Starting phenix.real_space_refine on Sun Aug 24 21:06:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ptn_17875/08_2025/8ptn_17875_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ptn_17875/08_2025/8ptn_17875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ptn_17875/08_2025/8ptn_17875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ptn_17875/08_2025/8ptn_17875.map" model { file = "/net/cci-nas-00/data/ceres_data/8ptn_17875/08_2025/8ptn_17875_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ptn_17875/08_2025/8ptn_17875_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 14431 2.51 5 N 4050 2.21 5 O 4378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s 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: 22976 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "B" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "C" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "D" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "E" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "F" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "a" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "b" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "c" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "d" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "e" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Time building chain proxies: 4.43, per 1000 atoms: 0.19 Number of scatterers: 22976 At special positions: 0 Unit cell: (130.624, 141.44, 163.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 4378 8.00 N 4050 7.00 C 14431 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 872.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5458 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 28 sheets defined 44.8% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 removed outlier: 3.636A pdb=" N LEU A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN A 8 " --> pdb=" O THR A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 30 through 46 removed outlier: 3.823A pdb=" N ILE A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 89 removed outlier: 3.627A pdb=" N ILE A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 153 through 166 Processing helix chain 'A' and resid 183 through 199 Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 235 through 255 removed outlier: 3.501A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 325 through 335 removed outlier: 3.534A pdb=" N GLU A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 removed outlier: 3.598A pdb=" N ALA A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.090A pdb=" N LEU A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 388 Processing helix chain 'A' and resid 392 through 405 removed outlier: 4.502A pdb=" N MET A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 416 removed outlier: 3.767A pdb=" N MET A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 9 removed outlier: 3.940A pdb=" N THR B 9 " --> pdb=" O GLU B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 22 Processing helix chain 'B' and resid 30 through 45 Processing helix chain 'B' and resid 82 through 89 removed outlier: 3.628A pdb=" N ILE B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 128 Processing helix chain 'B' and resid 153 through 166 removed outlier: 3.888A pdb=" N THR B 158 " --> pdb=" O THR B 154 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'B' and resid 212 through 223 removed outlier: 3.714A pdb=" N VAL B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 256 removed outlier: 3.573A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 removed outlier: 3.613A pdb=" N LEU B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 289 removed outlier: 3.734A pdb=" N VAL B 289 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 346 through 352 removed outlier: 3.648A pdb=" N LYS B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.608A pdb=" N LEU B 370 " --> pdb=" O LYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 388 Processing helix chain 'B' and resid 391 through 406 removed outlier: 4.509A pdb=" N MET B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR B 406 " --> pdb=" O LYS B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 418 removed outlier: 3.647A pdb=" N ARG B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 30 through 46 Processing helix chain 'C' and resid 82 through 89 removed outlier: 3.535A pdb=" N ILE C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 128 removed outlier: 3.771A pdb=" N ARG C 128 " --> pdb=" O PRO C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 166 removed outlier: 4.265A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'C' and resid 212 through 223 Processing helix chain 'C' and resid 235 through 255 removed outlier: 3.546A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 278 Processing helix chain 'C' and resid 294 through 302 removed outlier: 3.565A pdb=" N LYS C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 373 through 388 Processing helix chain 'C' and resid 391 through 405 removed outlier: 3.644A pdb=" N MET C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 418 Processing helix chain 'D' and resid 2 through 7 removed outlier: 3.563A pdb=" N LEU D 6 " --> pdb=" O ASN D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 22 Processing helix chain 'D' and resid 30 through 45 removed outlier: 3.804A pdb=" N SER D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 89 removed outlier: 3.766A pdb=" N ILE D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 155 through 166 removed outlier: 4.228A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 Processing helix chain 'D' and resid 212 through 223 Processing helix chain 'D' and resid 235 through 256 removed outlier: 3.568A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 278 Processing helix chain 'D' and resid 294 through 303 removed outlier: 3.956A pdb=" N LYS D 298 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG D 299 " --> pdb=" O HIS D 295 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE D 300 " --> pdb=" O ARG D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 335 Processing helix chain 'D' and resid 346 through 352 removed outlier: 3.695A pdb=" N ALA D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 363 removed outlier: 3.526A pdb=" N SER D 363 " --> pdb=" O TYR D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 391 through 403 Processing helix chain 'D' and resid 409 through 418 Processing helix chain 'E' and resid 2 through 9 removed outlier: 3.654A pdb=" N ASN E 8 " --> pdb=" O THR E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 22 Processing helix chain 'E' and resid 30 through 46 Processing helix chain 'E' and resid 82 through 89 removed outlier: 3.570A pdb=" N ILE E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 129 removed outlier: 3.696A pdb=" N ASN E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 166 Processing helix chain 'E' and resid 183 through 199 Processing helix chain 'E' and resid 212 through 223 Processing helix chain 'E' and resid 235 through 256 removed outlier: 3.528A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N HIS E 256 " --> pdb=" O ARG E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 278 Processing helix chain 'E' and resid 290 through 302 removed outlier: 3.967A pdb=" N ARG E 296 " --> pdb=" O ASN E 292 " (cutoff:3.500A) Proline residue: E 297 - end of helix Processing helix chain 'E' and resid 326 through 335 removed outlier: 4.371A pdb=" N VAL E 330 " --> pdb=" O LYS E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 Processing helix chain 'E' and resid 367 through 371 removed outlier: 3.861A pdb=" N LEU E 370 " --> pdb=" O LYS E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 388 Processing helix chain 'E' and resid 391 through 404 Processing helix chain 'E' and resid 408 through 418 Processing helix chain 'F' and resid 2 through 9 Processing helix chain 'F' and resid 10 through 21 Processing helix chain 'F' and resid 30 through 46 removed outlier: 3.573A pdb=" N GLY F 46 " --> pdb=" O HIS F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 89 removed outlier: 3.629A pdb=" N ILE F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 129 Processing helix chain 'F' and resid 153 through 166 Processing helix chain 'F' and resid 184 through 199 Processing helix chain 'F' and resid 212 through 223 removed outlier: 3.697A pdb=" N VAL F 216 " --> pdb=" O ARG F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 256 Processing helix chain 'F' and resid 266 through 278 removed outlier: 3.590A pdb=" N LEU F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 289 removed outlier: 3.850A pdb=" N VAL F 289 " --> pdb=" O THR F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 302 removed outlier: 3.640A pdb=" N ARG F 296 " --> pdb=" O ASN F 292 " (cutoff:3.500A) Proline residue: F 297 - end of helix Processing helix chain 'F' and resid 325 through 336 Processing helix chain 'F' and resid 337 through 339 No H-bonds generated for 'chain 'F' and resid 337 through 339' Processing helix chain 'F' and resid 347 through 352 Processing helix chain 'F' and resid 367 through 372 Processing helix chain 'F' and resid 373 through 388 Processing helix chain 'F' and resid 394 through 406 removed outlier: 4.097A pdb=" N THR F 406 " --> pdb=" O LYS F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 415 removed outlier: 4.232A pdb=" N PHE F 412 " --> pdb=" O THR F 408 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 23 removed outlier: 3.537A pdb=" N TYR a 13 " --> pdb=" O ASN a 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 23 removed outlier: 3.541A pdb=" N HIS b 23 " --> pdb=" O ALA b 19 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 23 Processing helix chain 'c' and resid 56 through 59 Processing helix chain 'd' and resid 9 through 23 Processing helix chain 'e' and resid 9 through 23 Processing helix chain 'e' and resid 45 through 49 removed outlier: 3.523A pdb=" N ASN e 48 " --> pdb=" O SER e 45 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 57 removed outlier: 3.785A pdb=" N ILE A 79 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU A 114 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG A 102 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N VAL A 116 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LYS A 100 " --> pdb=" O VAL A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 231 removed outlier: 6.328A pdb=" N LEU A 204 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N VAL A 228 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL A 206 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N SER A 230 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU A 208 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE A 316 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE A 262 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N THR A 318 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ARG A 173 " --> pdb=" O MET A 341 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LEU A 343 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU A 175 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 57 removed outlier: 3.524A pdb=" N LEU B 113 " --> pdb=" O TYR B 80 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 112 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LYS B 100 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N VAL B 116 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N SER B 98 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLU B 118 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR B 96 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE B 49 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.600A pdb=" N ASN B 306 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 144 through 145 removed outlier: 4.489A pdb=" N ILE B 168 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 226 through 231 removed outlier: 7.012A pdb=" N LEU B 204 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N VAL B 228 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL B 206 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N SER B 230 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU B 208 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE B 209 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY B 174 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ALA B 319 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE B 176 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG B 173 " --> pdb=" O MET B 341 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU B 343 " --> pdb=" O ARG B 173 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU B 175 " --> pdb=" O LEU B 343 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 50 through 57 removed outlier: 3.845A pdb=" N ILE C 79 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS C 100 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N VAL C 116 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N SER C 98 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLU C 118 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR C 96 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.723A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 226 through 231 removed outlier: 6.593A pdb=" N LEU C 204 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N VAL C 228 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL C 206 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N SER C 230 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU C 208 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE C 316 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE C 262 " --> pdb=" O ILE C 316 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N THR C 318 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU C 264 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N LEU C 320 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 284 through 285 removed outlier: 3.824A pdb=" N VAL C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 49 through 57 removed outlier: 3.959A pdb=" N ILE D 79 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 113 " --> pdb=" O TYR D 80 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU D 114 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ARG D 102 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N VAL D 116 " --> pdb=" O LYS D 100 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS D 100 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE D 49 " --> pdb=" O ILE D 101 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 138 through 139 removed outlier: 6.340A pdb=" N VAL D 260 " --> pdb=" O THR D 314 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ILE D 316 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE D 262 " --> pdb=" O ILE D 316 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N THR D 318 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU D 264 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N LEU D 320 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU D 226 " --> pdb=" O LEU D 204 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 138 through 139 removed outlier: 6.006A pdb=" N GLY D 174 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ALA D 319 " --> pdb=" O GLY D 174 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE D 176 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 49 through 57 removed outlier: 3.657A pdb=" N ILE E 79 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LYS E 100 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N VAL E 116 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N SER E 98 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLU E 118 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR E 96 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE E 49 " --> pdb=" O ILE E 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.545A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.545A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL E 260 " --> pdb=" O THR E 314 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE E 316 " --> pdb=" O VAL E 260 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE E 262 " --> pdb=" O ILE E 316 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N THR E 318 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU E 264 " --> pdb=" O THR E 318 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N LEU E 320 " --> pdb=" O LEU E 264 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU E 263 " --> pdb=" O MET E 205 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU E 226 " --> pdb=" O LEU E 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 79 through 81 removed outlier: 3.816A pdb=" N ILE F 49 " --> pdb=" O ILE F 101 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR F 96 " --> pdb=" O GLU F 118 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLU F 118 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N SER F 98 " --> pdb=" O VAL F 116 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL F 116 " --> pdb=" O SER F 98 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS F 100 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA F 112 " --> pdb=" O ARG F 102 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 260 through 264 removed outlier: 7.232A pdb=" N VAL F 260 " --> pdb=" O THR F 314 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N ILE F 316 " --> pdb=" O VAL F 260 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE F 262 " --> pdb=" O ILE F 316 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N THR F 318 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU F 264 " --> pdb=" O THR F 318 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N LEU F 320 " --> pdb=" O LEU F 264 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU F 175 " --> pdb=" O LEU F 343 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N LEU F 345 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL F 177 " --> pdb=" O LEU F 345 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N HIS F 344 " --> pdb=" O ASP F 359 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 206 through 211 removed outlier: 6.137A pdb=" N VAL F 206 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N SER F 230 " --> pdb=" O VAL F 206 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU F 208 " --> pdb=" O SER F 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'a' and resid 26 through 29 Processing sheet with id=AC3, first strand: chain 'a' and resid 40 through 46 removed outlier: 4.139A pdb=" N ASP a 42 " --> pdb=" O VAL a 53 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL a 53 " --> pdb=" O ASP a 42 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'b' and resid 61 through 63 removed outlier: 3.670A pdb=" N ASP b 42 " --> pdb=" O VAL b 53 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU b 55 " --> pdb=" O ALA b 40 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ALA b 40 " --> pdb=" O GLU b 55 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER b 70 " --> pdb=" O GLU b 29 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'c' and resid 35 through 38 removed outlier: 3.992A pdb=" N PHE c 71 " --> pdb=" O VAL c 79 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL c 79 " --> pdb=" O PHE c 71 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'c' and resid 40 through 46 removed outlier: 4.351A pdb=" N ASP c 42 " --> pdb=" O VAL c 53 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL c 53 " --> pdb=" O ASP c 42 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'd' and resid 25 through 29 removed outlier: 5.400A pdb=" N ALA d 40 " --> pdb=" O GLU d 55 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLU d 55 " --> pdb=" O ALA d 40 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP d 42 " --> pdb=" O VAL d 53 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'e' and resid 27 through 29 Processing sheet with id=AC9, first strand: chain 'e' and resid 40 through 44 removed outlier: 3.707A pdb=" N ASP e 42 " --> pdb=" O VAL e 53 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'e' and resid 70 through 71 removed outlier: 4.471A pdb=" N PHE e 71 " --> pdb=" O VAL e 79 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL e 79 " --> pdb=" O PHE e 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 1055 hydrogen bonds defined for protein. 3039 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.75 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7846 1.34 - 1.46: 4497 1.46 - 1.58: 10749 1.58 - 1.70: 0 1.70 - 1.82: 218 Bond restraints: 23310 Sorted by residual: bond pdb=" CB GLU e 17 " pdb=" CG GLU e 17 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.58e+00 bond pdb=" CA ASP B 322 " pdb=" CB ASP B 322 " ideal model delta sigma weight residual 1.530 1.556 -0.026 1.69e-02 3.50e+03 2.42e+00 bond pdb=" CB LYS D 326 " pdb=" CG LYS D 326 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.57e+00 bond pdb=" CB ASP B 322 " pdb=" CG ASP B 322 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.54e+00 bond pdb=" CB GLU D 329 " pdb=" CG GLU D 329 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.52e+00 ... (remaining 23305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 31070 2.83 - 5.66: 267 5.66 - 8.49: 45 8.49 - 11.32: 18 11.32 - 14.15: 7 Bond angle restraints: 31407 Sorted by residual: angle pdb=" CB MET E 147 " pdb=" CG MET E 147 " pdb=" SD MET E 147 " ideal model delta sigma weight residual 112.70 126.63 -13.93 3.00e+00 1.11e-01 2.15e+01 angle pdb=" N GLU A 333 " pdb=" CA GLU A 333 " pdb=" CB GLU A 333 " ideal model delta sigma weight residual 110.28 117.45 -7.17 1.55e+00 4.16e-01 2.14e+01 angle pdb=" CB MET F 415 " pdb=" CG MET F 415 " pdb=" SD MET F 415 " ideal model delta sigma weight residual 112.70 126.08 -13.38 3.00e+00 1.11e-01 1.99e+01 angle pdb=" CA ARG A 353 " pdb=" CB ARG A 353 " pdb=" CG ARG A 353 " ideal model delta sigma weight residual 114.10 122.99 -8.89 2.00e+00 2.50e-01 1.98e+01 angle pdb=" CB MET F 396 " pdb=" CG MET F 396 " pdb=" SD MET F 396 " ideal model delta sigma weight residual 112.70 125.33 -12.63 3.00e+00 1.11e-01 1.77e+01 ... (remaining 31402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 12578 17.77 - 35.54: 1470 35.54 - 53.31: 335 53.31 - 71.08: 62 71.08 - 88.85: 25 Dihedral angle restraints: 14470 sinusoidal: 6048 harmonic: 8422 Sorted by residual: dihedral pdb=" CA GLU A 414 " pdb=" C GLU A 414 " pdb=" N MET A 415 " pdb=" CA MET A 415 " ideal model delta harmonic sigma weight residual -180.00 -157.86 -22.14 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA HIS F 388 " pdb=" C HIS F 388 " pdb=" N PRO F 389 " pdb=" CA PRO F 389 " ideal model delta harmonic sigma weight residual 180.00 -162.04 -17.96 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA MET F 29 " pdb=" C MET F 29 " pdb=" N ARG F 30 " pdb=" CA ARG F 30 " ideal model delta harmonic sigma weight residual -180.00 -162.35 -17.65 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 14467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2334 0.033 - 0.065: 801 0.065 - 0.098: 294 0.098 - 0.131: 158 0.131 - 0.163: 10 Chirality restraints: 3597 Sorted by residual: chirality pdb=" CA MET A 396 " pdb=" N MET A 396 " pdb=" C MET A 396 " pdb=" CB MET A 396 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA MET A 186 " pdb=" N MET A 186 " pdb=" C MET A 186 " pdb=" CB MET A 186 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA MET F 21 " pdb=" N MET F 21 " pdb=" C MET F 21 " pdb=" CB MET F 21 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 3594 not shown) Planarity restraints: 4097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 322 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" C ASP B 322 " 0.051 2.00e-02 2.50e+03 pdb=" O ASP B 322 " -0.019 2.00e-02 2.50e+03 pdb=" N THR B 323 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 278 " 0.034 5.00e-02 4.00e+02 5.22e-02 4.35e+00 pdb=" N PRO D 279 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO D 279 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 279 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 322 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" C ASP C 322 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP C 322 " 0.013 2.00e-02 2.50e+03 pdb=" N THR C 323 " 0.012 2.00e-02 2.50e+03 ... (remaining 4094 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 331 2.64 - 3.21: 21693 3.21 - 3.77: 37204 3.77 - 4.34: 48637 4.34 - 4.90: 78780 Nonbonded interactions: 186645 Sorted by model distance: nonbonded pdb=" OD1 ASP d 42 " pdb=" N LEU d 43 " model vdw 2.077 3.120 nonbonded pdb=" OD1 ASP E 265 " pdb=" OG1 THR E 318 " model vdw 2.101 3.040 nonbonded pdb=" O LEU F 320 " pdb=" OH TYR F 332 " model vdw 2.101 3.040 nonbonded pdb=" O HIS C 42 " pdb=" OG SER C 45 " model vdw 2.115 3.040 nonbonded pdb=" O GLN F 374 " pdb=" NE2 GLN F 378 " model vdw 2.135 3.120 ... (remaining 186640 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } 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: 0.010 Normalize map: mean=0, sd=1: 3.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 17.960 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 : 0.003 0.048 23310 Z= 0.142 Angle : 0.710 14.155 31407 Z= 0.352 Chirality : 0.042 0.163 3597 Planarity : 0.004 0.053 4097 Dihedral : 15.969 88.852 9012 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.73 % Favored : 98.24 % Rotamer: Outliers : 0.48 % Allowed : 20.97 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.18 % 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: 0.48 (0.16), residues: 2896 helix: 1.09 (0.15), residues: 1205 sheet: 0.13 (0.26), residues: 400 loop : -0.26 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG F 87 TYR 0.012 0.001 TYR B 332 PHE 0.020 0.001 PHE F 301 TRP 0.013 0.001 TRP E 381 HIS 0.014 0.001 HIS a 22 Details of bonding type rmsd covalent geometry : bond 0.00305 (23310) covalent geometry : angle 0.70968 (31407) hydrogen bonds : bond 0.14262 ( 1048) hydrogen bonds : angle 5.94129 ( 3039) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 407 time to evaluate : 0.633 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: E 193 GLN cc_start: 0.8892 (tm-30) cc_final: 0.8625 (tm-30) REVERT: E 390 MET cc_start: 0.9090 (ptp) cc_final: 0.8578 (pmm) REVERT: F 110 TYR cc_start: 0.8745 (p90) cc_final: 0.8385 (p90) REVERT: F 345 LEU cc_start: 0.6270 (tp) cc_final: 0.5865 (tp) REVERT: a 25 MET cc_start: 0.5947 (pmm) cc_final: 0.5138 (tmm) REVERT: b 22 HIS cc_start: 0.8715 (m90) cc_final: 0.8313 (m90) REVERT: b 75 GLU cc_start: 0.9073 (pm20) cc_final: 0.8696 (pm20) REVERT: c 21 GLN cc_start: 0.9049 (mt0) cc_final: 0.8706 (mt0) REVERT: c 51 TYR cc_start: 0.8024 (m-80) cc_final: 0.7789 (m-80) REVERT: c 81 VAL cc_start: 0.9309 (t) cc_final: 0.9099 (m) REVERT: d 51 TYR cc_start: 0.8466 (m-80) cc_final: 0.8177 (m-80) REVERT: d 66 ASP cc_start: 0.8421 (p0) cc_final: 0.7610 (p0) outliers start: 12 outliers final: 6 residues processed: 414 average time/residue: 0.1391 time to fit residues: 90.0165 Evaluate side-chains 369 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 363 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain a residue 22 HIS Chi-restraints excluded: chain b residue 23 HIS Chi-restraints excluded: chain d residue 80 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN D 198 ASN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 21 GLN ** d 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 15 ASN ** e 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.107553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.072557 restraints weight = 73893.895| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.41 r_work: 0.3074 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23310 Z= 0.210 Angle : 0.646 12.726 31407 Z= 0.325 Chirality : 0.043 0.154 3597 Planarity : 0.004 0.106 4097 Dihedral : 4.531 51.961 3172 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.24 % Favored : 97.72 % Rotamer: Outliers : 2.90 % Allowed : 19.38 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.18 % 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: 0.47 (0.15), residues: 2896 helix: 1.13 (0.15), residues: 1212 sheet: -0.16 (0.25), residues: 437 loop : -0.21 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG a 46 TYR 0.021 0.002 TYR e 13 PHE 0.017 0.001 PHE F 398 TRP 0.015 0.001 TRP E 381 HIS 0.006 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00473 (23310) covalent geometry : angle 0.64609 (31407) hydrogen bonds : bond 0.03948 ( 1048) hydrogen bonds : angle 4.90699 ( 3039) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 382 time to evaluate : 0.650 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 52 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.6861 (t0) REVERT: B 234 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8362 (mp0) REVERT: C 155 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7527 (tm-30) REVERT: D 198 ASN cc_start: 0.8862 (OUTLIER) cc_final: 0.8545 (m110) REVERT: D 320 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9065 (mm) REVERT: E 193 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8788 (tm-30) REVERT: E 298 LYS cc_start: 0.8434 (tptt) cc_final: 0.7887 (tptp) REVERT: E 341 MET cc_start: 0.8471 (tmm) cc_final: 0.8219 (tmm) REVERT: E 390 MET cc_start: 0.9072 (ptp) cc_final: 0.8649 (pmm) REVERT: F 110 TYR cc_start: 0.8318 (p90) cc_final: 0.8011 (p90) REVERT: F 345 LEU cc_start: 0.6536 (tp) cc_final: 0.6129 (tp) REVERT: a 25 MET cc_start: 0.6974 (pmm) cc_final: 0.6099 (tmm) REVERT: b 17 GLU cc_start: 0.8538 (pt0) cc_final: 0.8195 (pt0) REVERT: b 25 MET cc_start: 0.8833 (tpp) cc_final: 0.8573 (tpp) REVERT: c 21 GLN cc_start: 0.9104 (mt0) cc_final: 0.8835 (mt0) REVERT: c 29 GLU cc_start: 0.9056 (mp0) cc_final: 0.8811 (mp0) REVERT: c 64 ARG cc_start: 0.7993 (ttt180) cc_final: 0.7714 (ttt180) REVERT: c 81 VAL cc_start: 0.9365 (t) cc_final: 0.9135 (m) REVERT: d 6 GLN cc_start: 0.9277 (mm-40) cc_final: 0.9060 (mm-40) REVERT: d 29 GLU cc_start: 0.8640 (mp0) cc_final: 0.8193 (mp0) REVERT: d 51 TYR cc_start: 0.9364 (m-80) cc_final: 0.8599 (m-80) REVERT: d 64 ARG cc_start: 0.8577 (mtm180) cc_final: 0.7846 (mtp-110) REVERT: e 9 ASN cc_start: 0.8836 (m-40) cc_final: 0.8625 (m-40) outliers start: 73 outliers final: 38 residues processed: 427 average time/residue: 0.1319 time to fit residues: 89.0797 Evaluate side-chains 401 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 358 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain e residue 8 ILE Chi-restraints excluded: chain e residue 20 CYS Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 49 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 244 optimal weight: 7.9990 chunk 239 optimal weight: 7.9990 chunk 147 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 281 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN D 120 ASN ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.108089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.073816 restraints weight = 72946.097| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.35 r_work: 0.3122 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23310 Z= 0.134 Angle : 0.612 11.336 31407 Z= 0.302 Chirality : 0.042 0.159 3597 Planarity : 0.004 0.103 4097 Dihedral : 4.145 39.961 3163 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.82 % Allowed : 20.25 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.18 % 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: 0.52 (0.16), residues: 2896 helix: 1.20 (0.15), residues: 1220 sheet: -0.20 (0.25), residues: 437 loop : -0.20 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG a 46 TYR 0.016 0.001 TYR B 332 PHE 0.016 0.001 PHE F 301 TRP 0.016 0.001 TRP E 381 HIS 0.006 0.001 HIS c 73 Details of bonding type rmsd covalent geometry : bond 0.00301 (23310) covalent geometry : angle 0.61170 (31407) hydrogen bonds : bond 0.03435 ( 1048) hydrogen bonds : angle 4.70671 ( 3039) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 379 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.8448 (pp20) cc_final: 0.8150 (pp20) REVERT: A 245 MET cc_start: 0.9354 (tpp) cc_final: 0.9012 (mmm) REVERT: D 320 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9015 (mm) REVERT: E 21 MET cc_start: 0.9090 (ppp) cc_final: 0.8597 (ppp) REVERT: E 193 GLN cc_start: 0.9030 (tm-30) cc_final: 0.8776 (tm-30) REVERT: E 308 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8825 (mm-30) REVERT: E 341 MET cc_start: 0.8521 (tmm) cc_final: 0.8194 (tmm) REVERT: F 21 MET cc_start: 0.7619 (pmm) cc_final: 0.7386 (pmm) REVERT: F 110 TYR cc_start: 0.8237 (p90) cc_final: 0.7952 (p90) REVERT: F 390 MET cc_start: 0.5429 (tmm) cc_final: 0.4791 (pmm) REVERT: a 25 MET cc_start: 0.6810 (pmm) cc_final: 0.5804 (tmm) REVERT: a 54 VAL cc_start: 0.6933 (OUTLIER) cc_final: 0.6487 (p) REVERT: b 17 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8272 (pt0) REVERT: b 18 LEU cc_start: 0.9293 (pp) cc_final: 0.9018 (pp) REVERT: b 22 HIS cc_start: 0.8714 (m90) cc_final: 0.8497 (m90) REVERT: b 25 MET cc_start: 0.8867 (tpp) cc_final: 0.8658 (tpp) REVERT: c 64 ARG cc_start: 0.8084 (ttt180) cc_final: 0.7823 (ttt180) REVERT: c 81 VAL cc_start: 0.9340 (t) cc_final: 0.9123 (m) REVERT: d 51 TYR cc_start: 0.9383 (m-80) cc_final: 0.8621 (m-80) REVERT: d 64 ARG cc_start: 0.8523 (mtm180) cc_final: 0.7971 (ttp-170) REVERT: d 66 ASP cc_start: 0.8811 (p0) cc_final: 0.8399 (p0) REVERT: e 14 ASP cc_start: 0.8490 (m-30) cc_final: 0.8233 (m-30) outliers start: 71 outliers final: 39 residues processed: 424 average time/residue: 0.1586 time to fit residues: 106.2920 Evaluate side-chains 388 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 345 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain a residue 54 VAL Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain d residue 15 ASN Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain e residue 8 ILE Chi-restraints excluded: chain e residue 20 CYS Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 49 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 159 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 203 optimal weight: 8.9990 chunk 190 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN B 292 ASN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 ASN D 120 ASN ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 HIS ** a 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.106243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.071710 restraints weight = 73602.255| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.34 r_work: 0.3064 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 23310 Z= 0.247 Angle : 0.666 9.562 31407 Z= 0.333 Chirality : 0.044 0.182 3597 Planarity : 0.004 0.105 4097 Dihedral : 4.263 20.070 3160 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.98 % Allowed : 21.53 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.18 % 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: 0.42 (0.15), residues: 2896 helix: 1.11 (0.15), residues: 1220 sheet: -0.30 (0.24), residues: 448 loop : -0.22 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 46 TYR 0.018 0.002 TYR B 332 PHE 0.016 0.001 PHE F 301 TRP 0.015 0.001 TRP E 381 HIS 0.007 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00553 (23310) covalent geometry : angle 0.66582 (31407) hydrogen bonds : bond 0.03762 ( 1048) hydrogen bonds : angle 4.76845 ( 3039) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 360 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8937 (mt) REVERT: A 244 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8207 (pp20) REVERT: C 60 ASP cc_start: 0.8801 (m-30) cc_final: 0.8482 (t0) REVERT: C 348 LYS cc_start: 0.9539 (tppt) cc_final: 0.9338 (tppt) REVERT: D 193 GLN cc_start: 0.8703 (mt0) cc_final: 0.8482 (mp10) REVERT: D 198 ASN cc_start: 0.8903 (OUTLIER) cc_final: 0.8616 (m110) REVERT: D 294 LEU cc_start: 0.9196 (tp) cc_final: 0.8854 (tt) REVERT: D 320 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9047 (mm) REVERT: D 342 GLU cc_start: 0.8142 (pm20) cc_final: 0.7872 (pm20) REVERT: E 21 MET cc_start: 0.9057 (ppp) cc_final: 0.8540 (ppp) REVERT: E 193 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8766 (tm-30) REVERT: E 341 MET cc_start: 0.8695 (tmm) cc_final: 0.8409 (tmm) REVERT: E 390 MET cc_start: 0.9208 (ptp) cc_final: 0.8567 (pmm) REVERT: F 30 ARG cc_start: 0.9246 (OUTLIER) cc_final: 0.8984 (tpp80) REVERT: F 110 TYR cc_start: 0.8344 (p90) cc_final: 0.8011 (p90) REVERT: F 390 MET cc_start: 0.5369 (tmm) cc_final: 0.4758 (pmm) REVERT: a 25 MET cc_start: 0.6913 (pmm) cc_final: 0.5907 (tmm) REVERT: a 54 VAL cc_start: 0.6857 (OUTLIER) cc_final: 0.6452 (p) REVERT: b 17 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8393 (pt0) REVERT: b 25 MET cc_start: 0.8947 (tpp) cc_final: 0.8747 (tpp) REVERT: b 75 GLU cc_start: 0.9200 (pm20) cc_final: 0.8871 (pm20) REVERT: c 6 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8408 (mm110) REVERT: c 29 GLU cc_start: 0.9040 (mp0) cc_final: 0.8837 (mp0) REVERT: c 64 ARG cc_start: 0.8182 (ttt180) cc_final: 0.7615 (ttt180) REVERT: c 81 VAL cc_start: 0.9366 (t) cc_final: 0.9135 (m) REVERT: d 6 GLN cc_start: 0.9221 (mm-40) cc_final: 0.9016 (mm-40) REVERT: d 29 GLU cc_start: 0.8699 (mp0) cc_final: 0.8260 (mp0) REVERT: d 51 TYR cc_start: 0.9387 (m-80) cc_final: 0.8625 (m-80) REVERT: d 64 ARG cc_start: 0.8512 (mtm180) cc_final: 0.8010 (ttp-170) REVERT: d 66 ASP cc_start: 0.8826 (p0) cc_final: 0.8448 (p0) outliers start: 75 outliers final: 47 residues processed: 414 average time/residue: 0.1425 time to fit residues: 92.9514 Evaluate side-chains 396 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 342 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 418 ARG Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain a residue 43 LEU Chi-restraints excluded: chain a residue 54 VAL Chi-restraints excluded: chain a residue 63 LEU Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain d residue 15 ASN Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain e residue 20 CYS Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 49 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 245 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 257 optimal weight: 9.9990 chunk 135 optimal weight: 0.0370 chunk 236 optimal weight: 40.0000 chunk 282 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 247 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN D 120 ASN ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN ** b 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.104853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.070247 restraints weight = 73732.282| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.39 r_work: 0.3020 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 23310 Z= 0.291 Angle : 0.697 13.792 31407 Z= 0.349 Chirality : 0.044 0.170 3597 Planarity : 0.004 0.078 4097 Dihedral : 4.409 21.978 3160 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.57 % Allowed : 22.56 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.18 % 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: 0.20 (0.15), residues: 2896 helix: 0.91 (0.15), residues: 1227 sheet: -0.48 (0.24), residues: 451 loop : -0.29 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 353 TYR 0.022 0.002 TYR D 197 PHE 0.018 0.002 PHE D 62 TRP 0.017 0.002 TRP E 381 HIS 0.008 0.001 HIS d 73 Details of bonding type rmsd covalent geometry : bond 0.00654 (23310) covalent geometry : angle 0.69742 (31407) hydrogen bonds : bond 0.03886 ( 1048) hydrogen bonds : angle 4.91119 ( 3039) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 361 time to evaluate : 0.940 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 139 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9032 (mt) REVERT: A 244 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8257 (pp20) REVERT: A 415 MET cc_start: 0.9106 (ppp) cc_final: 0.8809 (ppp) REVERT: B 329 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8567 (mm-30) REVERT: C 344 HIS cc_start: 0.8910 (OUTLIER) cc_final: 0.8494 (m170) REVERT: D 294 LEU cc_start: 0.9200 (tp) cc_final: 0.8905 (tt) REVERT: D 299 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8205 (mtm-85) REVERT: D 320 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9006 (mm) REVERT: E 21 MET cc_start: 0.9092 (ppp) cc_final: 0.8840 (ppp) REVERT: E 341 MET cc_start: 0.8769 (tmm) cc_final: 0.8433 (tmm) REVERT: E 390 MET cc_start: 0.9067 (ptp) cc_final: 0.8537 (pmm) REVERT: F 30 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8985 (tpp80) REVERT: F 110 TYR cc_start: 0.8020 (p90) cc_final: 0.7776 (p90) REVERT: F 390 MET cc_start: 0.5328 (tmm) cc_final: 0.4704 (pmm) REVERT: a 25 MET cc_start: 0.6922 (pmm) cc_final: 0.5930 (tmm) REVERT: a 54 VAL cc_start: 0.6710 (OUTLIER) cc_final: 0.6294 (p) REVERT: b 17 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8508 (pt0) REVERT: b 22 HIS cc_start: 0.9156 (m90) cc_final: 0.8919 (m90) REVERT: b 75 GLU cc_start: 0.9217 (pm20) cc_final: 0.8925 (pm20) REVERT: c 17 GLU cc_start: 0.8118 (pt0) cc_final: 0.7736 (pt0) REVERT: c 64 ARG cc_start: 0.8076 (ttt180) cc_final: 0.7607 (ttt180) REVERT: c 67 LYS cc_start: 0.8551 (mmtm) cc_final: 0.8328 (mmtm) REVERT: c 68 ILE cc_start: 0.8513 (mm) cc_final: 0.8108 (mm) REVERT: c 81 VAL cc_start: 0.9377 (t) cc_final: 0.9168 (m) REVERT: d 6 GLN cc_start: 0.9167 (mm-40) cc_final: 0.8898 (mm-40) REVERT: d 29 GLU cc_start: 0.8748 (mp0) cc_final: 0.8416 (mp0) REVERT: d 51 TYR cc_start: 0.9352 (m-80) cc_final: 0.8629 (m-80) REVERT: d 64 ARG cc_start: 0.8497 (mtm180) cc_final: 0.7987 (ttp-170) REVERT: d 66 ASP cc_start: 0.8728 (p0) cc_final: 0.8330 (p0) REVERT: e 14 ASP cc_start: 0.8593 (m-30) cc_final: 0.8342 (p0) outliers start: 90 outliers final: 65 residues processed: 426 average time/residue: 0.1401 time to fit residues: 94.5247 Evaluate side-chains 415 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 342 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain B residue 418 ARG Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 344 HIS Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 299 ARG Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 381 TRP Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain a residue 23 HIS Chi-restraints excluded: chain a residue 54 VAL Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 61 ARG Chi-restraints excluded: chain d residue 15 ASN Chi-restraints excluded: chain d residue 47 LYS Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain e residue 20 CYS Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 49 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 192 optimal weight: 6.9990 chunk 273 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 chunk 244 optimal weight: 30.0000 chunk 130 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 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 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 GLN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN b 21 GLN ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 23 HIS ** e 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.105132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.070485 restraints weight = 74158.685| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.36 r_work: 0.3016 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 23310 Z= 0.262 Angle : 0.703 11.945 31407 Z= 0.348 Chirality : 0.044 0.220 3597 Planarity : 0.004 0.116 4097 Dihedral : 4.425 21.386 3160 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.97 % Allowed : 22.44 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.18 % 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: 0.14 (0.15), residues: 2896 helix: 0.88 (0.15), residues: 1233 sheet: -0.60 (0.24), residues: 455 loop : -0.31 (0.18), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 109 TYR 0.025 0.002 TYR B 332 PHE 0.018 0.001 PHE F 398 TRP 0.018 0.002 TRP E 381 HIS 0.007 0.001 HIS d 73 Details of bonding type rmsd covalent geometry : bond 0.00590 (23310) covalent geometry : angle 0.70335 (31407) hydrogen bonds : bond 0.03792 ( 1048) hydrogen bonds : angle 4.88821 ( 3039) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 363 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9053 (mt) REVERT: A 244 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8226 (pp20) REVERT: A 299 ARG cc_start: 0.9044 (ttm110) cc_final: 0.8800 (ttm110) REVERT: A 415 MET cc_start: 0.9133 (ppp) cc_final: 0.8916 (ppp) REVERT: D 294 LEU cc_start: 0.9200 (tp) cc_final: 0.8871 (tt) REVERT: D 299 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8180 (mtm-85) REVERT: D 320 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8986 (mm) REVERT: D 342 GLU cc_start: 0.8129 (pm20) cc_final: 0.7853 (pm20) REVERT: E 21 MET cc_start: 0.9050 (ppp) cc_final: 0.8794 (ppp) REVERT: E 341 MET cc_start: 0.8776 (tmm) cc_final: 0.8431 (tmm) REVERT: E 390 MET cc_start: 0.9155 (ptp) cc_final: 0.8692 (pmm) REVERT: F 328 ASP cc_start: 0.8286 (t70) cc_final: 0.7909 (t0) REVERT: F 390 MET cc_start: 0.5274 (tmm) cc_final: 0.4681 (pmm) REVERT: a 25 MET cc_start: 0.6829 (pmm) cc_final: 0.5909 (tmm) REVERT: a 61 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7868 (ptt-90) REVERT: b 17 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8574 (pt0) REVERT: b 22 HIS cc_start: 0.9236 (m90) cc_final: 0.8951 (m90) REVERT: b 75 GLU cc_start: 0.9267 (pm20) cc_final: 0.8957 (pm20) REVERT: c 13 TYR cc_start: 0.7875 (t80) cc_final: 0.7302 (t80) REVERT: c 17 GLU cc_start: 0.8210 (pt0) cc_final: 0.7782 (pt0) REVERT: c 64 ARG cc_start: 0.8208 (ttt180) cc_final: 0.7912 (ttt180) REVERT: d 29 GLU cc_start: 0.8785 (mp0) cc_final: 0.8491 (mp0) REVERT: d 51 TYR cc_start: 0.9365 (m-80) cc_final: 0.8613 (m-80) REVERT: d 64 ARG cc_start: 0.8575 (mtm180) cc_final: 0.8260 (mtp-110) REVERT: d 66 ASP cc_start: 0.8748 (p0) cc_final: 0.8385 (p0) outliers start: 100 outliers final: 72 residues processed: 432 average time/residue: 0.1451 time to fit residues: 98.5770 Evaluate side-chains 436 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 358 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 299 ARG Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 381 TRP Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 401 ASN Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 353 ARG Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain a residue 23 HIS Chi-restraints excluded: chain a residue 61 ARG Chi-restraints excluded: chain a residue 63 LEU Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 61 ARG Chi-restraints excluded: chain d residue 15 ASN Chi-restraints excluded: chain d residue 47 LYS Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain e residue 20 CYS Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 28 LEU Chi-restraints excluded: chain e residue 49 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 198 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 211 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 237 optimal weight: 5.9990 chunk 241 optimal weight: 0.8980 chunk 285 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 23 HIS ** e 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.106494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.071793 restraints weight = 73800.272| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.40 r_work: 0.3035 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23310 Z= 0.152 Angle : 0.676 17.398 31407 Z= 0.329 Chirality : 0.043 0.184 3597 Planarity : 0.004 0.096 4097 Dihedral : 4.299 20.532 3160 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.30 % Allowed : 23.59 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.18 % 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: 0.31 (0.16), residues: 2896 helix: 1.07 (0.15), residues: 1227 sheet: -0.52 (0.24), residues: 453 loop : -0.27 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 109 TYR 0.026 0.002 TYR a 13 PHE 0.020 0.001 PHE F 398 TRP 0.017 0.002 TRP E 381 HIS 0.007 0.001 HIS C 344 Details of bonding type rmsd covalent geometry : bond 0.00349 (23310) covalent geometry : angle 0.67590 (31407) hydrogen bonds : bond 0.03366 ( 1048) hydrogen bonds : angle 4.70550 ( 3039) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 369 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8221 (pp20) REVERT: A 299 ARG cc_start: 0.9007 (ttm110) cc_final: 0.8753 (ttm110) REVERT: A 353 ARG cc_start: 0.8452 (mmm160) cc_final: 0.8119 (mmp-170) REVERT: A 415 MET cc_start: 0.9145 (ppp) cc_final: 0.8838 (ppp) REVERT: B 234 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8323 (mp0) REVERT: C 140 HIS cc_start: 0.8722 (OUTLIER) cc_final: 0.8018 (m90) REVERT: D 294 LEU cc_start: 0.9187 (tp) cc_final: 0.8927 (tt) REVERT: D 299 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8142 (mtm-85) REVERT: D 320 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8986 (mm) REVERT: E 21 MET cc_start: 0.9081 (ppp) cc_final: 0.8600 (ppp) REVERT: E 341 MET cc_start: 0.8818 (tmm) cc_final: 0.8420 (tmm) REVERT: E 390 MET cc_start: 0.9243 (ptp) cc_final: 0.8795 (pmm) REVERT: F 328 ASP cc_start: 0.8261 (t70) cc_final: 0.7994 (t0) REVERT: F 390 MET cc_start: 0.5340 (tmm) cc_final: 0.4730 (pmm) REVERT: a 13 TYR cc_start: 0.6365 (t80) cc_final: 0.6120 (t80) REVERT: a 25 MET cc_start: 0.7090 (pmm) cc_final: 0.6164 (tmm) REVERT: a 61 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7958 (ptt-90) REVERT: b 17 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8543 (pt0) REVERT: b 75 GLU cc_start: 0.9290 (pm20) cc_final: 0.8957 (pm20) REVERT: c 13 TYR cc_start: 0.7895 (t80) cc_final: 0.7332 (t80) REVERT: c 17 GLU cc_start: 0.8188 (pt0) cc_final: 0.7785 (pt0) REVERT: c 59 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7966 (pp20) REVERT: d 6 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8953 (mm-40) REVERT: d 50 GLU cc_start: 0.9120 (pm20) cc_final: 0.8905 (pm20) REVERT: d 51 TYR cc_start: 0.9412 (m-80) cc_final: 0.8612 (m-80) REVERT: d 64 ARG cc_start: 0.8608 (mtm180) cc_final: 0.8276 (mtp-110) REVERT: d 66 ASP cc_start: 0.8806 (p0) cc_final: 0.8438 (p0) outliers start: 83 outliers final: 56 residues processed: 419 average time/residue: 0.1668 time to fit residues: 109.4810 Evaluate side-chains 413 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 349 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 299 ARG Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 381 TRP Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 401 ASN Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 353 ARG Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain a residue 23 HIS Chi-restraints excluded: chain a residue 61 ARG Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 30 LEU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 59 GLU Chi-restraints excluded: chain c residue 61 ARG Chi-restraints excluded: chain d residue 15 ASN Chi-restraints excluded: chain d residue 47 LYS Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain e residue 20 CYS Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 49 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 107 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 268 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 285 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 234 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 241 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 23 HIS ** e 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.105564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.070964 restraints weight = 73712.588| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.35 r_work: 0.3027 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23310 Z= 0.219 Angle : 0.715 13.641 31407 Z= 0.350 Chirality : 0.044 0.208 3597 Planarity : 0.004 0.078 4097 Dihedral : 4.352 20.922 3160 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.22 % Allowed : 23.67 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.18 % 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: 0.28 (0.16), residues: 2896 helix: 1.02 (0.15), residues: 1229 sheet: -0.52 (0.24), residues: 444 loop : -0.27 (0.17), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG a 46 TYR 0.026 0.002 TYR a 13 PHE 0.023 0.001 PHE F 398 TRP 0.018 0.002 TRP E 381 HIS 0.007 0.001 HIS b 22 Details of bonding type rmsd covalent geometry : bond 0.00498 (23310) covalent geometry : angle 0.71467 (31407) hydrogen bonds : bond 0.03596 ( 1048) hydrogen bonds : angle 4.80436 ( 3039) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 361 time to evaluate : 0.938 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: A 244 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8231 (pp20) REVERT: A 415 MET cc_start: 0.9123 (ppp) cc_final: 0.8817 (ppp) REVERT: B 234 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8304 (mp0) REVERT: C 140 HIS cc_start: 0.8743 (OUTLIER) cc_final: 0.8006 (m90) REVERT: D 294 LEU cc_start: 0.9186 (tp) cc_final: 0.8845 (tt) REVERT: D 299 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8171 (mtm-85) REVERT: D 320 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8993 (mm) REVERT: D 342 GLU cc_start: 0.8105 (pm20) cc_final: 0.7854 (pm20) REVERT: E 21 MET cc_start: 0.9067 (ppp) cc_final: 0.8831 (ppp) REVERT: E 341 MET cc_start: 0.8856 (tmm) cc_final: 0.8448 (tmm) REVERT: E 390 MET cc_start: 0.9264 (ptp) cc_final: 0.8794 (pmm) REVERT: F 390 MET cc_start: 0.5236 (tmm) cc_final: 0.4675 (pmm) REVERT: a 13 TYR cc_start: 0.6509 (t80) cc_final: 0.6281 (t80) REVERT: a 54 VAL cc_start: 0.7100 (OUTLIER) cc_final: 0.6749 (p) REVERT: b 17 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8274 (pt0) REVERT: b 59 GLU cc_start: 0.8752 (pp20) cc_final: 0.8495 (pp20) REVERT: b 75 GLU cc_start: 0.9264 (pm20) cc_final: 0.8963 (pm20) REVERT: c 17 GLU cc_start: 0.8220 (pt0) cc_final: 0.7849 (pt0) REVERT: c 64 ARG cc_start: 0.7932 (ttt180) cc_final: 0.7359 (ttt180) REVERT: d 6 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8979 (mm-40) REVERT: d 29 GLU cc_start: 0.8719 (mp0) cc_final: 0.8413 (mp0) REVERT: d 50 GLU cc_start: 0.9101 (pm20) cc_final: 0.8896 (pm20) REVERT: d 51 TYR cc_start: 0.9420 (m-80) cc_final: 0.8681 (m-80) REVERT: d 64 ARG cc_start: 0.8619 (mtm180) cc_final: 0.8062 (mtm110) REVERT: d 66 ASP cc_start: 0.8776 (p0) cc_final: 0.8161 (p0) outliers start: 81 outliers final: 63 residues processed: 414 average time/residue: 0.1685 time to fit residues: 109.1759 Evaluate side-chains 428 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 358 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 299 ARG Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 381 TRP Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 401 ASN Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 353 ARG Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain a residue 23 HIS Chi-restraints excluded: chain a residue 54 VAL Chi-restraints excluded: chain a residue 61 ARG Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 30 LEU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 61 ARG Chi-restraints excluded: chain d residue 15 ASN Chi-restraints excluded: chain d residue 47 LYS Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain e residue 20 CYS Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 65 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 220 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 0.0010 chunk 134 optimal weight: 2.9990 chunk 252 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 119 optimal weight: 0.1980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 ASN ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 23 HIS ** e 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.107318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.072502 restraints weight = 73375.043| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.48 r_work: 0.3076 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23310 Z= 0.123 Angle : 0.691 14.359 31407 Z= 0.334 Chirality : 0.044 0.218 3597 Planarity : 0.004 0.077 4097 Dihedral : 4.214 21.134 3160 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.82 % Allowed : 24.19 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.18 % 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: 0.41 (0.16), residues: 2896 helix: 1.18 (0.15), residues: 1221 sheet: -0.43 (0.25), residues: 437 loop : -0.26 (0.17), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 109 TYR 0.023 0.001 TYR a 13 PHE 0.025 0.001 PHE F 398 TRP 0.018 0.001 TRP E 381 HIS 0.007 0.001 HIS b 22 Details of bonding type rmsd covalent geometry : bond 0.00279 (23310) covalent geometry : angle 0.69147 (31407) hydrogen bonds : bond 0.03087 ( 1048) hydrogen bonds : angle 4.62391 ( 3039) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 374 time to evaluate : 1.136 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 244 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8149 (pp20) REVERT: A 245 MET cc_start: 0.9253 (tpp) cc_final: 0.8913 (mmm) REVERT: A 299 ARG cc_start: 0.8962 (ttm110) cc_final: 0.8758 (ttm110) REVERT: A 341 MET cc_start: 0.9189 (ttm) cc_final: 0.8546 (tpt) REVERT: A 415 MET cc_start: 0.9100 (ppp) cc_final: 0.8799 (ppp) REVERT: B 234 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8134 (mp0) REVERT: C 140 HIS cc_start: 0.8689 (OUTLIER) cc_final: 0.7984 (m90) REVERT: C 221 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8008 (mtt90) REVERT: C 272 ARG cc_start: 0.8786 (ttm170) cc_final: 0.8238 (mtm180) REVERT: D 294 LEU cc_start: 0.9183 (tp) cc_final: 0.8895 (tt) REVERT: D 299 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8111 (mtm-85) REVERT: D 320 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8939 (mm) REVERT: D 342 GLU cc_start: 0.8012 (pm20) cc_final: 0.7776 (pm20) REVERT: D 416 MET cc_start: 0.9367 (tpt) cc_final: 0.9028 (tpt) REVERT: E 21 MET cc_start: 0.9155 (ppp) cc_final: 0.8702 (ppp) REVERT: E 341 MET cc_start: 0.8775 (tmm) cc_final: 0.8177 (tmm) REVERT: E 390 MET cc_start: 0.9266 (ptp) cc_final: 0.8819 (pmm) REVERT: F 390 MET cc_start: 0.5251 (tmm) cc_final: 0.4676 (pmm) REVERT: a 13 TYR cc_start: 0.6434 (t80) cc_final: 0.6215 (t80) REVERT: a 61 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8151 (pmt170) REVERT: b 17 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8050 (pt0) REVERT: b 59 GLU cc_start: 0.8745 (pp20) cc_final: 0.8523 (pp20) REVERT: b 67 LYS cc_start: 0.9353 (mtmm) cc_final: 0.9041 (pttp) REVERT: b 75 GLU cc_start: 0.9303 (pm20) cc_final: 0.8976 (pm20) REVERT: c 13 TYR cc_start: 0.7788 (t80) cc_final: 0.7567 (t80) REVERT: d 6 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8987 (mm-40) REVERT: d 50 GLU cc_start: 0.9114 (pm20) cc_final: 0.8783 (pm20) REVERT: d 51 TYR cc_start: 0.9404 (m-80) cc_final: 0.8627 (m-80) REVERT: d 64 ARG cc_start: 0.8611 (mtm180) cc_final: 0.8025 (mtm110) REVERT: d 66 ASP cc_start: 0.8777 (p0) cc_final: 0.8103 (p0) outliers start: 71 outliers final: 54 residues processed: 418 average time/residue: 0.1741 time to fit residues: 112.3685 Evaluate side-chains 405 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 343 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 299 ARG Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 381 TRP Chi-restraints excluded: chain D residue 415 MET Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 401 ASN Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 353 ARG Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain a residue 23 HIS Chi-restraints excluded: chain a residue 61 ARG Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 30 LEU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 61 ARG Chi-restraints excluded: chain d residue 15 ASN Chi-restraints excluded: chain d residue 47 LYS Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain e residue 20 CYS Chi-restraints excluded: chain e residue 27 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 109 optimal weight: 0.9990 chunk 223 optimal weight: 0.6980 chunk 266 optimal weight: 9.9990 chunk 131 optimal weight: 0.0470 chunk 53 optimal weight: 0.5980 chunk 159 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 0.0980 chunk 22 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN D 198 ASN D 374 GLN D 378 GLN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 23 HIS e 15 ASN ** e 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.107688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.073240 restraints weight = 73285.195| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.48 r_work: 0.3095 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23310 Z= 0.122 Angle : 0.726 17.826 31407 Z= 0.344 Chirality : 0.044 0.300 3597 Planarity : 0.004 0.094 4097 Dihedral : 4.163 22.271 3160 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.62 % Allowed : 24.86 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.18 % 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: 0.41 (0.16), residues: 2896 helix: 1.17 (0.15), residues: 1222 sheet: -0.31 (0.25), residues: 450 loop : -0.31 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 299 TYR 0.021 0.001 TYR a 13 PHE 0.028 0.001 PHE F 398 TRP 0.017 0.002 TRP E 381 HIS 0.004 0.001 HIS C 344 Details of bonding type rmsd covalent geometry : bond 0.00278 (23310) covalent geometry : angle 0.72643 (31407) hydrogen bonds : bond 0.03018 ( 1048) hydrogen bonds : angle 4.59077 ( 3039) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 358 time to evaluate : 0.980 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: A 244 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8156 (pp20) REVERT: A 245 MET cc_start: 0.9229 (tpp) cc_final: 0.8876 (mmm) REVERT: A 341 MET cc_start: 0.9247 (ttm) cc_final: 0.8569 (tpt) REVERT: A 415 MET cc_start: 0.9051 (ppp) cc_final: 0.8774 (ppp) REVERT: B 234 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8118 (mp0) REVERT: C 140 HIS cc_start: 0.8670 (OUTLIER) cc_final: 0.7929 (m90) REVERT: C 221 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8004 (mtt90) REVERT: C 272 ARG cc_start: 0.8758 (ttm170) cc_final: 0.8238 (mtm180) REVERT: D 294 LEU cc_start: 0.9180 (tp) cc_final: 0.8887 (tt) REVERT: D 299 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8106 (mtm-85) REVERT: D 320 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8926 (mm) REVERT: E 21 MET cc_start: 0.9152 (ppp) cc_final: 0.8689 (ppp) REVERT: E 301 PHE cc_start: 0.8917 (t80) cc_final: 0.8345 (t80) REVERT: E 381 TRP cc_start: 0.9351 (m100) cc_final: 0.8658 (m-90) REVERT: E 390 MET cc_start: 0.9165 (ptp) cc_final: 0.8778 (pmm) REVERT: E 415 MET cc_start: 0.9258 (ppp) cc_final: 0.9039 (ppp) REVERT: F 30 ARG cc_start: 0.9111 (mtp-110) cc_final: 0.8742 (ttp-170) REVERT: F 390 MET cc_start: 0.5219 (tmm) cc_final: 0.4619 (pmm) REVERT: F 396 MET cc_start: 0.7836 (mmm) cc_final: 0.7002 (pmm) REVERT: a 13 TYR cc_start: 0.6311 (t80) cc_final: 0.6096 (t80) REVERT: a 26 LEU cc_start: 0.6279 (tp) cc_final: 0.5662 (pp) REVERT: a 54 VAL cc_start: 0.7463 (OUTLIER) cc_final: 0.6794 (p) REVERT: a 61 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7588 (ptt-90) REVERT: b 17 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7985 (pt0) REVERT: b 67 LYS cc_start: 0.9384 (mtmm) cc_final: 0.9120 (pttp) REVERT: b 68 ILE cc_start: 0.9097 (mm) cc_final: 0.8847 (mm) REVERT: b 75 GLU cc_start: 0.9330 (pm20) cc_final: 0.8753 (pm20) REVERT: c 59 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7739 (pp20) REVERT: d 6 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8909 (mm-40) REVERT: d 50 GLU cc_start: 0.9182 (pm20) cc_final: 0.8887 (pm20) REVERT: d 51 TYR cc_start: 0.9348 (m-80) cc_final: 0.8665 (m-80) REVERT: d 64 ARG cc_start: 0.8543 (mtm180) cc_final: 0.7968 (mtm110) REVERT: d 66 ASP cc_start: 0.8628 (p0) cc_final: 0.7911 (p0) outliers start: 66 outliers final: 52 residues processed: 402 average time/residue: 0.1732 time to fit residues: 107.1468 Evaluate side-chains 418 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 356 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 299 ARG Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 381 TRP Chi-restraints excluded: chain D residue 415 MET Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 401 ASN Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 353 ARG Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain a residue 23 HIS Chi-restraints excluded: chain a residue 54 VAL Chi-restraints excluded: chain a residue 61 ARG Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 23 HIS Chi-restraints excluded: chain b residue 30 LEU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 59 GLU Chi-restraints excluded: chain c residue 61 ARG Chi-restraints excluded: chain d residue 15 ASN Chi-restraints excluded: chain d residue 47 LYS Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain e residue 20 CYS Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 153 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 104 optimal weight: 0.0670 chunk 110 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 178 optimal weight: 20.0000 chunk 260 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 chunk 235 optimal weight: 8.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN E 126 ASN ** a 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 23 HIS ** e 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.107425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.073050 restraints weight = 73501.254| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.46 r_work: 0.3075 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23310 Z= 0.140 Angle : 0.730 16.320 31407 Z= 0.348 Chirality : 0.044 0.236 3597 Planarity : 0.004 0.087 4097 Dihedral : 4.176 23.378 3160 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.74 % Allowed : 25.06 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.18 % 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: 0.40 (0.16), residues: 2896 helix: 1.17 (0.15), residues: 1222 sheet: -0.34 (0.25), residues: 456 loop : -0.31 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 299 TYR 0.021 0.001 TYR a 13 PHE 0.027 0.001 PHE F 398 TRP 0.023 0.002 TRP B 381 HIS 0.010 0.001 HIS b 22 Details of bonding type rmsd covalent geometry : bond 0.00324 (23310) covalent geometry : angle 0.73050 (31407) hydrogen bonds : bond 0.03147 ( 1048) hydrogen bonds : angle 4.56317 ( 3039) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6725.68 seconds wall clock time: 116 minutes 0.80 seconds (6960.80 seconds total)