Starting phenix.real_space_refine on Wed Aug 27 01:23:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jon_36461/08_2025/8jon_36461.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jon_36461/08_2025/8jon_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jon_36461/08_2025/8jon_36461.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jon_36461/08_2025/8jon_36461.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jon_36461/08_2025/8jon_36461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jon_36461/08_2025/8jon_36461.map" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: B, C, D, E, F Time building chain proxies: 10.43, per 1000 atoms: 0.23 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: 4.62 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.52 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: 13.24 Time building geometry restraints manager: 6.27 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: 0.07 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: 1.740 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: 0.290 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 48.780 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 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:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.280 ------------------------------------------------------------------------------- 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 : 0.014 0.870 23646 Z= 1.397 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (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 ARG 0.011 0.001 ARG C 170 TYR 0.006 0.001 TYR B 158 PHE 0.023 0.002 PHE B 423 TRP 0.011 0.002 TRP D 466 HIS 0.006 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00421 (23634) covalent geometry : angle 0.63096 (31950) hydrogen bonds : bond 0.14811 ( 1032) hydrogen bonds : angle 6.40726 ( 2862) Misc. bond : bond 0.61470 ( 12) *********************** 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 : 1.428 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: 0.6008 (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: 0.6670 (mm-30) REVERT: A 277 MET cc_start: 0.8529 (mtp) cc_final: 0.8225 (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: 0.6481 (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: 0.7849 (m-80) REVERT: A 472 ARG cc_start: 0.7124 (mtt-85) cc_final: 0.6808 (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: 0.6320 (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: 0.7994 (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: 0.6746 (mtpp) REVERT: C 422 GLN cc_start: 0.7179 (mp10) cc_final: 0.6728 (mm-40) REVERT: C 468 ASP cc_start: 0.8131 (t0) cc_final: 0.7771 (t70) REVERT: C 482 GLU cc_start: 0.6647 (tt0) cc_final: 0.5986 (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: 0.6331 (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: 0.6375 (tpt-90) REVERT: D 276 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6677 (mm-30) REVERT: D 277 MET cc_start: 0.8548 (mtp) cc_final: 0.8207 (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: 0.7919 (t70) REVERT: D 472 ARG cc_start: 0.7080 (mtt-85) cc_final: 0.6741 (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: 0.6992 (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: 0.6298 (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: 0.6770 (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: 0.6167 (tm-30) REVERT: F 65 TYR cc_start: 0.8008 (t80) cc_final: 0.7720 (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: 0.7966 (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: 0.8026 (m-30) REVERT: F 276 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6368 (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 482 GLU cc_start: 0.6649 (tt0) cc_final: 0.5985 (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: 1.3647 time to fit residues: 1190.4830 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 : 1.233 ------------------------------------------------------------------------------- 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 197 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 207 ASN A 422 GLN A 445 GLN B 90 ASN B 207 ASN B 422 GLN B 445 GLN C 90 ASN 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.144531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.116791 restraints weight = 66108.962| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.64 r_work: 0.3097 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 23646 Z= 0.343 Angle : 0.746 7.903 31950 Z= 0.389 Chirality : 0.049 0.165 3570 Planarity : 0.006 0.066 4092 Dihedral : 12.254 133.072 3548 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.21 % Allowed : 19.48 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.15), residues: 2898 helix: 0.88 (0.15), residues: 1086 sheet: -0.97 (0.18), residues: 702 loop : -0.32 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 197 TYR 0.019 0.002 TYR A 158 PHE 0.022 0.003 PHE E 32 TRP 0.007 0.002 TRP D 466 HIS 0.010 0.002 HIS D 246 Details of bonding type rmsd covalent geometry : bond 0.00744 (23634) covalent geometry : angle 0.74622 (31950) hydrogen bonds : bond 0.04694 ( 1032) hydrogen bonds : angle 5.66838 ( 2862) Misc. bond : bond 0.00469 ( 12) *********************** 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 708 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 628 time to evaluate : 0.847 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: A 30 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7660 (tp30) REVERT: A 72 ASP cc_start: 0.8341 (t0) cc_final: 0.7786 (m-30) REVERT: A 135 ASN cc_start: 0.8707 (t0) cc_final: 0.8414 (t0) REVERT: A 149 ASP cc_start: 0.8221 (t0) cc_final: 0.7580 (t0) REVERT: A 206 ASP cc_start: 0.8766 (m-30) cc_final: 0.8464 (m-30) REVERT: A 218 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7760 (mt-10) REVERT: A 273 ARG cc_start: 0.7924 (tpt170) cc_final: 0.7594 (tpt-90) REVERT: A 311 GLN cc_start: 0.8235 (mt0) cc_final: 0.7963 (mt0) REVERT: A 314 GLU cc_start: 0.7429 (mt-10) cc_final: 0.6921 (mt-10) REVERT: A 327 GLN cc_start: 0.8029 (tt0) cc_final: 0.7825 (tt0) REVERT: A 439 ASP cc_start: 0.8057 (m-30) cc_final: 0.7813 (m-30) REVERT: A 482 GLU cc_start: 0.7795 (tt0) cc_final: 0.7568 (tp30) REVERT: B 30 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7676 (tp30) REVERT: B 100 LYS cc_start: 0.8250 (tttt) cc_final: 0.8036 (ttpt) REVERT: B 142 LYS cc_start: 0.8278 (mttp) cc_final: 0.7794 (mmtm) REVERT: B 191 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8694 (mm-30) REVERT: B 273 ARG cc_start: 0.7998 (tpt170) cc_final: 0.7553 (tpt-90) REVERT: B 314 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7175 (mt-10) REVERT: B 325 ARG cc_start: 0.8617 (ttt-90) cc_final: 0.8303 (ttt-90) REVERT: B 439 ASP cc_start: 0.8089 (m-30) cc_final: 0.7838 (m-30) REVERT: B 450 ARG cc_start: 0.7887 (mtt180) cc_final: 0.7615 (mtt-85) REVERT: B 482 GLU cc_start: 0.7911 (tt0) cc_final: 0.7626 (tp30) REVERT: C 30 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7631 (tp30) REVERT: C 142 LYS cc_start: 0.8262 (mttp) cc_final: 0.7802 (mmtm) REVERT: C 191 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8705 (mm-30) REVERT: C 273 ARG cc_start: 0.7930 (tpt170) cc_final: 0.7592 (tmt170) REVERT: C 284 LYS cc_start: 0.7799 (tptt) cc_final: 0.7579 (ttmt) REVERT: C 304 LYS cc_start: 0.8771 (mmmm) cc_final: 0.8498 (mmpt) REVERT: C 439 ASP cc_start: 0.8136 (m-30) cc_final: 0.7896 (m-30) REVERT: C 450 ARG cc_start: 0.7972 (mtt180) cc_final: 0.7527 (mtt-85) REVERT: C 482 GLU cc_start: 0.7923 (tt0) cc_final: 0.7645 (tp30) REVERT: C 492 ARG cc_start: 0.7857 (mtp180) cc_final: 0.7418 (mtp85) REVERT: D 30 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7694 (tp30) REVERT: D 72 ASP cc_start: 0.8352 (t0) cc_final: 0.7799 (m-30) REVERT: D 135 ASN cc_start: 0.8740 (t0) cc_final: 0.8421 (t0) REVERT: D 149 ASP cc_start: 0.8196 (t0) cc_final: 0.7543 (t70) REVERT: D 206 ASP cc_start: 0.8758 (m-30) cc_final: 0.8441 (m-30) REVERT: D 218 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: D 273 ARG cc_start: 0.7937 (tpt170) cc_final: 0.7572 (tpt-90) REVERT: D 314 GLU cc_start: 0.7438 (mt-10) cc_final: 0.6919 (mt-10) REVERT: D 349 LYS cc_start: 0.8099 (ttmm) cc_final: 0.7886 (ttmp) REVERT: D 482 GLU cc_start: 0.7746 (tt0) cc_final: 0.7528 (tp30) REVERT: D 492 ARG cc_start: 0.7826 (mtp180) cc_final: 0.7451 (mtp85) REVERT: E 30 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7700 (tp30) REVERT: E 100 LYS cc_start: 0.8253 (tttt) cc_final: 0.8011 (ttpt) REVERT: E 135 ASN cc_start: 0.8717 (t0) cc_final: 0.8505 (t0) REVERT: E 142 LYS cc_start: 0.8268 (mttp) cc_final: 0.7792 (mmtm) REVERT: E 191 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8756 (mm-30) REVERT: E 273 ARG cc_start: 0.7999 (tpt170) cc_final: 0.7624 (tpt-90) REVERT: E 325 ARG cc_start: 0.8612 (ttt-90) cc_final: 0.8326 (ttt-90) REVERT: E 439 ASP cc_start: 0.8111 (m-30) cc_final: 0.7880 (m-30) REVERT: E 450 ARG cc_start: 0.8049 (mtt180) cc_final: 0.7781 (mtt-85) REVERT: E 482 GLU cc_start: 0.7909 (tt0) cc_final: 0.7640 (tp30) REVERT: E 492 ARG cc_start: 0.7849 (mtp180) cc_final: 0.7431 (mtp85) REVERT: F 30 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7619 (tp30) REVERT: F 100 LYS cc_start: 0.8184 (tttt) cc_final: 0.7968 (tttt) REVERT: F 135 ASN cc_start: 0.8688 (t0) cc_final: 0.8483 (t0) REVERT: F 142 LYS cc_start: 0.8267 (mttp) cc_final: 0.7805 (mmtm) REVERT: F 191 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.8705 (mm-30) REVERT: F 273 ARG cc_start: 0.7915 (tpt170) cc_final: 0.7582 (tmt170) REVERT: F 284 LYS cc_start: 0.7790 (tptt) cc_final: 0.7559 (ttmt) REVERT: F 304 LYS cc_start: 0.8768 (mmmm) cc_final: 0.8502 (mmpt) REVERT: F 450 ARG cc_start: 0.8165 (mtt180) cc_final: 0.7774 (mtt-85) REVERT: F 462 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8424 (tpt) REVERT: F 482 GLU cc_start: 0.7923 (tt0) cc_final: 0.7645 (tp30) REVERT: F 492 ARG cc_start: 0.7921 (mtp180) cc_final: 0.7435 (mtp85) outliers start: 80 outliers final: 34 residues processed: 672 average time/residue: 1.5931 time to fit residues: 1225.2793 Evaluate side-chains 550 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 509 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 218 GLU 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 99 GLN 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 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 188 ARG Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 218 GLU 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 99 GLN Chi-restraints excluded: chain E residue 188 ARG Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 191 GLU 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 191 GLU Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 462 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 174 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 94 optimal weight: 0.0170 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 overall best weight: 1.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN B 139 GLN B 177 GLN B 327 GLN B 345 GLN B 445 GLN C 139 GLN C 327 GLN D 327 GLN D 445 GLN E 139 GLN E 445 GLN F 139 GLN F 177 GLN F 327 GLN F 345 GLN F 445 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.151286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.125653 restraints weight = 67587.037| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.53 r_work: 0.3275 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23646 Z= 0.177 Angle : 0.588 7.003 31950 Z= 0.298 Chirality : 0.044 0.156 3570 Planarity : 0.004 0.049 4092 Dihedral : 10.422 119.594 3498 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.17 % Allowed : 20.64 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.16), residues: 2898 helix: 1.37 (0.16), residues: 1086 sheet: -1.36 (0.18), residues: 702 loop : -0.18 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 325 TYR 0.016 0.002 TYR F 158 PHE 0.015 0.002 PHE E 32 TRP 0.003 0.001 TRP C 96 HIS 0.003 0.001 HIS A 246 Details of bonding type rmsd covalent geometry : bond 0.00375 (23634) covalent geometry : angle 0.58819 (31950) hydrogen bonds : bond 0.03541 ( 1032) hydrogen bonds : angle 5.30963 ( 2862) Misc. bond : bond 0.00548 ( 12) *********************** 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 630 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 551 time to evaluate : 1.438 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: A 30 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7721 (tp30) REVERT: A 188 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.8596 (mtp180) REVERT: A 206 ASP cc_start: 0.8648 (m-30) cc_final: 0.8347 (m-30) REVERT: A 314 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6838 (mt-10) REVERT: A 349 LYS cc_start: 0.8138 (ttmm) cc_final: 0.7554 (mtpp) REVERT: A 450 ARG cc_start: 0.8018 (mtt180) cc_final: 0.7686 (mtt-85) REVERT: B 142 LYS cc_start: 0.8124 (mttp) cc_final: 0.7868 (mmtm) REVERT: B 166 ARG cc_start: 0.8559 (ttp-110) cc_final: 0.8350 (ttp-110) REVERT: B 256 MET cc_start: 0.5774 (OUTLIER) cc_final: 0.5436 (ptt) REVERT: B 284 LYS cc_start: 0.8111 (tttm) cc_final: 0.7744 (ttmt) REVERT: B 349 LYS cc_start: 0.8100 (ttmm) cc_final: 0.7319 (tttm) REVERT: B 439 ASP cc_start: 0.8029 (m-30) cc_final: 0.7745 (m-30) REVERT: B 450 ARG cc_start: 0.7932 (mtt180) cc_final: 0.7668 (mtt-85) REVERT: C 30 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7529 (tp30) REVERT: C 142 LYS cc_start: 0.8213 (mttp) cc_final: 0.7865 (mmtm) REVERT: C 206 ASP cc_start: 0.8634 (m-30) cc_final: 0.8423 (m-30) REVERT: C 275 ASP cc_start: 0.8786 (m-30) cc_final: 0.8349 (m-30) REVERT: C 327 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: C 349 LYS cc_start: 0.8112 (ttmm) cc_final: 0.7382 (tttm) REVERT: C 450 ARG cc_start: 0.7949 (mtt180) cc_final: 0.7582 (mtt-85) REVERT: C 492 ARG cc_start: 0.7915 (mtp180) cc_final: 0.7524 (mtp85) REVERT: D 30 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7688 (tp30) REVERT: D 188 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.8595 (mtp180) REVERT: D 206 ASP cc_start: 0.8649 (m-30) cc_final: 0.8343 (m-30) REVERT: D 314 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6861 (mt-10) REVERT: D 349 LYS cc_start: 0.8137 (ttmm) cc_final: 0.7555 (mtpp) REVERT: D 439 ASP cc_start: 0.8030 (m-30) cc_final: 0.7753 (m-30) REVERT: D 492 ARG cc_start: 0.7946 (mtp180) cc_final: 0.7636 (mtp85) REVERT: E 142 LYS cc_start: 0.8081 (mttp) cc_final: 0.7853 (mmtm) REVERT: E 166 ARG cc_start: 0.8559 (ttp-110) cc_final: 0.8325 (ttp-110) REVERT: E 349 LYS cc_start: 0.8095 (ttmm) cc_final: 0.7320 (tttm) REVERT: E 450 ARG cc_start: 0.8012 (mtt180) cc_final: 0.7761 (mtt-85) REVERT: E 492 ARG cc_start: 0.8001 (mtp180) cc_final: 0.7631 (mtp85) REVERT: F 142 LYS cc_start: 0.8185 (mttp) cc_final: 0.7865 (mmtm) REVERT: F 206 ASP cc_start: 0.8673 (m-30) cc_final: 0.8466 (m-30) REVERT: F 275 ASP cc_start: 0.8828 (m-30) cc_final: 0.8621 (m-30) REVERT: F 349 LYS cc_start: 0.8101 (ttmm) cc_final: 0.7381 (tttm) REVERT: F 450 ARG cc_start: 0.8069 (mtt180) cc_final: 0.7741 (mtt-85) REVERT: F 492 ARG cc_start: 0.7933 (mtp180) cc_final: 0.7494 (mtp85) outliers start: 79 outliers final: 35 residues processed: 596 average time/residue: 1.4958 time to fit residues: 1030.5832 Evaluate side-chains 554 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 515 time to evaluate : 1.323 ------------------------------------------------------------------------------- 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 267 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 222 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 486 SER Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 327 GLN 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 180 VAL Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 267 VAL 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 188 ARG Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 232 THR 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 F residue 21 GLU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 267 VAL 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 185 optimal weight: 8.9990 chunk 275 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 213 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 154 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 272 optimal weight: 4.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 327 GLN B 445 GLN C 445 GLN E 445 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.144222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.117683 restraints weight = 67662.624| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.52 r_work: 0.3176 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 23646 Z= 0.297 Angle : 0.665 7.804 31950 Z= 0.342 Chirality : 0.046 0.150 3570 Planarity : 0.005 0.057 4092 Dihedral : 11.532 127.694 3490 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.41 % Allowed : 21.24 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.15), residues: 2898 helix: 1.18 (0.16), residues: 1086 sheet: -1.47 (0.19), residues: 690 loop : -0.23 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 212 TYR 0.015 0.002 TYR B 239 PHE 0.020 0.002 PHE B 32 TRP 0.004 0.001 TRP D 466 HIS 0.006 0.002 HIS A 246 Details of bonding type rmsd covalent geometry : bond 0.00642 (23634) covalent geometry : angle 0.66470 (31950) hydrogen bonds : bond 0.04115 ( 1032) hydrogen bonds : angle 5.47236 ( 2862) Misc. bond : bond 0.00695 ( 12) *********************** 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 625 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 540 time to evaluate : 1.337 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 97 ASN cc_start: 0.8941 (t0) cc_final: 0.8729 (t160) REVERT: A 191 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8623 (mm-30) REVERT: A 256 MET cc_start: 0.5668 (OUTLIER) cc_final: 0.5232 (ptt) REVERT: A 314 GLU cc_start: 0.7436 (mt-10) cc_final: 0.6993 (mt-10) REVERT: A 423 PHE cc_start: 0.9016 (p90) cc_final: 0.8461 (p90) REVERT: A 450 ARG cc_start: 0.8267 (mtt180) cc_final: 0.8012 (mtt-85) REVERT: B 142 LYS cc_start: 0.8250 (mttp) cc_final: 0.8006 (mmtm) REVERT: B 256 MET cc_start: 0.5583 (OUTLIER) cc_final: 0.5122 (ptt) REVERT: B 311 GLN cc_start: 0.8342 (mt0) cc_final: 0.7999 (mt0) REVERT: B 313 LYS cc_start: 0.8688 (mmmt) cc_final: 0.8222 (mmmm) REVERT: B 450 ARG cc_start: 0.8185 (mtt180) cc_final: 0.7959 (mtt-85) REVERT: C 30 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7684 (tp30) REVERT: C 142 LYS cc_start: 0.8343 (mttp) cc_final: 0.8085 (mmtm) REVERT: C 191 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: C 256 MET cc_start: 0.5546 (OUTLIER) cc_final: 0.5179 (ptt) REVERT: C 492 ARG cc_start: 0.8014 (mtp180) cc_final: 0.7658 (mtp85) REVERT: D 97 ASN cc_start: 0.8949 (t0) cc_final: 0.8741 (t160) REVERT: D 206 ASP cc_start: 0.8705 (m-30) cc_final: 0.8475 (m-30) REVERT: D 256 MET cc_start: 0.5647 (OUTLIER) cc_final: 0.5237 (ptt) REVERT: D 314 GLU cc_start: 0.7412 (mt-10) cc_final: 0.6963 (mt-10) REVERT: D 492 ARG cc_start: 0.8107 (mtp180) cc_final: 0.7788 (mtp85) REVERT: E 142 LYS cc_start: 0.8218 (mttp) cc_final: 0.7995 (mmtm) REVERT: E 273 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7767 (tmt170) REVERT: E 311 GLN cc_start: 0.8310 (mt0) cc_final: 0.7969 (mt0) REVERT: E 450 ARG cc_start: 0.8188 (mtt180) cc_final: 0.7972 (mtt-85) REVERT: E 472 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7008 (mtm180) REVERT: E 492 ARG cc_start: 0.8110 (mtp180) cc_final: 0.7728 (mtp85) REVERT: F 142 LYS cc_start: 0.8355 (mttp) cc_final: 0.8072 (mmtm) REVERT: F 256 MET cc_start: 0.5702 (OUTLIER) cc_final: 0.5298 (ptt) REVERT: F 275 ASP cc_start: 0.8889 (m-30) cc_final: 0.8662 (m-30) REVERT: F 311 GLN cc_start: 0.8365 (mt0) cc_final: 0.8078 (mt0) REVERT: F 450 ARG cc_start: 0.8194 (mtt180) cc_final: 0.7928 (mtt-85) REVERT: F 492 ARG cc_start: 0.8020 (mtp180) cc_final: 0.7601 (mtp85) outliers start: 85 outliers final: 46 residues processed: 577 average time/residue: 1.5265 time to fit residues: 1015.0934 Evaluate side-chains 567 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 512 time to evaluate : 1.304 ------------------------------------------------------------------------------- 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 191 GLU 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 436 THR Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 147 SER 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 364 LEU Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 472 ARG 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 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 413 THR 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 273 ARG Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 99 GLN 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 273 ARG Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 472 ARG 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 413 THR 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 19 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 235 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 268 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.143095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.116733 restraints weight = 67929.220| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.51 r_work: 0.3167 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.5786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 23646 Z= 0.295 Angle : 0.653 7.687 31950 Z= 0.336 Chirality : 0.045 0.157 3570 Planarity : 0.005 0.058 4092 Dihedral : 11.334 127.866 3474 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.02 % Allowed : 20.52 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.16), residues: 2898 helix: 1.17 (0.16), residues: 1092 sheet: -1.54 (0.19), residues: 696 loop : -0.16 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 212 TYR 0.015 0.002 TYR B 239 PHE 0.021 0.002 PHE E 423 TRP 0.004 0.001 TRP A 466 HIS 0.006 0.001 HIS C 246 Details of bonding type rmsd covalent geometry : bond 0.00633 (23634) covalent geometry : angle 0.65341 (31950) hydrogen bonds : bond 0.03924 ( 1032) hydrogen bonds : angle 5.46479 ( 2862) Misc. bond : bond 0.00716 ( 12) *********************** 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 633 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 533 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8320 (mtp85) cc_final: 0.8075 (mtp85) REVERT: A 256 MET cc_start: 0.5659 (OUTLIER) cc_final: 0.5197 (ptt) REVERT: A 314 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7049 (mt-10) REVERT: A 423 PHE cc_start: 0.9033 (p90) cc_final: 0.8553 (p90) REVERT: A 450 ARG cc_start: 0.8257 (mtt180) cc_final: 0.8040 (mtt-85) REVERT: A 492 ARG cc_start: 0.8110 (mtp180) cc_final: 0.7779 (mtp85) REVERT: B 142 LYS cc_start: 0.8253 (mttp) cc_final: 0.8018 (mmtm) REVERT: B 256 MET cc_start: 0.5648 (OUTLIER) cc_final: 0.5178 (ptt) REVERT: B 313 LYS cc_start: 0.8709 (mmmt) cc_final: 0.8287 (mmmm) REVERT: B 484 LYS cc_start: 0.8449 (mmtt) cc_final: 0.8118 (mmtp) REVERT: B 492 ARG cc_start: 0.8153 (mtp180) cc_final: 0.7774 (mtp85) REVERT: C 70 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8043 (mt-10) REVERT: C 256 MET cc_start: 0.5625 (OUTLIER) cc_final: 0.5246 (ptt) REVERT: C 492 ARG cc_start: 0.8063 (mtp180) cc_final: 0.7690 (mtp85) REVERT: D 197 ARG cc_start: 0.8317 (mtp85) cc_final: 0.8072 (mtp85) REVERT: D 206 ASP cc_start: 0.8701 (m-30) cc_final: 0.8437 (m-30) REVERT: D 256 MET cc_start: 0.5667 (OUTLIER) cc_final: 0.5218 (ptt) REVERT: D 314 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7023 (mt-10) REVERT: D 423 PHE cc_start: 0.9034 (p90) cc_final: 0.8483 (p90) REVERT: D 462 MET cc_start: 0.8913 (tpt) cc_final: 0.8416 (tpt) REVERT: D 492 ARG cc_start: 0.8137 (mtp180) cc_final: 0.7807 (mtp85) REVERT: E 142 LYS cc_start: 0.8238 (mttp) cc_final: 0.8015 (mmtm) REVERT: E 275 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.8348 (m-30) REVERT: E 313 LYS cc_start: 0.8710 (mmmt) cc_final: 0.8274 (mmmm) REVERT: E 364 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.7926 (tp) REVERT: E 484 LYS cc_start: 0.8469 (mmtt) cc_final: 0.8163 (mmtp) REVERT: E 492 ARG cc_start: 0.8161 (mtp180) cc_final: 0.7771 (mtp85) REVERT: F 70 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8039 (mt-10) REVERT: F 142 LYS cc_start: 0.8367 (mttp) cc_final: 0.8084 (mmtm) REVERT: F 256 MET cc_start: 0.5650 (OUTLIER) cc_final: 0.5231 (ptt) REVERT: F 275 ASP cc_start: 0.8886 (m-30) cc_final: 0.8667 (m-30) REVERT: F 450 ARG cc_start: 0.8223 (mtt180) cc_final: 0.7979 (mtt-85) REVERT: F 492 ARG cc_start: 0.8038 (mtp180) cc_final: 0.7656 (mtp85) outliers start: 100 outliers final: 62 residues processed: 574 average time/residue: 1.5830 time to fit residues: 1041.3948 Evaluate side-chains 581 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 512 time to evaluate : 1.288 ------------------------------------------------------------------------------- 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 176 LYS 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 413 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 99 GLN 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 314 GLU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 472 ARG 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 154 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 413 THR 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 232 THR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 413 THR Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 99 GLN 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 267 VAL Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 275 ASP Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 364 LEU 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 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 314 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 125 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 266 optimal weight: 4.9990 chunk 216 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 57 optimal weight: 0.1980 chunk 163 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 393 ASN C 393 ASN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 393 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.146848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.121078 restraints weight = 68048.004| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.50 r_work: 0.3224 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23646 Z= 0.178 Angle : 0.585 6.978 31950 Z= 0.296 Chirality : 0.043 0.148 3570 Planarity : 0.004 0.051 4092 Dihedral : 10.188 119.036 3474 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.21 % Allowed : 21.97 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.16), residues: 2898 helix: 1.41 (0.16), residues: 1098 sheet: -1.63 (0.19), residues: 684 loop : -0.17 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 455 TYR 0.011 0.002 TYR A 239 PHE 0.022 0.002 PHE B 423 TRP 0.003 0.001 TRP A 335 HIS 0.002 0.001 HIS F 433 Details of bonding type rmsd covalent geometry : bond 0.00380 (23634) covalent geometry : angle 0.58469 (31950) hydrogen bonds : bond 0.03303 ( 1032) hydrogen bonds : angle 5.27953 ( 2862) Misc. bond : bond 0.00434 ( 12) *********************** 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: 80 poor density : 530 time to evaluate : 1.021 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 97 ASN cc_start: 0.8970 (t0) cc_final: 0.8739 (t160) REVERT: A 256 MET cc_start: 0.5536 (OUTLIER) cc_final: 0.5138 (ptt) REVERT: A 314 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6909 (mt-10) REVERT: A 450 ARG cc_start: 0.8253 (mtt180) cc_final: 0.8038 (mtt-85) REVERT: A 462 MET cc_start: 0.8829 (tpt) cc_final: 0.8490 (tpt) REVERT: A 484 LYS cc_start: 0.8500 (mmtt) cc_final: 0.8250 (mmtp) REVERT: B 142 LYS cc_start: 0.8185 (mttp) cc_final: 0.7953 (mmtm) REVERT: B 256 MET cc_start: 0.5641 (OUTLIER) cc_final: 0.5158 (ptt) REVERT: B 364 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.7992 (tp) REVERT: B 462 MET cc_start: 0.8714 (tpt) cc_final: 0.8456 (tpt) REVERT: B 484 LYS cc_start: 0.8424 (mmtt) cc_final: 0.8131 (mmtp) REVERT: C 70 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7963 (mt-10) REVERT: C 256 MET cc_start: 0.5574 (OUTLIER) cc_final: 0.5214 (ptt) REVERT: C 462 MET cc_start: 0.8938 (tpt) cc_final: 0.8469 (tpt) REVERT: C 492 ARG cc_start: 0.8038 (mtp180) cc_final: 0.7684 (mtp85) REVERT: C 501 ILE cc_start: 0.7676 (pt) cc_final: 0.7367 (pp) REVERT: D 97 ASN cc_start: 0.8951 (t0) cc_final: 0.8718 (t160) REVERT: D 206 ASP cc_start: 0.8566 (m-30) cc_final: 0.8285 (m-30) REVERT: D 256 MET cc_start: 0.5530 (OUTLIER) cc_final: 0.5090 (ptt) REVERT: D 273 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7841 (tmt170) REVERT: D 314 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6949 (mt-10) REVERT: D 450 ARG cc_start: 0.8250 (mtt180) cc_final: 0.8037 (mtt-85) REVERT: D 462 MET cc_start: 0.8835 (tpt) cc_final: 0.8473 (tpt) REVERT: D 492 ARG cc_start: 0.8052 (mtp180) cc_final: 0.7753 (mtp85) REVERT: E 142 LYS cc_start: 0.8158 (mttp) cc_final: 0.7942 (mmtm) REVERT: E 256 MET cc_start: 0.5439 (tmm) cc_final: 0.5128 (ptt) REVERT: E 273 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7867 (tmt170) REVERT: E 364 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.7906 (tp) REVERT: E 484 LYS cc_start: 0.8453 (mmtt) cc_final: 0.8169 (mmtp) REVERT: E 492 ARG cc_start: 0.8102 (mtp180) cc_final: 0.7737 (mtp85) REVERT: F 70 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7915 (mt-10) REVERT: F 256 MET cc_start: 0.5505 (OUTLIER) cc_final: 0.5133 (ptt) REVERT: F 275 ASP cc_start: 0.8856 (m-30) cc_final: 0.8632 (m-30) REVERT: F 450 ARG cc_start: 0.8190 (mtt180) cc_final: 0.7966 (mtt-85) REVERT: F 492 ARG cc_start: 0.7960 (mtp180) cc_final: 0.7559 (mtp85) REVERT: F 501 ILE cc_start: 0.7616 (pt) cc_final: 0.7244 (pp) outliers start: 80 outliers final: 56 residues processed: 558 average time/residue: 1.2246 time to fit residues: 789.9581 Evaluate side-chains 581 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 516 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 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 273 ARG Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain B residue 21 GLU 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 314 GLU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 472 ARG 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 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 314 GLU Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 436 THR 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 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 273 ARG Chi-restraints excluded: chain D residue 436 THR 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 267 VAL Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 275 ASP Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 436 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 154 VAL Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 314 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 68 optimal weight: 3.9990 chunk 253 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 270 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN C 249 ASN C 418 ASN F 418 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.140838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.113984 restraints weight = 67946.657| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.51 r_work: 0.3135 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.6136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 23646 Z= 0.379 Angle : 0.702 7.930 31950 Z= 0.363 Chirality : 0.047 0.165 3570 Planarity : 0.005 0.048 4092 Dihedral : 12.009 133.333 3474 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.98 % Allowed : 21.73 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.16), residues: 2898 helix: 1.09 (0.16), residues: 1098 sheet: -1.64 (0.19), residues: 744 loop : -0.06 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 455 TYR 0.016 0.002 TYR B 239 PHE 0.022 0.003 PHE B 423 TRP 0.005 0.002 TRP A 466 HIS 0.008 0.002 HIS A 246 Details of bonding type rmsd covalent geometry : bond 0.00827 (23634) covalent geometry : angle 0.70220 (31950) hydrogen bonds : bond 0.04258 ( 1032) hydrogen bonds : angle 5.47934 ( 2862) Misc. bond : bond 0.00886 ( 12) *********************** 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 611 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 512 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 MET cc_start: 0.5599 (OUTLIER) cc_final: 0.5128 (ptt) REVERT: A 314 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7122 (mt-10) REVERT: A 423 PHE cc_start: 0.9032 (p90) cc_final: 0.8484 (p90) REVERT: A 484 LYS cc_start: 0.8566 (mmtt) cc_final: 0.8308 (mmtp) REVERT: B 142 LYS cc_start: 0.8288 (mttp) cc_final: 0.8016 (mmtm) REVERT: B 313 LYS cc_start: 0.8729 (mmmt) cc_final: 0.8297 (mmmm) REVERT: B 484 LYS cc_start: 0.8502 (mmtt) cc_final: 0.8170 (mmtp) REVERT: C 70 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8032 (mt-10) REVERT: C 256 MET cc_start: 0.5644 (OUTLIER) cc_final: 0.5215 (ptt) REVERT: C 492 ARG cc_start: 0.8084 (mtp180) cc_final: 0.7733 (mtp85) REVERT: D 206 ASP cc_start: 0.8744 (m-30) cc_final: 0.8525 (m-30) REVERT: D 256 MET cc_start: 0.5632 (OUTLIER) cc_final: 0.5159 (ptt) REVERT: D 314 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7087 (mt-10) REVERT: D 423 PHE cc_start: 0.9020 (p90) cc_final: 0.8431 (p90) REVERT: D 450 ARG cc_start: 0.8349 (mtt180) cc_final: 0.7981 (mtt-85) REVERT: D 492 ARG cc_start: 0.8146 (mtp180) cc_final: 0.7807 (mtp85) REVERT: E 142 LYS cc_start: 0.8274 (mttp) cc_final: 0.8036 (mmtm) REVERT: E 256 MET cc_start: 0.5572 (tmm) cc_final: 0.5159 (ptt) REVERT: E 275 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8333 (m-30) REVERT: E 313 LYS cc_start: 0.8745 (mmmt) cc_final: 0.8325 (mmmm) REVERT: E 364 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8091 (tp) REVERT: E 484 LYS cc_start: 0.8531 (mmtt) cc_final: 0.8236 (mmtp) REVERT: E 492 ARG cc_start: 0.8176 (mtp180) cc_final: 0.7771 (mtp85) REVERT: F 70 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8030 (mt-10) REVERT: F 256 MET cc_start: 0.5693 (OUTLIER) cc_final: 0.5251 (ptt) REVERT: F 275 ASP cc_start: 0.8892 (m-30) cc_final: 0.8657 (m-30) REVERT: F 492 ARG cc_start: 0.8060 (mtp180) cc_final: 0.7658 (mtp85) REVERT: F 501 ILE cc_start: 0.7842 (pt) cc_final: 0.7597 (pp) outliers start: 99 outliers final: 66 residues processed: 554 average time/residue: 0.9294 time to fit residues: 594.7048 Evaluate side-chains 576 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 504 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 267 VAL Chi-restraints excluded: chain A residue 289 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 267 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 472 ARG 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 189 ILE Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 413 THR 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 232 THR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 273 ARG 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 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 267 VAL Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 275 ASP Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 364 LEU 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 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 189 ILE Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain F residue 436 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 265 optimal weight: 3.9990 chunk 233 optimal weight: 7.9990 chunk 171 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 279 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 187 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 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 = 0.144188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.118201 restraints weight = 67991.541| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.49 r_work: 0.3186 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.6120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 23646 Z= 0.230 Angle : 0.618 7.260 31950 Z= 0.315 Chirality : 0.043 0.150 3570 Planarity : 0.004 0.045 4092 Dihedral : 10.543 123.268 3468 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.13 % Allowed : 22.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.16), residues: 2898 helix: 1.24 (0.16), residues: 1098 sheet: -1.65 (0.19), residues: 696 loop : -0.15 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 472 TYR 0.013 0.002 TYR F 239 PHE 0.023 0.002 PHE B 423 TRP 0.003 0.001 TRP A 466 HIS 0.003 0.001 HIS F 433 Details of bonding type rmsd covalent geometry : bond 0.00490 (23634) covalent geometry : angle 0.61771 (31950) hydrogen bonds : bond 0.03592 ( 1032) hydrogen bonds : angle 5.36318 ( 2862) Misc. bond : bond 0.00572 ( 12) *********************** 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 607 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 529 time to evaluate : 0.794 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: A 256 MET cc_start: 0.5581 (OUTLIER) cc_final: 0.5110 (ptt) REVERT: A 314 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6980 (mt-10) REVERT: A 349 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7394 (tttm) REVERT: A 423 PHE cc_start: 0.9032 (p90) cc_final: 0.8515 (p90) REVERT: A 450 ARG cc_start: 0.8280 (mtt180) cc_final: 0.7924 (mtt-85) REVERT: A 462 MET cc_start: 0.8890 (tpt) cc_final: 0.8414 (tpt) REVERT: A 484 LYS cc_start: 0.8531 (mmtt) cc_final: 0.8266 (mmtp) REVERT: B 70 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8055 (mt-10) REVERT: B 142 LYS cc_start: 0.8252 (mttp) cc_final: 0.8045 (mmtm) REVERT: B 256 MET cc_start: 0.5476 (tmm) cc_final: 0.5087 (ptt) REVERT: B 364 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8102 (tp) REVERT: B 462 MET cc_start: 0.8815 (tpt) cc_final: 0.8491 (tpt) REVERT: B 484 LYS cc_start: 0.8453 (mmtt) cc_final: 0.8155 (mmtp) REVERT: C 70 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8011 (mt-10) REVERT: C 256 MET cc_start: 0.5543 (OUTLIER) cc_final: 0.5173 (ptt) REVERT: C 275 ASP cc_start: 0.8827 (m-30) cc_final: 0.8321 (m-30) REVERT: C 364 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8189 (tt) REVERT: C 492 ARG cc_start: 0.8095 (mtp180) cc_final: 0.7740 (mtp85) REVERT: D 206 ASP cc_start: 0.8614 (m-30) cc_final: 0.8315 (m-30) REVERT: D 256 MET cc_start: 0.5597 (OUTLIER) cc_final: 0.5108 (ptt) REVERT: D 273 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7824 (tmt170) REVERT: D 314 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6944 (mt-10) REVERT: D 423 PHE cc_start: 0.9024 (p90) cc_final: 0.8484 (p90) REVERT: D 450 ARG cc_start: 0.8317 (mtt180) cc_final: 0.7960 (mtt-85) REVERT: D 462 MET cc_start: 0.8924 (tpt) cc_final: 0.8444 (tpt) REVERT: D 492 ARG cc_start: 0.8088 (mtp180) cc_final: 0.7766 (mtp85) REVERT: E 70 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8064 (mt-10) REVERT: E 142 LYS cc_start: 0.8263 (mttp) cc_final: 0.8018 (mmtm) REVERT: E 256 MET cc_start: 0.5603 (OUTLIER) cc_final: 0.5229 (ptt) REVERT: E 273 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7891 (tmt170) REVERT: E 275 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8356 (m-30) REVERT: E 364 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8062 (tp) REVERT: E 484 LYS cc_start: 0.8512 (mmtt) cc_final: 0.8239 (mmtp) REVERT: E 492 ARG cc_start: 0.8119 (mtp180) cc_final: 0.7738 (mtp85) REVERT: F 70 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8027 (mt-10) REVERT: F 256 MET cc_start: 0.5615 (OUTLIER) cc_final: 0.5210 (ptt) REVERT: F 275 ASP cc_start: 0.8857 (m-30) cc_final: 0.8635 (m-30) REVERT: F 364 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8185 (tt) REVERT: F 492 ARG cc_start: 0.8017 (mtp180) cc_final: 0.7621 (mtp85) REVERT: F 501 ILE cc_start: 0.7835 (pt) cc_final: 0.7634 (pp) outliers start: 78 outliers final: 55 residues processed: 555 average time/residue: 0.8936 time to fit residues: 574.3111 Evaluate side-chains 582 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 515 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 436 THR 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 289 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 364 LEU 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 289 LEU Chi-restraints excluded: chain C residue 314 GLU 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 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 273 ARG Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 436 THR 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 273 ARG Chi-restraints excluded: chain E residue 275 ASP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 364 LEU 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 190 ASP Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain F residue 436 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 195 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 262 optimal weight: 0.9990 chunk 237 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 177 optimal weight: 0.1980 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.145468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.119650 restraints weight = 67550.820| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.49 r_work: 0.3205 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23646 Z= 0.200 Angle : 0.597 7.128 31950 Z= 0.303 Chirality : 0.043 0.151 3570 Planarity : 0.004 0.042 4092 Dihedral : 9.965 120.364 3459 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.97 % Allowed : 22.81 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.16), residues: 2898 helix: 1.36 (0.16), residues: 1098 sheet: -1.66 (0.20), residues: 696 loop : -0.10 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 472 TYR 0.011 0.002 TYR F 158 PHE 0.023 0.002 PHE F 423 TRP 0.003 0.001 TRP B 335 HIS 0.003 0.001 HIS E 246 Details of bonding type rmsd covalent geometry : bond 0.00428 (23634) covalent geometry : angle 0.59734 (31950) hydrogen bonds : bond 0.03380 ( 1032) hydrogen bonds : angle 5.28146 ( 2862) Misc. bond : bond 0.00501 ( 12) *********************** 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 603 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 529 time to evaluate : 0.745 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 97 ASN cc_start: 0.9002 (t0) cc_final: 0.8779 (t160) REVERT: A 256 MET cc_start: 0.5509 (OUTLIER) cc_final: 0.5098 (ptt) REVERT: A 314 GLU cc_start: 0.7437 (mt-10) cc_final: 0.6947 (mt-10) REVERT: A 364 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8100 (tt) REVERT: A 423 PHE cc_start: 0.9014 (p90) cc_final: 0.8546 (p90) REVERT: A 450 ARG cc_start: 0.8277 (mtt180) cc_final: 0.7907 (mtt-85) REVERT: A 462 MET cc_start: 0.8883 (tpt) cc_final: 0.8431 (tpt) REVERT: A 484 LYS cc_start: 0.8518 (mmtt) cc_final: 0.8283 (mmtp) REVERT: B 70 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8024 (mt-10) REVERT: B 142 LYS cc_start: 0.8244 (mttp) cc_final: 0.8015 (mmtm) REVERT: B 256 MET cc_start: 0.5456 (tmm) cc_final: 0.5126 (ptt) REVERT: B 275 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8326 (m-30) REVERT: B 364 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8105 (tp) REVERT: B 462 MET cc_start: 0.8791 (tpt) cc_final: 0.8470 (tpt) REVERT: B 484 LYS cc_start: 0.8471 (mmtt) cc_final: 0.8180 (mmtp) REVERT: C 70 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7975 (mt-10) REVERT: C 256 MET cc_start: 0.5488 (OUTLIER) cc_final: 0.5159 (ptt) REVERT: C 364 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8166 (tt) REVERT: D 206 ASP cc_start: 0.8569 (m-30) cc_final: 0.8266 (m-30) REVERT: D 256 MET cc_start: 0.5498 (OUTLIER) cc_final: 0.5092 (ptt) REVERT: D 314 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6931 (mt-10) REVERT: D 423 PHE cc_start: 0.9008 (p90) cc_final: 0.8512 (p90) REVERT: D 450 ARG cc_start: 0.8286 (mtt180) cc_final: 0.7931 (mtt-85) REVERT: D 462 MET cc_start: 0.8904 (tpt) cc_final: 0.8437 (tpt) REVERT: E 70 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8043 (mt-10) REVERT: E 142 LYS cc_start: 0.8244 (mttp) cc_final: 0.7983 (mmtm) REVERT: E 256 MET cc_start: 0.5571 (OUTLIER) cc_final: 0.5178 (ptt) REVERT: E 273 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7824 (tmt170) REVERT: E 275 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8352 (m-30) REVERT: E 364 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8047 (tp) REVERT: E 462 MET cc_start: 0.8786 (tpt) cc_final: 0.8458 (tpt) REVERT: E 484 LYS cc_start: 0.8465 (mmtt) cc_final: 0.8204 (mmtp) REVERT: F 70 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8068 (mt-10) REVERT: F 256 MET cc_start: 0.5591 (OUTLIER) cc_final: 0.5181 (ptt) REVERT: F 275 ASP cc_start: 0.8840 (m-30) cc_final: 0.8610 (m-30) REVERT: F 364 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8157 (tt) outliers start: 74 outliers final: 52 residues processed: 556 average time/residue: 0.8381 time to fit residues: 539.6312 Evaluate side-chains 587 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 522 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 364 LEU Chi-restraints excluded: chain A residue 383 SER 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 267 VAL Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 364 LEU 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 289 LEU Chi-restraints excluded: chain C residue 314 GLU 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 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 289 LEU 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 273 ARG Chi-restraints excluded: chain E residue 275 ASP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 364 LEU 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 190 ASP Chi-restraints excluded: chain F residue 256 MET Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 314 GLU 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 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 190 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 277 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 233 optimal weight: 4.9990 chunk 278 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 393 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.145295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.119339 restraints weight = 68226.730| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.50 r_work: 0.3199 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.6126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23646 Z= 0.207 Angle : 0.605 7.230 31950 Z= 0.306 Chirality : 0.043 0.150 3570 Planarity : 0.004 0.039 4092 Dihedral : 9.947 120.934 3456 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.81 % Allowed : 23.33 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.16), residues: 2898 helix: 1.38 (0.16), residues: 1098 sheet: -1.56 (0.20), residues: 678 loop : -0.13 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 472 TYR 0.011 0.002 TYR B 239 PHE 0.022 0.002 PHE B 423 TRP 0.003 0.001 TRP A 466 HIS 0.003 0.001 HIS E 246 Details of bonding type rmsd covalent geometry : bond 0.00444 (23634) covalent geometry : angle 0.60462 (31950) hydrogen bonds : bond 0.03391 ( 1032) hydrogen bonds : angle 5.27492 ( 2862) Misc. bond : bond 0.00519 ( 12) ********************** 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 598 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 528 time to evaluate : 0.733 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: A 256 MET cc_start: 0.5566 (OUTLIER) cc_final: 0.5152 (ptt) REVERT: A 314 GLU cc_start: 0.7430 (mt-10) cc_final: 0.6942 (mt-10) REVERT: A 423 PHE cc_start: 0.9006 (p90) cc_final: 0.8538 (p90) REVERT: A 450 ARG cc_start: 0.8292 (mtt180) cc_final: 0.7933 (mtt-85) REVERT: A 462 MET cc_start: 0.8886 (tpt) cc_final: 0.8429 (tpt) REVERT: A 484 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8267 (mmtp) REVERT: B 70 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8034 (mt-10) REVERT: B 113 SER cc_start: 0.8547 (p) cc_final: 0.8149 (m) REVERT: B 142 LYS cc_start: 0.8233 (mttp) cc_final: 0.8001 (mmtm) REVERT: B 256 MET cc_start: 0.5387 (tmm) cc_final: 0.5051 (ptt) REVERT: B 275 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8325 (m-30) REVERT: B 364 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8084 (tp) REVERT: B 462 MET cc_start: 0.8813 (tpt) cc_final: 0.8496 (tpt) REVERT: B 484 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8158 (mmtp) REVERT: C 70 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8044 (mt-10) REVERT: C 256 MET cc_start: 0.5532 (OUTLIER) cc_final: 0.5194 (ptt) REVERT: C 364 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8213 (tt) REVERT: D 206 ASP cc_start: 0.8566 (m-30) cc_final: 0.8260 (m-30) REVERT: D 256 MET cc_start: 0.5492 (OUTLIER) cc_final: 0.5090 (ptt) REVERT: D 314 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6976 (mt-10) REVERT: D 423 PHE cc_start: 0.9019 (p90) cc_final: 0.8533 (p90) REVERT: D 450 ARG cc_start: 0.8313 (mtt180) cc_final: 0.7971 (mtt-85) REVERT: D 462 MET cc_start: 0.8905 (tpt) cc_final: 0.8433 (tpt) REVERT: E 70 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8062 (mt-10) REVERT: E 142 LYS cc_start: 0.8252 (mttp) cc_final: 0.7978 (mmtm) REVERT: E 256 MET cc_start: 0.5599 (OUTLIER) cc_final: 0.5219 (ptt) REVERT: E 273 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7827 (tmt170) REVERT: E 364 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8066 (tp) REVERT: E 462 MET cc_start: 0.8791 (tpt) cc_final: 0.8465 (tpt) REVERT: E 484 LYS cc_start: 0.8472 (mmtt) cc_final: 0.8209 (mmtp) REVERT: F 70 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8056 (mt-10) REVERT: F 256 MET cc_start: 0.5529 (OUTLIER) cc_final: 0.5110 (ptt) REVERT: F 275 ASP cc_start: 0.8830 (m-30) cc_final: 0.8605 (m-30) REVERT: F 364 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8206 (tt) REVERT: F 484 LYS cc_start: 0.8551 (mmtp) cc_final: 0.8351 (mmtp) outliers start: 70 outliers final: 55 residues processed: 556 average time/residue: 0.8199 time to fit residues: 528.8822 Evaluate side-chains 581 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 515 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 383 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 436 THR 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 267 VAL Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 364 LEU 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 289 LEU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 413 THR 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 289 LEU Chi-restraints excluded: chain D residue 383 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 273 ARG Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 364 LEU 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 289 LEU Chi-restraints excluded: chain F residue 314 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 186 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 242 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 246 optimal weight: 0.7980 chunk 204 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN C 327 GLN E 327 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.146342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.120688 restraints weight = 68023.017| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.49 r_work: 0.3218 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23646 Z= 0.184 Angle : 0.591 7.093 31950 Z= 0.298 Chirality : 0.043 0.148 3570 Planarity : 0.004 0.041 4092 Dihedral : 9.682 119.204 3456 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.89 % Allowed : 23.33 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.16), residues: 2898 helix: 1.45 (0.16), residues: 1098 sheet: -1.63 (0.20), residues: 672 loop : -0.12 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 472 TYR 0.011 0.002 TYR C 158 PHE 0.021 0.002 PHE F 423 TRP 0.003 0.001 TRP D 96 HIS 0.003 0.001 HIS E 246 Details of bonding type rmsd covalent geometry : bond 0.00394 (23634) covalent geometry : angle 0.59145 (31950) hydrogen bonds : bond 0.03253 ( 1032) hydrogen bonds : angle 5.23781 ( 2862) Misc. bond : bond 0.00464 ( 12) =============================================================================== Job complete usr+sys time: 16590.74 seconds wall clock time: 281 minutes 17.63 seconds (16877.63 seconds total)