MET cc_start: 0.8753 (mtp) cc_final: 0.8399 (mtp) REVERT: E 284 LYS cc_start: 0.7777 (tttm) cc_final: 0.7302 (ttmp) REVERT: E 314 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6677 (mt-10) REVERT: E 349 LYS cc_start: 0.7465 (ttmp) cc_final: 0.6606 (tttm) REVERT: E 450 ARG cc_start: 0.7703 (mtt180) cc_final: 0.7326 (mtt-85) REVERT: E 462 MET cc_start: 0.8882 (tpt) cc_final: 0.8466 (tpt) REVERT: E 482 GLU cc_start: 0.7425 (tt0) cc_final: 0.6901 (tp30) REVERT: E 485 ASP cc_start: 0.6858 (m-30) cc_final: 0.6480 (t0) REVERT: E 492 ARG cc_start: 0.6920 (mtp180) cc_final: 0.6333 (mtp85) REVERT: F 30 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6751 (tp30) REVERT: F 70 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7236 (mt-10) REVERT: F 100 LYS cc_start: 0.7330 (tttt) cc_final: 0.6903 (ttpt) REVERT: F 139 GLN cc_start: 0.7535 (mt0) cc_final: 0.6876 (mm110) REVERT: F 142 LYS cc_start: 0.7871 (mttp) cc_final: 0.7125 (mmtm) REVERT: F 206 ASP cc_start: 0.8505 (m-30) cc_final: 0.8255 (m-30) REVERT: F 256 MET cc_start: 0.5548 (OUTLIER) cc_final: 0.5274 (ptt) REVERT: F 273 ARG cc_start: 0.7170 (tpt170) cc_final: 0.6271 (tmt170) REVERT: F 275 ASP cc_start: 0.8105 (m-30) cc_final: 0.7694 (m-30) REVERT: F 284 LYS cc_start: 0.7424 (tptt) cc_final: 0.7049 (ttmt) REVERT: F 314 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6843 (mt-10) REVERT: F 450 ARG cc_start: 0.7821 (mtt90) cc_final: 0.7546 (mtt-85) REVERT: F 472 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.5602 (mtm180) REVERT: F 482 GLU cc_start: 0.7409 (tt0) cc_final: 0.6871 (tp30) REVERT: F 492 ARG cc_start: 0.6779 (mtp180) cc_final: 0.6154 (mtp85) outliers start: 73 outliers final: 41 residues processed: 573 average time/residue: 2.8826 time to fit residues: 1914.4717 Evaluate side-chains 569 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 519 time to evaluate : 3.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 275 ASP Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 486 SER Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 472 ARG Chi-restraints excluded: chain F residue 486 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 2.9990 chunk 250 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 278 optimal weight: 7.9990 chunk 231 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN C 327 GLN D 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.5613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23634 Z= 0.337 Angle : 0.616 7.570 31950 Z= 0.314 Chirality : 0.044 0.145 3570 Planarity : 0.004 0.047 4092 Dihedral : 10.759 124.395 3471 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.25 % Allowed : 21.69 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.16), residues: 2898 helix: 1.35 (0.16), residues: 1098 sheet: -1.58 (0.19), residues: 684 loop : -0.22 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 466 HIS 0.004 0.001 HIS D 246 PHE 0.019 0.002 PHE D 423 TYR 0.015 0.002 TYR A 239 ARG 0.006 0.000 ARG F 325 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 529 time to evaluate : 3.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6765 (tp30) REVERT: A 34 ASP cc_start: 0.8167 (m-30) cc_final: 0.7841 (m-30) REVERT: A 70 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7211 (mt-10) REVERT: A 100 LYS cc_start: 0.7315 (tttt) cc_final: 0.6949 (ttpt) REVERT: A 139 GLN cc_start: 0.7517 (mt0) cc_final: 0.7084 (mm-40) REVERT: A 197 ARG cc_start: 0.7795 (mtp85) cc_final: 0.7538 (mtp85) REVERT: A 206 ASP cc_start: 0.8517 (m-30) cc_final: 0.8238 (m-30) REVERT: A 216 GLU cc_start: 0.7411 (tp30) cc_final: 0.7043 (tm-30) REVERT: A 256 MET cc_start: 0.5447 (OUTLIER) cc_final: 0.5181 (ptt) REVERT: A 259 THR cc_start: 0.6568 (OUTLIER) cc_final: 0.6364 (m) REVERT: A 273 ARG cc_start: 0.7370 (tpt170) cc_final: 0.6580 (tmt170) REVERT: A 314 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6368 (mt-10) REVERT: A 349 LYS cc_start: 0.7538 (ttmm) cc_final: 0.7317 (ttmp) REVERT: A 364 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7339 (tp) REVERT: A 423 PHE cc_start: 0.8890 (p90) cc_final: 0.8216 (p90) REVERT: A 445 GLN cc_start: 0.8215 (pt0) cc_final: 0.7908 (pt0) REVERT: A 450 ARG cc_start: 0.7841 (mtt180) cc_final: 0.7412 (mtt-85) REVERT: A 472 ARG cc_start: 0.7584 (mtt-85) cc_final: 0.6992 (mtp85) REVERT: A 482 GLU cc_start: 0.7351 (tt0) cc_final: 0.6812 (tp30) REVERT: A 485 ASP cc_start: 0.6768 (m-30) cc_final: 0.6422 (t0) REVERT: B 30 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6936 (tp30) REVERT: B 85 GLN cc_start: 0.7222 (mm110) cc_final: 0.6952 (mp10) REVERT: B 100 LYS cc_start: 0.7358 (tttt) cc_final: 0.7093 (ttpt) REVERT: B 139 GLN cc_start: 0.7600 (mt0) cc_final: 0.6933 (mm-40) REVERT: B 142 LYS cc_start: 0.7754 (mttp) cc_final: 0.7025 (mmtm) REVERT: B 256 MET cc_start: 0.5482 (OUTLIER) cc_final: 0.5050 (ptt) REVERT: B 273 ARG cc_start: 0.7129 (tpt170) cc_final: 0.6550 (tpt-90) REVERT: B 275 ASP cc_start: 0.8311 (m-30) cc_final: 0.7900 (m-30) REVERT: B 314 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6700 (mt-10) REVERT: B 450 ARG cc_start: 0.7748 (mtt180) cc_final: 0.7410 (mtt-85) REVERT: B 462 MET cc_start: 0.8955 (tpt) cc_final: 0.8481 (tpt) REVERT: B 482 GLU cc_start: 0.7536 (tt0) cc_final: 0.6876 (tp30) REVERT: B 485 ASP cc_start: 0.6824 (m-30) cc_final: 0.6421 (t0) REVERT: B 501 ILE cc_start: 0.6880 (OUTLIER) cc_final: 0.6516 (pp) REVERT: C 30 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6761 (tp30) REVERT: C 70 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7228 (mt-10) REVERT: C 100 LYS cc_start: 0.7335 (tttt) cc_final: 0.7010 (ttpt) REVERT: C 139 GLN cc_start: 0.7604 (mt0) cc_final: 0.7192 (mm-40) REVERT: C 142 LYS cc_start: 0.7865 (mttp) cc_final: 0.7585 (mmtp) REVERT: C 256 MET cc_start: 0.5365 (OUTLIER) cc_final: 0.5034 (ptt) REVERT: C 273 ARG cc_start: 0.7131 (tpt170) cc_final: 0.6276 (tmt170) REVERT: C 284 LYS cc_start: 0.7422 (tptt) cc_final: 0.7040 (ttmt) REVERT: C 294 THR cc_start: 0.8897 (p) cc_final: 0.8648 (t) REVERT: C 314 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6893 (mt-10) REVERT: C 450 ARG cc_start: 0.7870 (mtt90) cc_final: 0.7657 (mtt-85) REVERT: C 452 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7578 (tp30) REVERT: C 462 MET cc_start: 0.8873 (tpt) cc_final: 0.8391 (tpt) REVERT: C 472 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.5678 (mtm180) REVERT: C 482 GLU cc_start: 0.7442 (tt0) cc_final: 0.6880 (tp30) REVERT: C 492 ARG cc_start: 0.6894 (mtp180) cc_final: 0.6340 (mtp85) REVERT: D 30 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6764 (tp30) REVERT: D 34 ASP cc_start: 0.8150 (m-30) cc_final: 0.7827 (m-30) REVERT: D 70 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7187 (mt-10) REVERT: D 100 LYS cc_start: 0.7301 (tttt) cc_final: 0.6933 (ttpt) REVERT: D 139 GLN cc_start: 0.7529 (mt0) cc_final: 0.7096 (mm-40) REVERT: D 142 LYS cc_start: 0.7543 (mtmt) cc_final: 0.7338 (mmtp) REVERT: D 197 ARG cc_start: 0.7811 (mtp85) cc_final: 0.7550 (mtp85) REVERT: D 206 ASP cc_start: 0.8522 (m-30) cc_final: 0.8218 (m-30) REVERT: D 216 GLU cc_start: 0.7474 (tp30) cc_final: 0.7145 (tm-30) REVERT: D 256 MET cc_start: 0.5479 (OUTLIER) cc_final: 0.5145 (ptt) REVERT: D 314 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6440 (mt-10) REVERT: D 349 LYS cc_start: 0.7521 (ttmm) cc_final: 0.7310 (ttmp) REVERT: D 364 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7337 (tp) REVERT: D 423 PHE cc_start: 0.8888 (p90) cc_final: 0.8205 (p90) REVERT: D 445 GLN cc_start: 0.8237 (pt0) cc_final: 0.7917 (pt0) REVERT: D 450 ARG cc_start: 0.7843 (mtt180) cc_final: 0.7405 (mtt-85) REVERT: D 482 GLU cc_start: 0.7335 (tt0) cc_final: 0.6805 (tp30) REVERT: D 485 ASP cc_start: 0.6933 (m-30) cc_final: 0.6486 (t0) REVERT: D 492 ARG cc_start: 0.6875 (mtp180) cc_final: 0.6383 (mtp85) REVERT: E 30 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6931 (tp30) REVERT: E 85 GLN cc_start: 0.7213 (mm110) cc_final: 0.6937 (mp10) REVERT: E 100 LYS cc_start: 0.7357 (tttt) cc_final: 0.7079 (ttpt) REVERT: E 139 GLN cc_start: 0.7593 (mt0) cc_final: 0.6935 (mm-40) REVERT: E 142 LYS cc_start: 0.7759 (mttp) cc_final: 0.7030 (mmtm) REVERT: E 256 MET cc_start: 0.5349 (OUTLIER) cc_final: 0.5016 (ptt) REVERT: E 273 ARG cc_start: 0.7257 (tpt170) cc_final: 0.6460 (tmt170) REVERT: E 313 LYS cc_start: 0.8274 (mmmt) cc_final: 0.7799 (mmmm) REVERT: E 314 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6700 (mt-10) REVERT: E 450 ARG cc_start: 0.7751 (mtt180) cc_final: 0.7400 (mtt-85) REVERT: E 462 MET cc_start: 0.8940 (tpt) cc_final: 0.8451 (tpt) REVERT: E 482 GLU cc_start: 0.7475 (tt0) cc_final: 0.6851 (tp30) REVERT: E 485 ASP cc_start: 0.6890 (m-30) cc_final: 0.6437 (t0) REVERT: E 492 ARG cc_start: 0.6939 (mtp180) cc_final: 0.6352 (mtp85) REVERT: E 501 ILE cc_start: 0.6896 (OUTLIER) cc_final: 0.6535 (pp) REVERT: F 30 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6766 (tp30) REVERT: F 70 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7224 (mt-10) REVERT: F 100 LYS cc_start: 0.7310 (tttt) cc_final: 0.6922 (ttpt) REVERT: F 139 GLN cc_start: 0.7591 (mt0) cc_final: 0.7184 (mm-40) REVERT: F 142 LYS cc_start: 0.7865 (mttp) cc_final: 0.7583 (mmtp) REVERT: F 256 MET cc_start: 0.5528 (OUTLIER) cc_final: 0.5148 (ptt) REVERT: F 273 ARG cc_start: 0.7180 (tpt170) cc_final: 0.6306 (tmt170) REVERT: F 275 ASP cc_start: 0.8124 (m-30) cc_final: 0.7688 (m-30) REVERT: F 284 LYS cc_start: 0.7412 (tptt) cc_final: 0.7037 (ttmt) REVERT: F 314 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6880 (mt-10) REVERT: F 450 ARG cc_start: 0.7883 (mtt90) cc_final: 0.7677 (mtt-85) REVERT: F 472 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.5625 (mtm180) REVERT: F 482 GLU cc_start: 0.7448 (tt0) cc_final: 0.6884 (tp30) REVERT: F 492 ARG cc_start: 0.6889 (mtp180) cc_final: 0.6276 (mtp85) outliers start: 81 outliers final: 53 residues processed: 558 average time/residue: 3.1361 time to fit residues: 2017.3276 Evaluate side-chains 579 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 512 time to evaluate : 3.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 413 THR Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 486 SER Chi-restraints excluded: chain E residue 501 ILE Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain F residue 472 ARG Chi-restraints excluded: chain F residue 486 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 234 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 277 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN A 418 ASN B 418 ASN D 393 ASN D 418 ASN E 418 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.5833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 23634 Z= 0.394 Angle : 0.641 7.635 31950 Z= 0.328 Chirality : 0.045 0.144 3570 Planarity : 0.005 0.050 4092 Dihedral : 11.056 126.409 3471 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.61 % Allowed : 20.76 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.16), residues: 2898 helix: 1.26 (0.16), residues: 1098 sheet: -1.68 (0.19), residues: 696 loop : -0.21 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 96 HIS 0.005 0.001 HIS A 246 PHE 0.021 0.002 PHE C 423 TYR 0.018 0.002 TYR D 239 ARG 0.006 0.001 ARG C 222 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 533 time to evaluate : 3.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6751 (tp30) REVERT: A 34 ASP cc_start: 0.8165 (m-30) cc_final: 0.7837 (m-30) REVERT: A 70 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7239 (mt-10) REVERT: A 100 LYS cc_start: 0.7308 (tttt) cc_final: 0.6912 (ttpt) REVERT: A 139 GLN cc_start: 0.7568 (mt0) cc_final: 0.7090 (mm-40) REVERT: A 216 GLU cc_start: 0.7435 (tp30) cc_final: 0.7071 (tm-30) REVERT: A 256 MET cc_start: 0.5399 (OUTLIER) cc_final: 0.5036 (ptt) REVERT: A 273 ARG cc_start: 0.7310 (tpt170) cc_final: 0.6546 (tmt170) REVERT: A 314 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6409 (mt-10) REVERT: A 349 LYS cc_start: 0.7543 (ttmm) cc_final: 0.6497 (tttm) REVERT: A 364 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7340 (tp) REVERT: A 423 PHE cc_start: 0.8912 (p90) cc_final: 0.8216 (p90) REVERT: A 445 GLN cc_start: 0.8226 (pt0) cc_final: 0.7916 (pt0) REVERT: A 450 ARG cc_start: 0.7877 (mtt180) cc_final: 0.7464 (mtt-85) REVERT: A 472 ARG cc_start: 0.7627 (mtt-85) cc_final: 0.7039 (mtp85) REVERT: A 482 GLU cc_start: 0.7336 (tt0) cc_final: 0.6836 (tp30) REVERT: A 485 ASP cc_start: 0.6782 (m-30) cc_final: 0.6390 (t0) REVERT: B 30 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6957 (tp30) REVERT: B 85 GLN cc_start: 0.7268 (mm110) cc_final: 0.6966 (mp10) REVERT: B 100 LYS cc_start: 0.7347 (tttt) cc_final: 0.7069 (ttpt) REVERT: B 139 GLN cc_start: 0.7622 (mt0) cc_final: 0.6954 (mm-40) REVERT: B 142 LYS cc_start: 0.7783 (mttp) cc_final: 0.7031 (mmtm) REVERT: B 256 MET cc_start: 0.5416 (OUTLIER) cc_final: 0.5074 (ptt) REVERT: B 259 THR cc_start: 0.6485 (OUTLIER) cc_final: 0.6187 (m) REVERT: B 273 ARG cc_start: 0.7132 (tpt170) cc_final: 0.6365 (tmt170) REVERT: B 275 ASP cc_start: 0.8269 (m-30) cc_final: 0.7857 (m-30) REVERT: B 313 LYS cc_start: 0.8329 (mmmt) cc_final: 0.7849 (mmmm) REVERT: B 314 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6820 (mt-10) REVERT: B 450 ARG cc_start: 0.7751 (mtt180) cc_final: 0.7406 (mtt-85) REVERT: B 482 GLU cc_start: 0.7549 (tt0) cc_final: 0.6884 (tp30) REVERT: B 485 ASP cc_start: 0.6868 (m-30) cc_final: 0.6368 (t0) REVERT: B 501 ILE cc_start: 0.6923 (OUTLIER) cc_final: 0.6592 (pp) REVERT: C 30 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6818 (tp30) REVERT: C 70 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7244 (mt-10) REVERT: C 100 LYS cc_start: 0.7303 (tttt) cc_final: 0.6973 (ttpt) REVERT: C 139 GLN cc_start: 0.7672 (mt0) cc_final: 0.7231 (mm-40) REVERT: C 142 LYS cc_start: 0.7843 (mttp) cc_final: 0.7558 (mmtp) REVERT: C 256 MET cc_start: 0.5383 (OUTLIER) cc_final: 0.5023 (ptt) REVERT: C 273 ARG cc_start: 0.7128 (tpt170) cc_final: 0.6201 (tpt-90) REVERT: C 284 LYS cc_start: 0.7496 (tttt) cc_final: 0.7081 (ttmt) REVERT: C 294 THR cc_start: 0.8915 (p) cc_final: 0.8660 (t) REVERT: C 314 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6932 (mt-10) REVERT: C 450 ARG cc_start: 0.7916 (mtt90) cc_final: 0.7492 (mtt-85) REVERT: C 452 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7578 (tp30) REVERT: C 472 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.5611 (mtm180) REVERT: C 482 GLU cc_start: 0.7468 (tt0) cc_final: 0.6908 (tp30) REVERT: C 485 ASP cc_start: 0.6879 (m-30) cc_final: 0.6424 (t0) REVERT: C 501 ILE cc_start: 0.6882 (pt) cc_final: 0.6457 (pp) REVERT: D 30 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6750 (tp30) REVERT: D 34 ASP cc_start: 0.8143 (m-30) cc_final: 0.7831 (m-30) REVERT: D 70 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7392 (mt-10) REVERT: D 72 ASP cc_start: 0.7907 (t70) cc_final: 0.7681 (m-30) REVERT: D 100 LYS cc_start: 0.7291 (tttt) cc_final: 0.6894 (ttpt) REVERT: D 139 GLN cc_start: 0.7567 (mt0) cc_final: 0.7088 (mm-40) REVERT: D 216 GLU cc_start: 0.7490 (tp30) cc_final: 0.7171 (tm-30) REVERT: D 256 MET cc_start: 0.5407 (OUTLIER) cc_final: 0.5022 (ptt) REVERT: D 259 THR cc_start: 0.6518 (OUTLIER) cc_final: 0.6182 (m) REVERT: D 314 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6463 (mt-10) REVERT: D 349 LYS cc_start: 0.7540 (ttmm) cc_final: 0.6499 (tttm) REVERT: D 364 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7338 (tp) REVERT: D 423 PHE cc_start: 0.8898 (p90) cc_final: 0.8186 (p90) REVERT: D 445 GLN cc_start: 0.8229 (pt0) cc_final: 0.7907 (pt0) REVERT: D 450 ARG cc_start: 0.7874 (mtt180) cc_final: 0.7458 (mtt-85) REVERT: D 482 GLU cc_start: 0.7321 (tt0) cc_final: 0.6834 (tp30) REVERT: D 485 ASP cc_start: 0.6878 (m-30) cc_final: 0.6445 (t0) REVERT: E 30 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6952 (tp30) REVERT: E 85 GLN cc_start: 0.7325 (mm110) cc_final: 0.6956 (mp10) REVERT: E 100 LYS cc_start: 0.7336 (tttt) cc_final: 0.7061 (ttpt) REVERT: E 139 GLN cc_start: 0.7614 (mt0) cc_final: 0.6951 (mm-40) REVERT: E 142 LYS cc_start: 0.7785 (mttp) cc_final: 0.7031 (mmtm) REVERT: E 256 MET cc_start: 0.5382 (OUTLIER) cc_final: 0.5002 (ptt) REVERT: E 273 ARG cc_start: 0.7182 (tpt170) cc_final: 0.6437 (tmt170) REVERT: E 314 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6752 (mt-10) REVERT: E 450 ARG cc_start: 0.7752 (mtt180) cc_final: 0.7432 (mtt-85) REVERT: E 482 GLU cc_start: 0.7489 (tt0) cc_final: 0.6862 (tp30) REVERT: E 485 ASP cc_start: 0.6862 (m-30) cc_final: 0.6348 (t0) REVERT: E 501 ILE cc_start: 0.6921 (OUTLIER) cc_final: 0.6584 (pp) REVERT: F 30 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6795 (tp30) REVERT: F 70 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7227 (mt-10) REVERT: F 100 LYS cc_start: 0.7283 (tttt) cc_final: 0.6931 (ttpt) REVERT: F 139 GLN cc_start: 0.7675 (mt0) cc_final: 0.7233 (mm-40) REVERT: F 142 LYS cc_start: 0.7842 (mttp) cc_final: 0.7556 (mmtp) REVERT: F 256 MET cc_start: 0.5502 (OUTLIER) cc_final: 0.5159 (ptt) REVERT: F 259 THR cc_start: 0.6521 (OUTLIER) cc_final: 0.6212 (m) REVERT: F 273 ARG cc_start: 0.7170 (tpt170) cc_final: 0.6549 (tpt-90) REVERT: F 275 ASP cc_start: 0.8128 (m-30) cc_final: 0.7690 (m-30) REVERT: F 284 LYS cc_start: 0.7467 (tttt) cc_final: 0.7019 (ttmt) REVERT: F 314 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6938 (mt-10) REVERT: F 450 ARG cc_start: 0.7884 (mtt90) cc_final: 0.7412 (mtt-85) REVERT: F 482 GLU cc_start: 0.7482 (tt0) cc_final: 0.6914 (tp30) REVERT: F 485 ASP cc_start: 0.6866 (m-30) cc_final: 0.6445 (t0) REVERT: F 501 ILE cc_start: 0.6927 (pt) cc_final: 0.6610 (pp) outliers start: 90 outliers final: 58 residues processed: 570 average time/residue: 3.2104 time to fit residues: 2117.2511 Evaluate side-chains 593 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 520 time to evaluate : 3.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 413 THR Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 486 SER Chi-restraints excluded: chain E residue 501 ILE Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain F residue 486 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 218 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.5962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 23634 Z= 0.442 Angle : 0.662 7.711 31950 Z= 0.340 Chirality : 0.045 0.142 3570 Planarity : 0.005 0.052 4092 Dihedral : 11.394 128.564 3471 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.69 % Allowed : 20.92 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.16), residues: 2898 helix: 1.19 (0.16), residues: 1098 sheet: -1.65 (0.19), residues: 696 loop : -0.20 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 466 HIS 0.005 0.001 HIS D 246 PHE 0.020 0.002 PHE D 32 TYR 0.019 0.002 TYR D 239 ARG 0.007 0.001 ARG C 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 524 time to evaluate : 3.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6765 (tp30) REVERT: A 34 ASP cc_start: 0.8156 (m-30) cc_final: 0.7829 (m-30) REVERT: A 70 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7250 (mt-10) REVERT: A 72 ASP cc_start: 0.7916 (t70) cc_final: 0.7687 (m-30) REVERT: A 100 LYS cc_start: 0.7280 (tttt) cc_final: 0.6891 (ttpt) REVERT: A 139 GLN cc_start: 0.7591 (mt0) cc_final: 0.7102 (mm-40) REVERT: A 216 GLU cc_start: 0.7457 (tp30) cc_final: 0.7150 (tm-30) REVERT: A 256 MET cc_start: 0.5376 (OUTLIER) cc_final: 0.4972 (ptt) REVERT: A 259 THR cc_start: 0.6497 (OUTLIER) cc_final: 0.6264 (p) REVERT: A 273 ARG cc_start: 0.7301 (tpt170) cc_final: 0.6572 (tmt170) REVERT: A 314 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6449 (mt-10) REVERT: A 364 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7409 (tp) REVERT: A 423 PHE cc_start: 0.8914 (p90) cc_final: 0.8188 (p90) REVERT: A 445 GLN cc_start: 0.8239 (pt0) cc_final: 0.7877 (pt0) REVERT: A 450 ARG cc_start: 0.7908 (mtt180) cc_final: 0.7500 (mtt-85) REVERT: A 472 ARG cc_start: 0.7657 (mtt-85) cc_final: 0.7020 (mtp85) REVERT: A 482 GLU cc_start: 0.7367 (tt0) cc_final: 0.6869 (tp30) REVERT: A 485 ASP cc_start: 0.6831 (m-30) cc_final: 0.6418 (t0) REVERT: B 30 GLU cc_start: 0.7282 (mm-30) cc_final: 0.6915 (tp30) REVERT: B 85 GLN cc_start: 0.7350 (mm110) cc_final: 0.6980 (mp10) REVERT: B 100 LYS cc_start: 0.7359 (tttt) cc_final: 0.7083 (ttpt) REVERT: B 139 GLN cc_start: 0.7626 (mt0) cc_final: 0.7002 (mm-40) REVERT: B 142 LYS cc_start: 0.7794 (mttp) cc_final: 0.7061 (mmtm) REVERT: B 273 ARG cc_start: 0.7161 (tpt170) cc_final: 0.6334 (tmt170) REVERT: B 275 ASP cc_start: 0.8291 (m-30) cc_final: 0.7882 (m-30) REVERT: B 314 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6658 (mt-10) REVERT: B 450 ARG cc_start: 0.7765 (mtt180) cc_final: 0.7420 (mtt-85) REVERT: B 482 GLU cc_start: 0.7556 (tt0) cc_final: 0.6860 (tp30) REVERT: B 484 LYS cc_start: 0.7693 (mmtt) cc_final: 0.7254 (mmtp) REVERT: B 485 ASP cc_start: 0.6848 (m-30) cc_final: 0.6314 (t0) REVERT: B 501 ILE cc_start: 0.7004 (OUTLIER) cc_final: 0.6663 (pp) REVERT: C 30 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6833 (tp30) REVERT: C 70 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7287 (mt-10) REVERT: C 100 LYS cc_start: 0.7289 (tttt) cc_final: 0.6936 (ttpt) REVERT: C 139 GLN cc_start: 0.7663 (mt0) cc_final: 0.7230 (mm-40) REVERT: C 142 LYS cc_start: 0.7858 (mttp) cc_final: 0.7574 (mmtp) REVERT: C 256 MET cc_start: 0.5386 (OUTLIER) cc_final: 0.5018 (ptt) REVERT: C 273 ARG cc_start: 0.7100 (tpt170) cc_final: 0.6178 (tpt-90) REVERT: C 284 LYS cc_start: 0.7491 (tttt) cc_final: 0.7026 (ttmt) REVERT: C 294 THR cc_start: 0.8921 (p) cc_final: 0.8660 (t) REVERT: C 450 ARG cc_start: 0.7916 (mtt90) cc_final: 0.7465 (mtt-85) REVERT: C 452 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7564 (tp30) REVERT: C 472 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.5636 (mtm180) REVERT: C 482 GLU cc_start: 0.7494 (tt0) cc_final: 0.6928 (tp30) REVERT: C 485 ASP cc_start: 0.6865 (m-30) cc_final: 0.6404 (t0) REVERT: C 501 ILE cc_start: 0.6951 (pt) cc_final: 0.6648 (pp) REVERT: D 30 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6767 (tp30) REVERT: D 34 ASP cc_start: 0.8158 (m-30) cc_final: 0.7828 (m-30) REVERT: D 70 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7388 (mt-10) REVERT: D 72 ASP cc_start: 0.7925 (t70) cc_final: 0.7688 (m-30) REVERT: D 100 LYS cc_start: 0.7273 (tttt) cc_final: 0.6942 (ttpt) REVERT: D 139 GLN cc_start: 0.7577 (mt0) cc_final: 0.7088 (mm-40) REVERT: D 216 GLU cc_start: 0.7505 (tp30) cc_final: 0.7182 (tm-30) REVERT: D 256 MET cc_start: 0.5398 (OUTLIER) cc_final: 0.5014 (ptt) REVERT: D 259 THR cc_start: 0.6480 (OUTLIER) cc_final: 0.6257 (p) REVERT: D 314 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6498 (mt-10) REVERT: D 349 LYS cc_start: 0.7543 (ttmm) cc_final: 0.6498 (tttm) REVERT: D 364 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7409 (tp) REVERT: D 423 PHE cc_start: 0.8904 (p90) cc_final: 0.8167 (p90) REVERT: D 445 GLN cc_start: 0.8243 (pt0) cc_final: 0.7920 (pt0) REVERT: D 450 ARG cc_start: 0.7909 (mtt180) cc_final: 0.7495 (mtt-85) REVERT: D 482 GLU cc_start: 0.7347 (tt0) cc_final: 0.6875 (tp30) REVERT: D 485 ASP cc_start: 0.6906 (m-30) cc_final: 0.6438 (t0) REVERT: E 30 GLU cc_start: 0.7282 (mm-30) cc_final: 0.6915 (tp30) REVERT: E 85 GLN cc_start: 0.7330 (mm110) cc_final: 0.6962 (mp10) REVERT: E 100 LYS cc_start: 0.7355 (tttt) cc_final: 0.7072 (ttpt) REVERT: E 139 GLN cc_start: 0.7622 (mt0) cc_final: 0.7000 (mm-40) REVERT: E 142 LYS cc_start: 0.7792 (mttp) cc_final: 0.7070 (mmtm) REVERT: E 256 MET cc_start: 0.5362 (OUTLIER) cc_final: 0.4961 (ptt) REVERT: E 314 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6665 (mt-10) REVERT: E 450 ARG cc_start: 0.7786 (mtt180) cc_final: 0.7454 (mtt-85) REVERT: E 482 GLU cc_start: 0.7528 (tt0) cc_final: 0.6881 (tp30) REVERT: E 485 ASP cc_start: 0.6890 (m-30) cc_final: 0.6392 (t0) REVERT: E 501 ILE cc_start: 0.6993 (OUTLIER) cc_final: 0.6652 (pp) REVERT: F 30 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6832 (tp30) REVERT: F 70 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7271 (mt-10) REVERT: F 100 LYS cc_start: 0.7298 (tttt) cc_final: 0.6856 (tttt) REVERT: F 139 GLN cc_start: 0.7665 (mt0) cc_final: 0.7230 (mm-40) REVERT: F 142 LYS cc_start: 0.7856 (mttp) cc_final: 0.7570 (mmtp) REVERT: F 256 MET cc_start: 0.5489 (OUTLIER) cc_final: 0.5130 (ptt) REVERT: F 275 ASP cc_start: 0.8130 (m-30) cc_final: 0.7695 (m-30) REVERT: F 284 LYS cc_start: 0.7464 (tttt) cc_final: 0.7006 (ttmt) REVERT: F 450 ARG cc_start: 0.7892 (mtt90) cc_final: 0.7422 (mtt-85) REVERT: F 482 GLU cc_start: 0.7501 (tt0) cc_final: 0.6943 (tp30) REVERT: F 485 ASP cc_start: 0.6878 (m-30) cc_final: 0.6382 (t0) REVERT: F 492 ARG cc_start: 0.6888 (mtp180) cc_final: 0.6319 (mtp85) REVERT: F 501 ILE cc_start: 0.7005 (pt) cc_final: 0.6742 (pp) outliers start: 92 outliers final: 61 residues processed: 561 average time/residue: 3.1655 time to fit residues: 2036.3198 Evaluate side-chains 580 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 506 time to evaluate : 3.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 413 THR Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 486 SER Chi-restraints excluded: chain E residue 501 ILE Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 383 SER Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain F residue 486 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 4.9990 chunk 265 optimal weight: 3.9990 chunk 242 optimal weight: 0.5980 chunk 258 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 203 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 233 optimal weight: 0.5980 chunk 244 optimal weight: 0.8980 chunk 257 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.5828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23634 Z= 0.203 Angle : 0.569 6.799 31950 Z= 0.285 Chirality : 0.043 0.144 3570 Planarity : 0.004 0.047 4092 Dihedral : 9.500 114.246 3468 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.53 % Allowed : 22.45 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.16), residues: 2898 helix: 1.47 (0.16), residues: 1098 sheet: -1.71 (0.20), residues: 672 loop : -0.15 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 335 HIS 0.001 0.000 HIS F 433 PHE 0.021 0.002 PHE C 423 TYR 0.018 0.002 TYR B 406 ARG 0.009 0.000 ARG C 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 536 time to evaluate : 3.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6755 (tp30) REVERT: A 34 ASP cc_start: 0.8132 (m-30) cc_final: 0.7833 (m-30) REVERT: A 70 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7264 (mt-10) REVERT: A 72 ASP cc_start: 0.7806 (t70) cc_final: 0.7579 (m-30) REVERT: A 100 LYS cc_start: 0.7315 (tttt) cc_final: 0.6924 (ttpt) REVERT: A 139 GLN cc_start: 0.7507 (mt0) cc_final: 0.7101 (mm-40) REVERT: A 206 ASP cc_start: 0.8414 (m-30) cc_final: 0.8174 (m-30) REVERT: A 216 GLU cc_start: 0.7350 (tp30) cc_final: 0.7004 (tm-30) REVERT: A 256 MET cc_start: 0.5264 (OUTLIER) cc_final: 0.4966 (ptt) REVERT: A 273 ARG cc_start: 0.7293 (tpt170) cc_final: 0.6548 (tmt170) REVERT: A 314 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6442 (mt-10) REVERT: A 349 LYS cc_start: 0.7550 (ttmm) cc_final: 0.7324 (ttmp) REVERT: A 364 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7325 (tp) REVERT: A 445 GLN cc_start: 0.8194 (pt0) cc_final: 0.7818 (pt0) REVERT: A 450 ARG cc_start: 0.7823 (mtt180) cc_final: 0.7406 (mtt-85) REVERT: A 472 ARG cc_start: 0.7492 (mtt-85) cc_final: 0.7086 (mtp85) REVERT: A 482 GLU cc_start: 0.7339 (tt0) cc_final: 0.6786 (tp30) REVERT: A 485 ASP cc_start: 0.6775 (m-30) cc_final: 0.6367 (t0) REVERT: B 30 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6877 (tp30) REVERT: B 85 GLN cc_start: 0.7307 (mm110) cc_final: 0.6916 (mp10) REVERT: B 100 LYS cc_start: 0.7416 (tttt) cc_final: 0.7142 (ttpt) REVERT: B 139 GLN cc_start: 0.7567 (mt0) cc_final: 0.6915 (mm-40) REVERT: B 142 LYS cc_start: 0.7730 (mttp) cc_final: 0.6963 (mmtm) REVERT: B 256 MET cc_start: 0.5261 (OUTLIER) cc_final: 0.4962 (ptt) REVERT: B 275 ASP cc_start: 0.8249 (m-30) cc_final: 0.7839 (m-30) REVERT: B 314 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6741 (mt-10) REVERT: B 450 ARG cc_start: 0.7751 (mtt180) cc_final: 0.7402 (mtt-85) REVERT: B 462 MET cc_start: 0.8891 (tpt) cc_final: 0.8417 (tpt) REVERT: B 482 GLU cc_start: 0.7452 (tt0) cc_final: 0.6796 (tp30) REVERT: B 485 ASP cc_start: 0.6891 (m-30) cc_final: 0.6474 (t0) REVERT: B 501 ILE cc_start: 0.6920 (pt) cc_final: 0.6601 (pp) REVERT: C 30 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6773 (tp30) REVERT: C 70 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7264 (mt-10) REVERT: C 100 LYS cc_start: 0.7333 (tttt) cc_final: 0.6954 (ttpt) REVERT: C 139 GLN cc_start: 0.7580 (mt0) cc_final: 0.7162 (mm-40) REVERT: C 142 LYS cc_start: 0.7827 (mttp) cc_final: 0.7554 (mmtp) REVERT: C 256 MET cc_start: 0.5430 (OUTLIER) cc_final: 0.5117 (ptt) REVERT: C 273 ARG cc_start: 0.7135 (tpt170) cc_final: 0.6881 (mmp80) REVERT: C 284 LYS cc_start: 0.7504 (tttt) cc_final: 0.7090 (ttmt) REVERT: C 294 THR cc_start: 0.8845 (p) cc_final: 0.8632 (t) REVERT: C 423 PHE cc_start: 0.8909 (p90) cc_final: 0.8050 (p90) REVERT: C 450 ARG cc_start: 0.7817 (mtt90) cc_final: 0.7444 (mtt-85) REVERT: C 452 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7454 (tp30) REVERT: C 482 GLU cc_start: 0.7460 (tt0) cc_final: 0.6908 (tp30) REVERT: C 485 ASP cc_start: 0.6949 (m-30) cc_final: 0.6440 (t0) REVERT: C 501 ILE cc_start: 0.6867 (pt) cc_final: 0.6505 (pp) REVERT: D 30 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6765 (tp30) REVERT: D 34 ASP cc_start: 0.8125 (m-30) cc_final: 0.7821 (m-30) REVERT: D 70 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7190 (mt-10) REVERT: D 72 ASP cc_start: 0.7791 (t70) cc_final: 0.7584 (m-30) REVERT: D 100 LYS cc_start: 0.7296 (tttt) cc_final: 0.6903 (ttpt) REVERT: D 139 GLN cc_start: 0.7505 (mt0) cc_final: 0.6830 (mm-40) REVERT: D 142 LYS cc_start: 0.7971 (mmtp) cc_final: 0.7182 (mmtm) REVERT: D 197 ARG cc_start: 0.7663 (mtp85) cc_final: 0.7196 (mtp85) REVERT: D 206 ASP cc_start: 0.8407 (m-30) cc_final: 0.8161 (m-30) REVERT: D 216 GLU cc_start: 0.7428 (tp30) cc_final: 0.7118 (tm-30) REVERT: D 256 MET cc_start: 0.5310 (OUTLIER) cc_final: 0.4978 (ptt) REVERT: D 314 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6487 (mt-10) REVERT: D 349 LYS cc_start: 0.7532 (ttmm) cc_final: 0.7317 (ttmp) REVERT: D 364 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7296 (tp) REVERT: D 445 GLN cc_start: 0.8178 (pt0) cc_final: 0.7857 (pt0) REVERT: D 450 ARG cc_start: 0.7821 (mtt180) cc_final: 0.7408 (mtt-85) REVERT: D 482 GLU cc_start: 0.7313 (tt0) cc_final: 0.6795 (tp30) REVERT: D 485 ASP cc_start: 0.6899 (m-30) cc_final: 0.6473 (t0) REVERT: E 30 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6876 (tp30) REVERT: E 85 GLN cc_start: 0.7263 (mm110) cc_final: 0.6904 (mp10) REVERT: E 100 LYS cc_start: 0.7397 (tttt) cc_final: 0.7130 (ttpt) REVERT: E 139 GLN cc_start: 0.7559 (mt0) cc_final: 0.6908 (mm-40) REVERT: E 142 LYS cc_start: 0.7726 (mttp) cc_final: 0.6972 (mmtm) REVERT: E 256 MET cc_start: 0.5371 (OUTLIER) cc_final: 0.5035 (ptt) REVERT: E 273 ARG cc_start: 0.7238 (tpt170) cc_final: 0.6899 (mmt-90) REVERT: E 314 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6611 (mt-10) REVERT: E 349 LYS cc_start: 0.7475 (ttmp) cc_final: 0.6571 (tttm) REVERT: E 450 ARG cc_start: 0.7762 (mtt180) cc_final: 0.7417 (mtt-85) REVERT: E 462 MET cc_start: 0.8889 (tpt) cc_final: 0.8403 (tpt) REVERT: E 482 GLU cc_start: 0.7421 (tt0) cc_final: 0.6804 (tp30) REVERT: E 485 ASP cc_start: 0.6885 (m-30) cc_final: 0.6416 (t0) REVERT: E 501 ILE cc_start: 0.6946 (pt) cc_final: 0.6619 (pp) REVERT: F 30 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6771 (tp30) REVERT: F 70 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7317 (mt-10) REVERT: F 100 LYS cc_start: 0.7337 (tttt) cc_final: 0.6974 (ttpt) REVERT: F 139 GLN cc_start: 0.7580 (mt0) cc_final: 0.7162 (mm-40) REVERT: F 142 LYS cc_start: 0.7828 (mttp) cc_final: 0.7554 (mmtp) REVERT: F 206 ASP cc_start: 0.8329 (m-30) cc_final: 0.8113 (m-30) REVERT: F 256 MET cc_start: 0.5457 (OUTLIER) cc_final: 0.5132 (ptt) REVERT: F 275 ASP cc_start: 0.8091 (m-30) cc_final: 0.7642 (m-30) REVERT: F 284 LYS cc_start: 0.7459 (tttt) cc_final: 0.7051 (ttmt) REVERT: F 450 ARG cc_start: 0.7815 (mtt90) cc_final: 0.7452 (mtt-85) REVERT: F 482 GLU cc_start: 0.7448 (tt0) cc_final: 0.6869 (tp30) REVERT: F 485 ASP cc_start: 0.6938 (m-30) cc_final: 0.6425 (t0) REVERT: F 501 ILE cc_start: 0.6993 (pt) cc_final: 0.6707 (pp) outliers start: 63 outliers final: 44 residues processed: 555 average time/residue: 3.0535 time to fit residues: 1963.4852 Evaluate side-chains 580 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 527 time to evaluate : 3.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 486 SER Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain F residue 486 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 2.9990 chunk 273 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 chunk 286 optimal weight: 3.9990 chunk 264 optimal weight: 0.7980 chunk 228 optimal weight: 6.9990 chunk 23 optimal weight: 0.0170 chunk 176 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 overall best weight: 0.6822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23634 Z= 0.194 Angle : 0.561 6.867 31950 Z= 0.279 Chirality : 0.042 0.141 3570 Planarity : 0.004 0.042 4092 Dihedral : 8.893 109.559 3456 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.17 % Allowed : 23.13 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.16), residues: 2898 helix: 1.62 (0.16), residues: 1098 sheet: -1.77 (0.20), residues: 672 loop : -0.11 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 335 HIS 0.002 0.001 HIS F 433 PHE 0.022 0.002 PHE D 423 TYR 0.009 0.001 TYR D 198 ARG 0.008 0.000 ARG C 222 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 523 time to evaluate : 2.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6799 (tp30) REVERT: A 34 ASP cc_start: 0.8096 (m-30) cc_final: 0.7789 (m-30) REVERT: A 70 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7210 (mt-10) REVERT: A 72 ASP cc_start: 0.7748 (t70) cc_final: 0.7543 (m-30) REVERT: A 100 LYS cc_start: 0.7260 (tttt) cc_final: 0.6891 (ttpt) REVERT: A 139 GLN cc_start: 0.7518 (mt0) cc_final: 0.7095 (mm-40) REVERT: A 206 ASP cc_start: 0.8368 (m-30) cc_final: 0.8090 (m-30) REVERT: A 216 GLU cc_start: 0.7290 (tp30) cc_final: 0.6970 (tm-30) REVERT: A 256 MET cc_start: 0.5181 (OUTLIER) cc_final: 0.4926 (ptt) REVERT: A 273 ARG cc_start: 0.7315 (tpt170) cc_final: 0.6585 (tmt170) REVERT: A 314 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6599 (mt-10) REVERT: A 349 LYS cc_start: 0.7512 (ttmm) cc_final: 0.7288 (ttmp) REVERT: A 364 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7219 (tp) REVERT: A 450 ARG cc_start: 0.7809 (mtt180) cc_final: 0.7424 (mtt-85) REVERT: A 472 ARG cc_start: 0.7493 (mtt-85) cc_final: 0.7083 (mtp85) REVERT: A 482 GLU cc_start: 0.7306 (tt0) cc_final: 0.6788 (tp30) REVERT: A 484 LYS cc_start: 0.7775 (mmtt) cc_final: 0.7455 (mmtt) REVERT: A 485 ASP cc_start: 0.6715 (m-30) cc_final: 0.6379 (t0) REVERT: B 30 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6894 (tp30) REVERT: B 85 GLN cc_start: 0.7279 (mm110) cc_final: 0.6882 (mp10) REVERT: B 100 LYS cc_start: 0.7402 (tttt) cc_final: 0.7131 (ttpt) REVERT: B 113 SER cc_start: 0.8236 (p) cc_final: 0.7769 (m) REVERT: B 139 GLN cc_start: 0.7548 (mt0) cc_final: 0.6902 (mm-40) REVERT: B 142 LYS cc_start: 0.7718 (mttp) cc_final: 0.6997 (mmtm) REVERT: B 256 MET cc_start: 0.5223 (OUTLIER) cc_final: 0.4974 (ptt) REVERT: B 275 ASP cc_start: 0.8235 (m-30) cc_final: 0.7816 (m-30) REVERT: B 314 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6739 (mt-10) REVERT: B 450 ARG cc_start: 0.7806 (mtt180) cc_final: 0.7463 (mtt-85) REVERT: B 462 MET cc_start: 0.8879 (tpt) cc_final: 0.8440 (tpt) REVERT: B 482 GLU cc_start: 0.7356 (tt0) cc_final: 0.6702 (tp30) REVERT: B 485 ASP cc_start: 0.6870 (m-30) cc_final: 0.6427 (t0) REVERT: B 501 ILE cc_start: 0.6898 (pt) cc_final: 0.6560 (pp) REVERT: C 30 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6755 (tp30) REVERT: C 100 LYS cc_start: 0.7313 (tttt) cc_final: 0.6939 (ttpt) REVERT: C 139 GLN cc_start: 0.7585 (mt0) cc_final: 0.7197 (mm110) REVERT: C 142 LYS cc_start: 0.7834 (mttp) cc_final: 0.7565 (mmtp) REVERT: C 256 MET cc_start: 0.5392 (OUTLIER) cc_final: 0.5083 (ptt) REVERT: C 284 LYS cc_start: 0.7466 (tttt) cc_final: 0.7066 (ttmt) REVERT: C 364 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7269 (tp) REVERT: C 450 ARG cc_start: 0.7844 (mtt90) cc_final: 0.7561 (mtt-85) REVERT: C 452 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7425 (tp30) REVERT: C 482 GLU cc_start: 0.7419 (tt0) cc_final: 0.6861 (tp30) REVERT: C 501 ILE cc_start: 0.6865 (pt) cc_final: 0.6480 (pp) REVERT: D 30 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6758 (tp30) REVERT: D 34 ASP cc_start: 0.8096 (m-30) cc_final: 0.7779 (m-30) REVERT: D 100 LYS cc_start: 0.7238 (tttt) cc_final: 0.6868 (ttpt) REVERT: D 139 GLN cc_start: 0.7492 (mt0) cc_final: 0.6838 (mm-40) REVERT: D 142 LYS cc_start: 0.7937 (mmtp) cc_final: 0.7164 (mmtm) REVERT: D 216 GLU cc_start: 0.7353 (tp30) cc_final: 0.7039 (tm-30) REVERT: D 256 MET cc_start: 0.5313 (OUTLIER) cc_final: 0.4970 (ptt) REVERT: D 314 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6592 (mt-10) REVERT: D 349 LYS cc_start: 0.7506 (ttmm) cc_final: 0.7292 (ttmp) REVERT: D 364 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7218 (tp) REVERT: D 445 GLN cc_start: 0.8196 (pt0) cc_final: 0.7857 (pt0) REVERT: D 450 ARG cc_start: 0.7828 (mtt180) cc_final: 0.7442 (mtt-85) REVERT: D 482 GLU cc_start: 0.7290 (tt0) cc_final: 0.6770 (tp30) REVERT: D 485 ASP cc_start: 0.6942 (m-30) cc_final: 0.6531 (t0) REVERT: E 30 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6873 (tp30) REVERT: E 85 GLN cc_start: 0.7231 (mm110) cc_final: 0.6887 (mp10) REVERT: E 100 LYS cc_start: 0.7384 (tttt) cc_final: 0.7099 (ttpt) REVERT: E 139 GLN cc_start: 0.7553 (mt0) cc_final: 0.6911 (mm-40) REVERT: E 142 LYS cc_start: 0.7707 (mttp) cc_final: 0.7009 (mmtm) REVERT: E 256 MET cc_start: 0.5244 (OUTLIER) cc_final: 0.4929 (ptt) REVERT: E 314 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6624 (mt-10) REVERT: E 349 LYS cc_start: 0.7461 (ttmp) cc_final: 0.6563 (tttm) REVERT: E 450 ARG cc_start: 0.7791 (mtt180) cc_final: 0.7452 (mtt-85) REVERT: E 462 MET cc_start: 0.8873 (tpt) cc_final: 0.8432 (tpt) REVERT: E 482 GLU cc_start: 0.7346 (tt0) cc_final: 0.6731 (tp30) REVERT: E 485 ASP cc_start: 0.6985 (m-30) cc_final: 0.6505 (t0) REVERT: E 501 ILE cc_start: 0.6903 (pt) cc_final: 0.6540 (pp) REVERT: F 30 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6752 (tp30) REVERT: F 100 LYS cc_start: 0.7308 (tttt) cc_final: 0.6967 (ttpt) REVERT: F 139 GLN cc_start: 0.7586 (mt0) cc_final: 0.7198 (mm110) REVERT: F 142 LYS cc_start: 0.7831 (mttp) cc_final: 0.7560 (mmtp) REVERT: F 256 MET cc_start: 0.5418 (OUTLIER) cc_final: 0.5074 (ptt) REVERT: F 275 ASP cc_start: 0.8075 (m-30) cc_final: 0.7622 (m-30) REVERT: F 284 LYS cc_start: 0.7466 (tttt) cc_final: 0.7063 (ttmt) REVERT: F 364 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7212 (tp) REVERT: F 450 ARG cc_start: 0.7818 (mtt90) cc_final: 0.7528 (mtt-85) REVERT: F 482 GLU cc_start: 0.7394 (tt0) cc_final: 0.6840 (tp30) REVERT: F 501 ILE cc_start: 0.7009 (pt) cc_final: 0.6711 (pp) outliers start: 54 outliers final: 41 residues processed: 543 average time/residue: 2.7834 time to fit residues: 1738.9205 Evaluate side-chains 565 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 513 time to evaluate : 5.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 275 ASP Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 486 SER Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 486 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 6.9990 chunk 243 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 228 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 234 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.144023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.117934 restraints weight = 67772.538| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.49 r_work: 0.3182 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.5985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 23634 Z= 0.394 Angle : 0.644 7.792 31950 Z= 0.328 Chirality : 0.045 0.143 3570 Planarity : 0.005 0.058 4092 Dihedral : 10.515 127.256 3456 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.37 % Allowed : 23.25 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.16), residues: 2898 helix: 1.37 (0.16), residues: 1098 sheet: -1.64 (0.20), residues: 672 loop : -0.07 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 96 HIS 0.005 0.001 HIS A 246 PHE 0.022 0.002 PHE D 423 TYR 0.017 0.002 TYR D 239 ARG 0.005 0.001 ARG C 325 =============================================================================== Job complete usr+sys time: 25557.49 seconds wall clock time: 450 minutes 50.03 seconds (27050.03 seconds total)