Starting phenix.real_space_refine on Tue Aug 26 09:10:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jo2_36453/08_2025/8jo2_36453_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jo2_36453/08_2025/8jo2_36453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jo2_36453/08_2025/8jo2_36453_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jo2_36453/08_2025/8jo2_36453_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jo2_36453/08_2025/8jo2_36453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jo2_36453/08_2025/8jo2_36453.map" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 130 5.49 5 S 145 5.16 5 C 21750 2.51 5 N 6278 2.21 5 O 7065 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s 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: 35368 Number of models: 1 Model: "" Number of chains: 10 Chain: "1" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1338 Classifications: {'DNA': 65} Link IDs: {'rna3p': 64} Chain: "2" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1332 Classifications: {'DNA': 65} Link IDs: {'rna3p': 64} Chain: "A" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 10570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10570 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "D" Number of atoms: 10474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1351, 10474 Classifications: {'peptide': 1351} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1295} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4022 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 15, 'TRANS': 481} Chain breaks: 1 Chain: "H" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1726 Classifications: {'peptide': 219} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 212} Chain: "I" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1726 Classifications: {'peptide': 219} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 212} Time building chain proxies: 7.48, per 1000 atoms: 0.21 Number of scatterers: 35368 At special positions: 0 Unit cell: (151.248, 193.992, 202.212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 145 16.00 P 130 15.00 O 7065 8.00 N 6278 7.00 C 21750 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 8286 Ramachandran restraints generated. 4143 Oldfield, 0 Emsley, 4143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7728 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 52 sheets defined 44.5% alpha, 14.2% beta 37 base pairs and 100 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.702A pdb=" N ALA A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.950A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.732A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 51 removed outlier: 3.977A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N MET B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.724A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 removed outlier: 3.831A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 231 removed outlier: 3.674A pdb=" N PHE B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 212 removed outlier: 4.113A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 4.019A pdb=" N ARG C 247 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.614A pdb=" N ALA C 293 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 290 through 294' Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.928A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 408 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.705A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.975A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 494 through 509 removed outlier: 4.397A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 527 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.717A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 704 through 711 Processing helix chain 'C' and resid 811 through 815 removed outlier: 3.890A pdb=" N ASP C 814 " --> pdb=" O ASN C 811 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.587A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 980 Processing helix chain 'C' and resid 986 through 992 removed outlier: 3.856A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 992 " --> pdb=" O LYS C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.817A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.593A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 3.509A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1311 Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.738A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.701A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU D 100 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 117 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 193 through 208 removed outlier: 4.069A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 4.059A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 286 removed outlier: 4.307A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.529A pdb=" N LEU D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.792A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 removed outlier: 3.555A pdb=" N TYR D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.548A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.563A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.950A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 613 through 636 removed outlier: 3.683A pdb=" N THR D 617 " --> pdb=" O GLY D 613 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 670 Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.357A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.654A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.536A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 895 through 900 removed outlier: 3.712A pdb=" N GLY D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.590A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 1063 through 1067 Processing helix chain 'D' and resid 1136 through 1147 removed outlier: 3.877A pdb=" N ARG D1140 " --> pdb=" O GLY D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.915A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 Processing helix chain 'D' and resid 1280 through 1290 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 4.068A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN D1326 " --> pdb=" O ALA D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1353 Processing helix chain 'D' and resid 1361 through 1375 removed outlier: 4.438A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 15 through 32 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 80 removed outlier: 3.890A pdb=" N LEU E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 90 removed outlier: 4.551A pdb=" N SER F 86 " --> pdb=" O GLN F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 108 removed outlier: 4.120A pdb=" N VAL F 108 " --> pdb=" O GLU F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 137 removed outlier: 4.004A pdb=" N TYR F 137 " --> pdb=" O SER F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 152 removed outlier: 4.186A pdb=" N ILE F 141 " --> pdb=" O TYR F 137 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR F 148 " --> pdb=" O LEU F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 155 No H-bonds generated for 'chain 'F' and resid 153 through 155' Processing helix chain 'F' and resid 159 through 165 Processing helix chain 'F' and resid 213 through 236 removed outlier: 3.511A pdb=" N ALA F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 257 Processing helix chain 'F' and resid 262 through 296 removed outlier: 4.155A pdb=" N MET F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN F 294 " --> pdb=" O LEU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 309 removed outlier: 3.771A pdb=" N THR F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 322 removed outlier: 3.579A pdb=" N MET F 322 " --> pdb=" O ALA F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 329 removed outlier: 3.528A pdb=" N GLU F 328 " --> pdb=" O LYS F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 332 No H-bonds generated for 'chain 'F' and resid 330 through 332' Processing helix chain 'F' and resid 333 through 352 removed outlier: 3.624A pdb=" N HIS F 338 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU F 348 " --> pdb=" O LEU F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 392 removed outlier: 3.649A pdb=" N LYS F 377 " --> pdb=" O ARG F 373 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ARG F 385 " --> pdb=" O GLU F 381 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU F 386 " --> pdb=" O ALA F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 419 Processing helix chain 'F' and resid 420 through 424 Processing helix chain 'F' and resid 426 through 446 removed outlier: 4.263A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA F 444 " --> pdb=" O THR F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 475 Processing helix chain 'F' and resid 479 through 488 Processing helix chain 'F' and resid 490 through 501 Processing helix chain 'F' and resid 518 through 522 Processing helix chain 'F' and resid 537 through 550 Processing helix chain 'F' and resid 552 through 564 Processing helix chain 'F' and resid 572 through 580 Processing helix chain 'F' and resid 585 through 598 Processing helix chain 'F' and resid 605 through 612 removed outlier: 3.599A pdb=" N SER F 609 " --> pdb=" O GLU F 605 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE F 610 " --> pdb=" O VAL F 606 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU F 611 " --> pdb=" O LEU F 607 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP F 612 " --> pdb=" O ARG F 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 605 through 612' Processing helix chain 'H' and resid 9 through 24 Processing helix chain 'H' and resid 32 through 43 Processing helix chain 'H' and resid 58 through 69 removed outlier: 4.009A pdb=" N PHE H 62 " --> pdb=" O ASP H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 94 Processing helix chain 'H' and resid 104 through 121 Processing helix chain 'H' and resid 151 through 164 Processing helix chain 'H' and resid 170 through 179 Processing helix chain 'H' and resid 189 through 202 Processing helix chain 'I' and resid 9 through 23 Processing helix chain 'I' and resid 32 through 43 Processing helix chain 'I' and resid 58 through 69 Processing helix chain 'I' and resid 83 through 94 Processing helix chain 'I' and resid 104 through 120 Processing helix chain 'I' and resid 136 through 139 Processing helix chain 'I' and resid 151 through 164 Processing helix chain 'I' and resid 170 through 179 removed outlier: 3.619A pdb=" N LEU I 174 " --> pdb=" O HIS I 170 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR I 179 " --> pdb=" O TYR I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 202 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 4.963A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 116 removed outlier: 4.368A pdb=" N THR A 101 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 18 removed outlier: 4.929A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 115 through 116 removed outlier: 4.140A pdb=" N THR B 101 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.651A pdb=" N GLY B 108 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.414A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.725A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.664A pdb=" N SER C 147 " --> pdb=" O ARG C 529 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 160 removed outlier: 3.700A pdb=" N ASP C 185 " --> pdb=" O ARG C 197 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 284 through 286 removed outlier: 4.642A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.106A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 301 through 302 removed outlier: 7.179A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.610A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC2, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.278A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 748 through 751 removed outlier: 5.721A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC5, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC6, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 4.280A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.670A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AC9, first strand: chain 'C' and resid 876 through 878 Processing sheet with id=AD1, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.733A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1268 through 1270 Processing sheet with id=AD3, first strand: chain 'C' and resid 1335 through 1341 removed outlier: 3.537A pdb=" N LYS D 21 " --> pdb=" O GLU C1338 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA D 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.722A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 9.889A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 9.798A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 159 through 160 removed outlier: 5.587A pdb=" N VAL D 146 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LYS D 179 " --> pdb=" O VAL D 146 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 252 through 254 removed outlier: 6.089A pdb=" N PHE D 260 " --> pdb=" O ILE F 505 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 350 through 357 removed outlier: 7.307A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN D 448 " --> pdb=" O GLY D 367 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD9, first strand: chain 'D' and resid 706 through 709 Processing sheet with id=AE1, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE2, first strand: chain 'D' and resid 825 through 827 removed outlier: 6.603A pdb=" N GLU D 827 " --> pdb=" O VAL D 831 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL D 831 " --> pdb=" O GLU D 827 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 901 through 902 removed outlier: 3.718A pdb=" N HIS D 907 " --> pdb=" O ASP D 902 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 958 through 961 removed outlier: 4.048A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1002 through 1003 Processing sheet with id=AE6, first strand: chain 'D' and resid 1027 through 1028 removed outlier: 3.586A pdb=" N ALA D1122 " --> pdb=" O VAL D1027 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1033 through 1034 Processing sheet with id=AE8, first strand: chain 'D' and resid 1060 through 1061 Processing sheet with id=AE9, first strand: chain 'D' and resid 1187 through 1191 Processing sheet with id=AF1, first strand: chain 'D' and resid 1277 through 1279 Processing sheet with id=AF2, first strand: chain 'H' and resid 27 through 30 removed outlier: 6.254A pdb=" N ILE H 48 " --> pdb=" O LEU H 76 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU H 78 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU H 50 " --> pdb=" O LEU H 78 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL H 75 " --> pdb=" O ASP H 97 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU H 99 " --> pdb=" O VAL H 75 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ILE H 77 " --> pdb=" O LEU H 99 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 126 through 129 Processing sheet with id=AF4, first strand: chain 'H' and resid 206 through 208 Processing sheet with id=AF5, first strand: chain 'I' and resid 27 through 30 removed outlier: 6.593A pdb=" N ILE I 3 " --> pdb=" O ASP I 28 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL I 30 " --> pdb=" O ILE I 3 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL I 5 " --> pdb=" O VAL I 30 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU I 4 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE I 48 " --> pdb=" O LEU I 76 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU I 78 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LEU I 50 " --> pdb=" O LEU I 78 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LEU I 99 " --> pdb=" O VAL I 75 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE I 77 " --> pdb=" O LEU I 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'I' and resid 127 through 129 removed outlier: 3.515A pdb=" N LEU I 140 " --> pdb=" O ASN I 135 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL I 141 " --> pdb=" O LEU I 148 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 206 through 208 removed outlier: 3.751A pdb=" N MET I 215 " --> pdb=" O ARG I 207 " (cutoff:3.500A) 1519 hydrogen bonds defined for protein. 4317 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 100 stacking parallelities Total time for adding SS restraints: 8.96 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5876 1.30 - 1.43: 8929 1.43 - 1.56: 20847 1.56 - 1.69: 258 1.69 - 1.81: 257 Bond restraints: 36167 Sorted by residual: bond pdb=" C PRO A 52 " pdb=" O PRO A 52 " ideal model delta sigma weight residual 1.234 1.169 0.065 1.08e-02 8.57e+03 3.63e+01 bond pdb=" C ILE B 223 " pdb=" O ILE B 223 " ideal model delta sigma weight residual 1.237 1.301 -0.064 1.13e-02 7.83e+03 3.18e+01 bond pdb=" N PHE B 231 " pdb=" CA PHE B 231 " ideal model delta sigma weight residual 1.457 1.514 -0.057 1.29e-02 6.01e+03 1.96e+01 bond pdb=" C GLU B 226 " pdb=" O GLU B 226 " ideal model delta sigma weight residual 1.237 1.285 -0.048 1.17e-02 7.31e+03 1.70e+01 bond pdb=" N VAL B 64 " pdb=" CA VAL B 64 " ideal model delta sigma weight residual 1.459 1.506 -0.048 1.19e-02 7.06e+03 1.61e+01 ... (remaining 36162 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 46917 2.35 - 4.70: 2284 4.70 - 7.04: 168 7.04 - 9.39: 24 9.39 - 11.74: 9 Bond angle restraints: 49402 Sorted by residual: angle pdb=" C ILE C1079 " pdb=" N ASN C1080 " pdb=" CA ASN C1080 " ideal model delta sigma weight residual 120.67 132.16 -11.49 1.34e+00 5.57e-01 7.35e+01 angle pdb=" C ASN C 519 " pdb=" CA ASN C 519 " pdb=" CB ASN C 519 " ideal model delta sigma weight residual 110.22 100.96 9.26 1.32e+00 5.74e-01 4.92e+01 angle pdb=" CA PHE F 401 " pdb=" CB PHE F 401 " pdb=" CG PHE F 401 " ideal model delta sigma weight residual 113.80 120.38 -6.58 1.00e+00 1.00e+00 4.32e+01 angle pdb=" C SER D 503 " pdb=" N GLN D 504 " pdb=" CA GLN D 504 " ideal model delta sigma weight residual 121.54 109.80 11.74 1.91e+00 2.74e-01 3.78e+01 angle pdb=" O3' DT 2 48 " pdb=" C3' DT 2 48 " pdb=" C2' DT 2 48 " ideal model delta sigma weight residual 111.50 102.35 9.15 1.50e+00 4.44e-01 3.72e+01 ... (remaining 49397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.92: 20818 34.92 - 69.85: 1070 69.85 - 104.77: 59 104.77 - 139.69: 4 139.69 - 174.61: 5 Dihedral angle restraints: 21956 sinusoidal: 9965 harmonic: 11991 Sorted by residual: dihedral pdb=" C ASN C 519 " pdb=" N ASN C 519 " pdb=" CA ASN C 519 " pdb=" CB ASN C 519 " ideal model delta harmonic sigma weight residual -122.60 -109.77 -12.83 0 2.50e+00 1.60e-01 2.63e+01 dihedral pdb=" N LEU H 116 " pdb=" C LEU H 116 " pdb=" CA LEU H 116 " pdb=" CB LEU H 116 " ideal model delta harmonic sigma weight residual 122.80 110.45 12.35 0 2.50e+00 1.60e-01 2.44e+01 dihedral pdb=" CA GLU D1291 " pdb=" C GLU D1291 " pdb=" N LEU D1292 " pdb=" CA LEU D1292 " ideal model delta harmonic sigma weight residual 180.00 156.10 23.90 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 21953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 5077 0.103 - 0.206: 508 0.206 - 0.309: 42 0.309 - 0.413: 6 0.413 - 0.516: 1 Chirality restraints: 5634 Sorted by residual: chirality pdb=" CB VAL B 232 " pdb=" CA VAL B 232 " pdb=" CG1 VAL B 232 " pdb=" CG2 VAL B 232 " both_signs ideal model delta sigma weight residual False -2.63 -2.11 -0.52 2.00e-01 2.50e+01 6.65e+00 chirality pdb=" CA MET A 51 " pdb=" N MET A 51 " pdb=" C MET A 51 " pdb=" CB MET A 51 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CA ARG D 709 " pdb=" N ARG D 709 " pdb=" C ARG D 709 " pdb=" CB ARG D 709 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 5631 not shown) Planarity restraints: 6004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO H 185 " 0.022 2.00e-02 2.50e+03 4.50e-02 2.03e+01 pdb=" C PRO H 185 " -0.078 2.00e-02 2.50e+03 pdb=" O PRO H 185 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA H 186 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 196 " 0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C VAL C 196 " -0.069 2.00e-02 2.50e+03 pdb=" O VAL C 196 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG C 197 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 50 " 0.016 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C SER A 50 " -0.059 2.00e-02 2.50e+03 pdb=" O SER A 50 " 0.022 2.00e-02 2.50e+03 pdb=" N MET A 51 " 0.020 2.00e-02 2.50e+03 ... (remaining 6001 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 485 2.63 - 3.20: 32763 3.20 - 3.77: 55513 3.77 - 4.33: 77613 4.33 - 4.90: 124826 Nonbonded interactions: 291200 Sorted by model distance: nonbonded pdb=" O VAL C 884 " pdb=" OG SER C 917 " model vdw 2.068 3.040 nonbonded pdb=" O SER I 89 " pdb=" OG1 THR I 93 " model vdw 2.074 3.040 nonbonded pdb=" OG SER D 949 " pdb=" O ALA D1018 " model vdw 2.105 3.040 nonbonded pdb=" O SER A 50 " pdb=" OG SER A 50 " model vdw 2.138 3.040 nonbonded pdb=" NH1 ARG C 197 " pdb=" O ARG C 201 " model vdw 2.150 3.120 ... (remaining 291195 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 233) selection = chain 'B' } ncs_group { reference = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 35.050 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 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 : 0.011 0.090 36167 Z= 0.539 Angle : 1.062 11.740 49402 Z= 0.678 Chirality : 0.064 0.516 5634 Planarity : 0.005 0.045 6004 Dihedral : 18.635 174.613 14228 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.22 % Allowed : 3.26 % Favored : 94.51 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.12), residues: 4143 helix: -0.65 (0.12), residues: 1687 sheet: -1.60 (0.23), residues: 470 loop : -1.95 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG C1301 TYR 0.033 0.003 TYR I 175 PHE 0.047 0.003 PHE D1325 TRP 0.013 0.002 TRP I 142 HIS 0.016 0.002 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.01059 (36167) covalent geometry : angle 1.06179 (49402) hydrogen bonds : bond 0.15248 ( 1609) hydrogen bonds : angle 7.39701 ( 4501) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8286 Ramachandran restraints generated. 4143 Oldfield, 0 Emsley, 4143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8286 Ramachandran restraints generated. 4143 Oldfield, 0 Emsley, 4143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 681 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8462 (ptm) cc_final: 0.8227 (ttp) REVERT: A 183 ILE cc_start: 0.8123 (tt) cc_final: 0.7899 (mt) REVERT: B 17 GLU cc_start: 0.7048 (tt0) cc_final: 0.6299 (mp0) REVERT: B 139 SER cc_start: 0.6928 (p) cc_final: 0.6653 (t) REVERT: B 142 MET cc_start: 0.7613 (ptp) cc_final: 0.7392 (ptt) REVERT: C 340 ASP cc_start: 0.7248 (t0) cc_final: 0.7010 (t0) REVERT: C 542 ARG cc_start: 0.7492 (mtm-85) cc_final: 0.6745 (tpt170) REVERT: C 805 MET cc_start: 0.8999 (ptm) cc_final: 0.8788 (ptm) REVERT: C 815 SER cc_start: 0.8960 (OUTLIER) cc_final: 0.8649 (m) REVERT: C 1040 ASP cc_start: 0.5818 (m-30) cc_final: 0.5446 (m-30) REVERT: D 69 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7395 (mt-10) REVERT: D 80 HIS cc_start: 0.6934 (m-70) cc_final: 0.6610 (m90) REVERT: D 677 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.7014 (mt-10) REVERT: E 35 LYS cc_start: 0.7940 (ptpt) cc_final: 0.7682 (ptpp) REVERT: E 47 THR cc_start: 0.8120 (m) cc_final: 0.7601 (p) REVERT: F 273 MET cc_start: 0.3836 (ttm) cc_final: 0.2757 (mtt) REVERT: F 322 MET cc_start: 0.0623 (tpt) cc_final: 0.0148 (mtm) REVERT: F 451 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7477 (mtp-110) REVERT: I 197 LEU cc_start: 0.7169 (tp) cc_final: 0.6726 (mm) outliers start: 79 outliers final: 10 residues processed: 736 average time/residue: 0.7816 time to fit residues: 666.3682 Evaluate side-chains 361 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 348 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 892 GLU Chi-restraints excluded: chain C residue 1258 PRO Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 677 GLU Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1152 GLU Chi-restraints excluded: chain D residue 1188 GLU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain F residue 451 ARG Chi-restraints excluded: chain H residue 50 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.0870 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 8.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 84 ASN A 137 ASN B 18 GLN B 227 GLN C 518 ASN C 568 ASN C 658 GLN C 659 GLN C1134 GLN C1209 GLN C1220 GLN C1236 ASN C1244 HIS D 45 ASN D 157 GLN D 164 GLN D 232 ASN D 294 ASN D 341 ASN D 545 HIS D 667 GLN D 777 HIS D 897 HIS D 929 GLN D1366 HIS E 15 ASN E 61 ASN F 128 ASN F 129 GLN F 271 ASN F 309 ASN F 357 GLN F 362 ASN F 400 GLN F 437 GLN F 472 GLN F 589 GLN F 600 HIS I 193 HIS Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.218314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.143271 restraints weight = 43346.428| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.77 r_work: 0.3504 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36167 Z= 0.151 Angle : 0.625 9.687 49402 Z= 0.335 Chirality : 0.043 0.182 5634 Planarity : 0.004 0.045 6004 Dihedral : 19.382 178.913 6059 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.70 % Allowed : 14.18 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.13), residues: 4143 helix: 0.59 (0.12), residues: 1719 sheet: -1.19 (0.22), residues: 497 loop : -1.37 (0.14), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C1301 TYR 0.020 0.002 TYR H 25 PHE 0.029 0.002 PHE H 62 TRP 0.009 0.001 TRP D1020 HIS 0.008 0.001 HIS C1116 Details of bonding type rmsd covalent geometry : bond 0.00333 (36167) covalent geometry : angle 0.62501 (49402) hydrogen bonds : bond 0.04303 ( 1609) hydrogen bonds : angle 5.08662 ( 4501) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8286 Ramachandran restraints generated. 4143 Oldfield, 0 Emsley, 4143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8286 Ramachandran restraints generated. 4143 Oldfield, 0 Emsley, 4143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 407 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: B 17 GLU cc_start: 0.7598 (tt0) cc_final: 0.6159 (mp0) REVERT: B 65 LEU cc_start: 0.7859 (mm) cc_final: 0.7267 (pt) REVERT: B 71 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.7072 (mtpm) REVERT: C 20 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.6803 (pp30) REVERT: C 160 ASP cc_start: 0.6636 (t70) cc_final: 0.6391 (t0) REVERT: C 200 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6623 (mtp85) REVERT: C 340 ASP cc_start: 0.7572 (t0) cc_final: 0.7203 (t0) REVERT: C 542 ARG cc_start: 0.7874 (mtm-85) cc_final: 0.6949 (tmm-80) REVERT: C 947 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6984 (tt0) REVERT: C 1040 ASP cc_start: 0.6188 (m-30) cc_final: 0.5794 (m-30) REVERT: C 1233 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8656 (mt) REVERT: D 69 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7716 (mt-10) REVERT: D 164 GLN cc_start: 0.6718 (tt0) cc_final: 0.5895 (mp10) REVERT: D 200 GLN cc_start: 0.6989 (tp40) cc_final: 0.6506 (mp10) REVERT: D 648 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: D 706 VAL cc_start: 0.8646 (m) cc_final: 0.8358 (m) REVERT: D 725 MET cc_start: 0.9010 (mtt) cc_final: 0.8737 (mtt) REVERT: D 736 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.7857 (mt0) REVERT: D 785 ASP cc_start: 0.7555 (t70) cc_final: 0.7038 (m-30) REVERT: D 812 ASP cc_start: 0.8273 (m-30) cc_final: 0.8072 (t0) REVERT: D 867 GLN cc_start: 0.8066 (mm110) cc_final: 0.6974 (tm-30) REVERT: D 1342 ASP cc_start: 0.8541 (p0) cc_final: 0.7819 (p0) REVERT: E 47 THR cc_start: 0.7935 (m) cc_final: 0.7283 (p) REVERT: E 56 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6985 (mp0) REVERT: F 111 LEU cc_start: 0.5000 (mp) cc_final: 0.4775 (mm) REVERT: F 322 MET cc_start: 0.1595 (tpt) cc_final: 0.0544 (mmm) REVERT: F 369 GLU cc_start: 0.7530 (tp30) cc_final: 0.7282 (tp30) REVERT: F 413 MET cc_start: 0.7651 (mtm) cc_final: 0.7286 (mtp) REVERT: F 451 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7725 (mtp-110) REVERT: F 526 THR cc_start: 0.8069 (OUTLIER) cc_final: 0.7812 (p) REVERT: F 541 ARG cc_start: 0.6035 (OUTLIER) cc_final: 0.5587 (ttp80) REVERT: F 591 GLU cc_start: 0.5645 (OUTLIER) cc_final: 0.5428 (pt0) REVERT: F 606 VAL cc_start: 0.4769 (p) cc_final: 0.4481 (t) REVERT: H 18 LEU cc_start: 0.2460 (mm) cc_final: 0.2125 (tp) REVERT: H 50 LEU cc_start: 0.2885 (OUTLIER) cc_final: 0.2289 (pt) REVERT: H 162 MET cc_start: 0.5017 (mtp) cc_final: 0.4739 (mtp) REVERT: H 210 ARG cc_start: 0.1601 (ttt90) cc_final: 0.1384 (mtt-85) REVERT: I 71 MET cc_start: -0.0111 (tmm) cc_final: -0.0409 (tpt) REVERT: I 162 MET cc_start: 0.5125 (mmm) cc_final: 0.4781 (mmm) REVERT: I 210 ARG cc_start: 0.4085 (mmm160) cc_final: 0.3214 (mmm160) outliers start: 96 outliers final: 20 residues processed: 470 average time/residue: 0.7814 time to fit residues: 428.4647 Evaluate side-chains 365 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 332 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 943 LYS Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain D residue 1152 GLU Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 451 ARG Chi-restraints excluded: chain F residue 526 THR Chi-restraints excluded: chain F residue 541 ARG Chi-restraints excluded: chain F residue 591 GLU Chi-restraints excluded: chain H residue 50 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 308 optimal weight: 6.9990 chunk 193 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 417 optimal weight: 20.0000 chunk 300 optimal weight: 20.0000 chunk 187 optimal weight: 0.1980 chunk 216 optimal weight: 0.8980 chunk 137 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 248 optimal weight: 0.5980 chunk 170 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN C 658 GLN C 760 ASN C1236 ASN D 489 ASN D 667 GLN D 805 GLN D 897 HIS E 15 ASN E 61 ASN F 128 ASN F 383 ASN F 396 ASN F 469 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.216607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.136381 restraints weight = 42722.291| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.29 r_work: 0.3438 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 36167 Z= 0.141 Angle : 0.573 9.263 49402 Z= 0.306 Chirality : 0.042 0.175 5634 Planarity : 0.004 0.045 6004 Dihedral : 19.082 179.874 6039 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.12 % Allowed : 16.48 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.13), residues: 4143 helix: 1.05 (0.13), residues: 1730 sheet: -0.97 (0.23), residues: 493 loop : -1.15 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1301 TYR 0.019 0.001 TYR D 144 PHE 0.024 0.002 PHE H 62 TRP 0.009 0.001 TRP C 183 HIS 0.012 0.001 HIS I 119 Details of bonding type rmsd covalent geometry : bond 0.00329 (36167) covalent geometry : angle 0.57251 (49402) hydrogen bonds : bond 0.04009 ( 1609) hydrogen bonds : angle 4.70778 ( 4501) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8286 Ramachandran restraints generated. 4143 Oldfield, 0 Emsley, 4143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8286 Ramachandran restraints generated. 4143 Oldfield, 0 Emsley, 4143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 365 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8612 (mmtt) cc_final: 0.7940 (mtpm) REVERT: A 122 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8196 (mp0) REVERT: B 17 GLU cc_start: 0.7740 (tt0) cc_final: 0.6147 (mp0) REVERT: B 65 LEU cc_start: 0.7933 (mm) cc_final: 0.7369 (pt) REVERT: B 71 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.7051 (mtpm) REVERT: B 214 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: C 20 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.6938 (pp30) REVERT: C 41 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7484 (mt0) REVERT: C 160 ASP cc_start: 0.6701 (t70) cc_final: 0.6344 (t0) REVERT: C 340 ASP cc_start: 0.7464 (t0) cc_final: 0.7245 (t70) REVERT: C 365 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7665 (mm-30) REVERT: C 441 GLU cc_start: 0.7501 (pm20) cc_final: 0.7141 (pm20) REVERT: C 542 ARG cc_start: 0.7761 (mtm-85) cc_final: 0.6938 (tmm-80) REVERT: C 876 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8078 (mm-30) REVERT: C 968 GLU cc_start: 0.4250 (mm-30) cc_final: 0.3363 (tp30) REVERT: C 1040 ASP cc_start: 0.6343 (m-30) cc_final: 0.6143 (m-30) REVERT: C 1233 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8663 (mt) REVERT: C 1242 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8767 (mttp) REVERT: D 69 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7885 (mt-10) REVERT: D 136 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7735 (mt-10) REVERT: D 164 GLN cc_start: 0.6655 (tt0) cc_final: 0.5954 (mp10) REVERT: D 190 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7334 (mttt) REVERT: D 200 GLN cc_start: 0.7099 (tp40) cc_final: 0.6527 (mp10) REVERT: D 321 LYS cc_start: 0.7574 (mmpt) cc_final: 0.6872 (tttt) REVERT: D 414 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7744 (tp30) REVERT: D 521 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8384 (ttpt) REVERT: D 599 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8303 (ttpp) REVERT: D 648 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: D 664 ILE cc_start: 0.6605 (OUTLIER) cc_final: 0.6343 (tt) REVERT: D 736 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.7820 (mt0) REVERT: D 785 ASP cc_start: 0.7506 (t70) cc_final: 0.6979 (m-30) REVERT: D 805 GLN cc_start: 0.7824 (tp40) cc_final: 0.7125 (tt0) REVERT: D 867 GLN cc_start: 0.8056 (mm110) cc_final: 0.7015 (tm-30) REVERT: D 1152 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6357 (tm-30) REVERT: D 1369 ARG cc_start: 0.5107 (mtm110) cc_final: 0.4692 (mtp180) REVERT: E 47 THR cc_start: 0.7772 (m) cc_final: 0.7185 (p) REVERT: E 56 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6776 (mp0) REVERT: F 369 GLU cc_start: 0.7376 (tp30) cc_final: 0.7161 (tp30) REVERT: F 413 MET cc_start: 0.7641 (mtm) cc_final: 0.7288 (mtp) REVERT: F 451 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7855 (mtp-110) REVERT: F 507 MET cc_start: 0.8026 (ttp) cc_final: 0.7721 (mtt) REVERT: F 526 THR cc_start: 0.8059 (OUTLIER) cc_final: 0.7846 (p) REVERT: F 606 VAL cc_start: 0.4771 (p) cc_final: 0.4531 (t) REVERT: H 50 LEU cc_start: 0.3208 (OUTLIER) cc_final: 0.2558 (pt) REVERT: I 162 MET cc_start: 0.5079 (mmm) cc_final: 0.4718 (mmm) REVERT: I 207 ARG cc_start: 0.4514 (mmt180) cc_final: 0.4233 (mtp85) outliers start: 111 outliers final: 30 residues processed: 441 average time/residue: 0.7649 time to fit residues: 392.9000 Evaluate side-chains 375 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 326 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 876 GLU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1242 LYS Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 521 LYS Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 599 LYS Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain D residue 1152 GLU Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 451 ARG Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 526 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain I residue 54 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 68 optimal weight: 3.9990 chunk 212 optimal weight: 0.7980 chunk 332 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 401 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 331 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 186 ASN C 799 ASN C1236 ASN D 545 HIS D 667 GLN D1259 GLN F 128 ASN F 472 GLN I 170 HIS I 196 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.215292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.135238 restraints weight = 42584.078| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.16 r_work: 0.3447 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36167 Z= 0.131 Angle : 0.550 11.985 49402 Z= 0.293 Chirality : 0.041 0.188 5634 Planarity : 0.004 0.043 6004 Dihedral : 18.909 179.619 6039 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.38 % Allowed : 18.20 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.13), residues: 4143 helix: 1.33 (0.13), residues: 1732 sheet: -0.84 (0.23), residues: 483 loop : -0.96 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 647 TYR 0.017 0.001 TYR D 631 PHE 0.019 0.001 PHE F 316 TRP 0.010 0.001 TRP C 183 HIS 0.010 0.001 HIS I 119 Details of bonding type rmsd covalent geometry : bond 0.00304 (36167) covalent geometry : angle 0.55038 (49402) hydrogen bonds : bond 0.03761 ( 1609) hydrogen bonds : angle 4.51681 ( 4501) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8286 Ramachandran restraints generated. 4143 Oldfield, 0 Emsley, 4143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8286 Ramachandran restraints generated. 4143 Oldfield, 0 Emsley, 4143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 360 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7132 (mtp85) REVERT: A 25 LYS cc_start: 0.8568 (mmtt) cc_final: 0.7921 (mtpp) REVERT: A 122 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8111 (mp0) REVERT: B 17 GLU cc_start: 0.7772 (tt0) cc_final: 0.6126 (mp0) REVERT: B 65 LEU cc_start: 0.7987 (mm) cc_final: 0.7388 (pt) REVERT: B 127 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7470 (mm110) REVERT: B 214 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: C 20 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.6921 (pp30) REVERT: C 41 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7435 (mt0) REVERT: C 160 ASP cc_start: 0.6756 (t70) cc_final: 0.6377 (t0) REVERT: C 340 ASP cc_start: 0.7402 (t0) cc_final: 0.7179 (t70) REVERT: C 365 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7644 (mm-30) REVERT: C 369 MET cc_start: 0.7558 (tmm) cc_final: 0.7294 (tmm) REVERT: C 370 MET cc_start: 0.6831 (OUTLIER) cc_final: 0.6315 (mmp) REVERT: C 441 GLU cc_start: 0.7504 (pm20) cc_final: 0.7147 (pm20) REVERT: C 542 ARG cc_start: 0.7701 (mtm-85) cc_final: 0.6894 (tmm-80) REVERT: C 625 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7473 (pm20) REVERT: C 951 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.6673 (tmm) REVERT: C 1040 ASP cc_start: 0.6327 (m-30) cc_final: 0.6103 (m-30) REVERT: C 1233 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8724 (mt) REVERT: C 1242 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8713 (mttp) REVERT: C 1319 MET cc_start: 0.8766 (tpp) cc_final: 0.8492 (tpp) REVERT: D 18 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7514 (m-30) REVERT: D 69 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7713 (tt0) REVERT: D 129 ASP cc_start: 0.7630 (t70) cc_final: 0.7157 (t0) REVERT: D 190 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7368 (mttt) REVERT: D 200 GLN cc_start: 0.6727 (tp40) cc_final: 0.6491 (mp10) REVERT: D 321 LYS cc_start: 0.7693 (mmpt) cc_final: 0.7464 (tppt) REVERT: D 414 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7735 (tp30) REVERT: D 416 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7849 (pt) REVERT: D 545 HIS cc_start: 0.8162 (OUTLIER) cc_final: 0.7938 (p-80) REVERT: D 599 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8486 (ttpp) REVERT: D 648 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: D 664 ILE cc_start: 0.6578 (OUTLIER) cc_final: 0.6291 (tt) REVERT: D 707 ILE cc_start: 0.6427 (OUTLIER) cc_final: 0.6000 (tt) REVERT: D 785 ASP cc_start: 0.7513 (t70) cc_final: 0.6999 (m-30) REVERT: D 805 GLN cc_start: 0.7691 (tp40) cc_final: 0.7201 (tt0) REVERT: D 1095 MET cc_start: 0.3333 (tpt) cc_final: 0.3036 (tpt) REVERT: D 1138 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6820 (mt) REVERT: D 1369 ARG cc_start: 0.5221 (mtm110) cc_final: 0.4749 (mtp-110) REVERT: D 1370 MET cc_start: 0.6308 (OUTLIER) cc_final: 0.5454 (mmm) REVERT: E 47 THR cc_start: 0.7789 (OUTLIER) cc_final: 0.7318 (p) REVERT: E 56 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6824 (mp0) REVERT: F 365 MET cc_start: 0.6842 (tpt) cc_final: 0.6545 (tpp) REVERT: F 413 MET cc_start: 0.7588 (mtm) cc_final: 0.7282 (mtp) REVERT: F 451 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7992 (ttp80) REVERT: F 474 MET cc_start: 0.7417 (mtp) cc_final: 0.6814 (mmt) REVERT: F 541 ARG cc_start: 0.6363 (OUTLIER) cc_final: 0.5646 (ttp80) REVERT: F 561 MET cc_start: 0.6575 (mtp) cc_final: 0.6311 (mtt) REVERT: F 591 GLU cc_start: 0.6154 (OUTLIER) cc_final: 0.5889 (pt0) REVERT: F 606 VAL cc_start: 0.4838 (p) cc_final: 0.4596 (t) REVERT: H 50 LEU cc_start: 0.3247 (OUTLIER) cc_final: 0.2607 (pt) REVERT: H 162 MET cc_start: 0.4664 (mtp) cc_final: 0.3742 (tpp) REVERT: H 209 VAL cc_start: 0.3816 (t) cc_final: 0.3245 (m) REVERT: H 210 ARG cc_start: 0.1471 (ttt90) cc_final: 0.1137 (mmm-85) REVERT: I 69 GLU cc_start: 0.1573 (OUTLIER) cc_final: 0.0992 (pt0) REVERT: I 162 MET cc_start: 0.5129 (mmm) cc_final: 0.4763 (mmm) REVERT: I 207 ARG cc_start: 0.4557 (mmt180) cc_final: 0.4252 (mtp85) outliers start: 120 outliers final: 34 residues processed: 431 average time/residue: 0.8505 time to fit residues: 429.6475 Evaluate side-chains 405 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 343 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 625 GLU Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1242 LYS Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 599 LYS Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 273 MET Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 451 ARG Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 541 ARG Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 591 GLU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 69 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 85 optimal weight: 2.9990 chunk 389 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 340 optimal weight: 20.0000 chunk 385 optimal weight: 20.0000 chunk 115 optimal weight: 2.9990 chunk 285 optimal weight: 10.0000 chunk 338 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 186 ASN C1236 ASN D 186 GLN D 545 HIS D 667 GLN D 897 HIS E 15 ASN F 128 ASN F 357 GLN F 545 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.211694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.134049 restraints weight = 42112.079| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.80 r_work: 0.3340 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 36167 Z= 0.256 Angle : 0.668 11.040 49402 Z= 0.353 Chirality : 0.046 0.267 5634 Planarity : 0.005 0.063 6004 Dihedral : 18.967 176.831 6036 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.28 % Allowed : 18.87 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.13), residues: 4143 helix: 1.02 (0.12), residues: 1731 sheet: -0.80 (0.23), residues: 487 loop : -0.98 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1246 TYR 0.025 0.002 TYR D 631 PHE 0.029 0.002 PHE D 57 TRP 0.023 0.002 TRP C 183 HIS 0.012 0.002 HIS C 526 Details of bonding type rmsd covalent geometry : bond 0.00630 (36167) covalent geometry : angle 0.66833 (49402) hydrogen bonds : bond 0.04850 ( 1609) hydrogen bonds : angle 4.81651 ( 4501) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8286 Ramachandran restraints generated. 4143 Oldfield, 0 Emsley, 4143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8286 Ramachandran restraints generated. 4143 Oldfield, 0 Emsley, 4143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 355 time to evaluate : 1.367 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 12 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7194 (mtp85) REVERT: A 25 LYS cc_start: 0.8612 (mmtt) cc_final: 0.8115 (mtpp) REVERT: A 215 GLU cc_start: 0.8214 (tt0) cc_final: 0.8011 (tm-30) REVERT: B 58 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7611 (mt-10) REVERT: B 65 LEU cc_start: 0.8104 (mm) cc_final: 0.7413 (pt) REVERT: B 127 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7479 (mm110) REVERT: B 214 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: C 20 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.6927 (pp30) REVERT: C 39 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7848 (pt) REVERT: C 41 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7246 (mt0) REVERT: C 160 ASP cc_start: 0.6932 (t70) cc_final: 0.6465 (t0) REVERT: C 542 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.6897 (tmm-80) REVERT: C 950 GLU cc_start: 0.7816 (tp30) cc_final: 0.7446 (tp30) REVERT: C 951 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.6706 (tmm) REVERT: C 1066 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8541 (mmm) REVERT: C 1233 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8699 (mt) REVERT: C 1242 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8736 (mttp) REVERT: D 18 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7566 (m-30) REVERT: D 69 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7974 (mt-10) REVERT: D 200 GLN cc_start: 0.6726 (tp40) cc_final: 0.6413 (mp10) REVERT: D 321 LYS cc_start: 0.8112 (mmpt) cc_final: 0.7889 (tppt) REVERT: D 414 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7755 (tt0) REVERT: D 453 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8610 (m) REVERT: D 648 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: D 707 ILE cc_start: 0.6799 (OUTLIER) cc_final: 0.6306 (tp) REVERT: D 785 ASP cc_start: 0.7600 (t70) cc_final: 0.7352 (t70) REVERT: D 805 GLN cc_start: 0.7870 (tp40) cc_final: 0.7256 (tt0) REVERT: D 867 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7075 (tm-30) REVERT: D 1189 MET cc_start: 0.6310 (mmm) cc_final: 0.5906 (mmm) REVERT: D 1278 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6473 (pp20) REVERT: D 1369 ARG cc_start: 0.5356 (mtm110) cc_final: 0.4708 (mtp-110) REVERT: D 1370 MET cc_start: 0.6298 (OUTLIER) cc_final: 0.5676 (mpm) REVERT: E 47 THR cc_start: 0.7809 (OUTLIER) cc_final: 0.7275 (p) REVERT: E 56 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6907 (mp0) REVERT: F 365 MET cc_start: 0.6894 (tpt) cc_final: 0.6642 (tpp) REVERT: F 413 MET cc_start: 0.7617 (mtm) cc_final: 0.7244 (mtp) REVERT: F 451 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8497 (tmm160) REVERT: F 474 MET cc_start: 0.7461 (mtp) cc_final: 0.6988 (mmt) REVERT: F 545 HIS cc_start: 0.6596 (t70) cc_final: 0.6381 (t70) REVERT: F 567 MET cc_start: 0.7216 (tpt) cc_final: 0.6982 (tpp) REVERT: F 568 ASN cc_start: 0.7023 (t0) cc_final: 0.6822 (t0) REVERT: F 606 VAL cc_start: 0.4739 (p) cc_final: 0.4531 (t) REVERT: H 50 LEU cc_start: 0.3191 (OUTLIER) cc_final: 0.2848 (mp) REVERT: H 209 VAL cc_start: 0.4128 (t) cc_final: 0.3510 (m) REVERT: I 69 GLU cc_start: 0.1543 (OUTLIER) cc_final: 0.0980 (pt0) REVERT: I 162 MET cc_start: 0.5118 (mmm) cc_final: 0.4767 (mmm) outliers start: 152 outliers final: 68 residues processed: 451 average time/residue: 0.8265 time to fit residues: 440.2189 Evaluate side-chains 418 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 328 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 407 ARG Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 625 GLU Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1242 LYS Chi-restraints excluded: chain C residue 1324 ASN Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 521 LYS Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 599 LYS Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1188 GLU Chi-restraints excluded: chain D residue 1278 GLU Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 451 ARG Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 69 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 371 optimal weight: 0.0060 chunk 235 optimal weight: 0.7980 chunk 142 optimal weight: 0.5980 chunk 146 optimal weight: 2.9990 chunk 386 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 288 optimal weight: 9.9990 chunk 309 optimal weight: 2.9990 chunk 388 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 310 optimal weight: 2.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 799 ASN C1236 ASN D 186 GLN D 545 HIS D 667 GLN E 15 ASN F 128 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.214468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.137448 restraints weight = 42296.000| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.89 r_work: 0.3384 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36167 Z= 0.135 Angle : 0.552 10.982 49402 Z= 0.293 Chirality : 0.041 0.194 5634 Planarity : 0.004 0.045 6004 Dihedral : 18.788 175.694 6036 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.60 % Allowed : 20.11 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.13), residues: 4143 helix: 1.33 (0.13), residues: 1735 sheet: -0.68 (0.23), residues: 489 loop : -0.84 (0.14), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 647 TYR 0.016 0.001 TYR D 631 PHE 0.021 0.001 PHE F 316 TRP 0.012 0.001 TRP C 183 HIS 0.009 0.001 HIS I 119 Details of bonding type rmsd covalent geometry : bond 0.00313 (36167) covalent geometry : angle 0.55198 (49402) hydrogen bonds : bond 0.03768 ( 1609) hydrogen bonds : angle 4.53255 ( 4501) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8286 Ramachandran restraints generated. 4143 Oldfield, 0 Emsley, 4143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8286 Ramachandran restraints generated. 4143 Oldfield, 0 Emsley, 4143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 337 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7162 (mtp85) REVERT: A 25 LYS cc_start: 0.8489 (mmtt) cc_final: 0.8058 (mtpp) REVERT: A 172 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8624 (mp) REVERT: B 58 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7484 (mt-10) REVERT: B 65 LEU cc_start: 0.8079 (mm) cc_final: 0.7342 (pt) REVERT: B 71 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7189 (mtpm) REVERT: B 127 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7528 (mm-40) REVERT: B 214 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: C 20 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.6995 (pp30) REVERT: C 39 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7574 (pt) REVERT: C 41 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7286 (mt0) REVERT: C 160 ASP cc_start: 0.6897 (t70) cc_final: 0.6452 (t0) REVERT: C 315 MET cc_start: 0.4889 (OUTLIER) cc_final: 0.4616 (pmt) REVERT: C 370 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.6471 (mmp) REVERT: C 441 GLU cc_start: 0.7633 (pm20) cc_final: 0.7308 (pm20) REVERT: C 625 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: C 738 GLU cc_start: 0.7898 (tp30) cc_final: 0.7407 (mt-10) REVERT: C 951 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.6598 (tmm) REVERT: C 968 GLU cc_start: 0.3879 (mm-30) cc_final: 0.2997 (pp20) REVERT: C 1233 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8714 (mt) REVERT: D 69 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7898 (mt-10) REVERT: D 81 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.6920 (ptp90) REVERT: D 129 ASP cc_start: 0.7560 (t70) cc_final: 0.7118 (t0) REVERT: D 151 MET cc_start: 0.3262 (OUTLIER) cc_final: 0.2929 (tmt) REVERT: D 289 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7524 (m-30) REVERT: D 414 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7828 (tp30) REVERT: D 416 ILE cc_start: 0.8248 (tt) cc_final: 0.7930 (pp) REVERT: D 604 MET cc_start: 0.9144 (ttp) cc_final: 0.8943 (ttm) REVERT: D 648 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: D 785 ASP cc_start: 0.7572 (t70) cc_final: 0.7005 (m-30) REVERT: D 805 GLN cc_start: 0.7734 (tp40) cc_final: 0.7235 (tt0) REVERT: D 867 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7046 (tm-30) REVERT: D 1138 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6751 (mt) REVERT: D 1278 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6286 (pp20) REVERT: D 1298 VAL cc_start: 0.4700 (OUTLIER) cc_final: 0.4475 (m) REVERT: D 1369 ARG cc_start: 0.5265 (mtm110) cc_final: 0.4632 (mtp-110) REVERT: D 1370 MET cc_start: 0.6294 (mpp) cc_final: 0.5675 (mpm) REVERT: E 47 THR cc_start: 0.7781 (OUTLIER) cc_final: 0.7339 (p) REVERT: E 56 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6895 (mp0) REVERT: F 297 MET cc_start: 0.0557 (OUTLIER) cc_final: 0.0312 (mtp) REVERT: F 413 MET cc_start: 0.7495 (mtm) cc_final: 0.7199 (mtp) REVERT: F 451 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8076 (ttp-110) REVERT: F 474 MET cc_start: 0.7376 (mtp) cc_final: 0.6930 (mmt) REVERT: F 545 HIS cc_start: 0.6548 (t70) cc_final: 0.6313 (t70) REVERT: F 567 MET cc_start: 0.7130 (tpt) cc_final: 0.6904 (tpp) REVERT: F 606 VAL cc_start: 0.4646 (p) cc_final: 0.4435 (t) REVERT: H 1 MET cc_start: 0.1521 (tpp) cc_final: 0.1308 (ttt) REVERT: H 50 LEU cc_start: 0.3339 (OUTLIER) cc_final: 0.2981 (mp) REVERT: H 162 MET cc_start: 0.4393 (mtp) cc_final: 0.3774 (tpp) REVERT: H 209 VAL cc_start: 0.3838 (t) cc_final: 0.2961 (m) REVERT: I 69 GLU cc_start: 0.1416 (OUTLIER) cc_final: 0.0877 (pt0) REVERT: I 162 MET cc_start: 0.5229 (mmm) cc_final: 0.4982 (mmm) outliers start: 128 outliers final: 45 residues processed: 423 average time/residue: 0.7602 time to fit residues: 381.0574 Evaluate side-chains 393 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 322 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 407 ARG Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 625 GLU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain D residue 1278 GLU Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 451 ARG Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 69 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 343 optimal weight: 5.9990 chunk 324 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 392 optimal weight: 9.9990 chunk 383 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 339 optimal weight: 6.9990 chunk 310 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN C 799 ASN C1236 ASN D 667 GLN D 716 GLN D 897 HIS F 128 ASN H 109 ASN H 120 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.211080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.131231 restraints weight = 42131.197| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.24 r_work: 0.3321 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 36167 Z= 0.239 Angle : 0.648 12.062 49402 Z= 0.342 Chirality : 0.045 0.245 5634 Planarity : 0.005 0.058 6004 Dihedral : 18.849 173.960 6036 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.77 % Allowed : 20.53 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.13), residues: 4143 helix: 1.04 (0.12), residues: 1742 sheet: -0.82 (0.22), residues: 500 loop : -0.89 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1156 TYR 0.021 0.002 TYR D 631 PHE 0.030 0.002 PHE C 337 TRP 0.024 0.002 TRP C 183 HIS 0.013 0.002 HIS C 526 Details of bonding type rmsd covalent geometry : bond 0.00586 (36167) covalent geometry : angle 0.64757 (49402) hydrogen bonds : bond 0.04671 ( 1609) hydrogen bonds : angle 4.74935 ( 4501) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8286 Ramachandran restraints generated. 4143 Oldfield, 0 Emsley, 4143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8286 Ramachandran restraints generated. 4143 Oldfield, 0 Emsley, 4143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 321 time to evaluate : 1.320 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 12 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7302 (mtp85) REVERT: A 25 LYS cc_start: 0.8603 (mmtt) cc_final: 0.8214 (mtpp) REVERT: A 172 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8796 (mp) REVERT: A 204 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: B 25 LYS cc_start: 0.8430 (mtpm) cc_final: 0.8123 (mtpt) REVERT: B 58 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7730 (mt-10) REVERT: B 65 LEU cc_start: 0.8119 (mm) cc_final: 0.7415 (pt) REVERT: B 71 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7331 (mtpm) REVERT: B 127 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7545 (mm-40) REVERT: B 143 ARG cc_start: 0.7629 (mpp-170) cc_final: 0.7341 (mpp-170) REVERT: B 214 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: C 20 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.6965 (pp30) REVERT: C 39 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7779 (pt) REVERT: C 41 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7219 (mt0) REVERT: C 160 ASP cc_start: 0.6882 (t70) cc_final: 0.6404 (t0) REVERT: C 200 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6773 (mtm110) REVERT: C 202 ARG cc_start: 0.7237 (mtm110) cc_final: 0.6889 (mtp180) REVERT: C 300 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.6841 (m-30) REVERT: C 315 MET cc_start: 0.4993 (OUTLIER) cc_final: 0.4720 (pmm) REVERT: C 370 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6522 (mmp) REVERT: C 546 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7655 (mm-30) REVERT: C 951 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.6729 (tmm) REVERT: C 968 GLU cc_start: 0.3819 (mm-30) cc_final: 0.3086 (pp20) REVERT: C 1026 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7076 (mp0) REVERT: C 1066 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8583 (mmm) REVERT: C 1171 ARG cc_start: 0.8258 (ttp-110) cc_final: 0.8039 (ttp-170) REVERT: C 1233 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8703 (mt) REVERT: D 18 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7609 (m-30) REVERT: D 69 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8142 (mt-10) REVERT: D 129 ASP cc_start: 0.7684 (t70) cc_final: 0.7203 (t0) REVERT: D 289 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7656 (m-30) REVERT: D 414 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7946 (tp30) REVERT: D 453 VAL cc_start: 0.8911 (OUTLIER) cc_final: 0.8631 (m) REVERT: D 648 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: D 785 ASP cc_start: 0.7659 (t70) cc_final: 0.7412 (t70) REVERT: D 805 GLN cc_start: 0.7972 (tp40) cc_final: 0.7367 (tt0) REVERT: D 867 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7186 (tm-30) REVERT: D 1095 MET cc_start: 0.2843 (tpt) cc_final: 0.1295 (ttm) REVERT: D 1298 VAL cc_start: 0.4640 (OUTLIER) cc_final: 0.4410 (m) REVERT: D 1369 ARG cc_start: 0.5537 (mtm110) cc_final: 0.4832 (mtp-110) REVERT: D 1370 MET cc_start: 0.6459 (mpp) cc_final: 0.5799 (mpm) REVERT: E 47 THR cc_start: 0.7977 (OUTLIER) cc_final: 0.7387 (p) REVERT: E 56 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6985 (mp0) REVERT: F 297 MET cc_start: 0.0750 (ptm) cc_final: 0.0464 (mtm) REVERT: F 413 MET cc_start: 0.7675 (mtm) cc_final: 0.7361 (mtp) REVERT: F 451 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8514 (tmm160) REVERT: F 474 MET cc_start: 0.7527 (mtp) cc_final: 0.7134 (mmt) REVERT: F 567 MET cc_start: 0.6979 (tpt) cc_final: 0.6778 (tpp) REVERT: F 606 VAL cc_start: 0.4762 (p) cc_final: 0.4554 (t) REVERT: H 1 MET cc_start: 0.1511 (tpp) cc_final: 0.1062 (ttm) REVERT: I 69 GLU cc_start: 0.1386 (OUTLIER) cc_final: 0.0831 (pt0) REVERT: I 71 MET cc_start: -0.0148 (tmm) cc_final: -0.0873 (tpt) REVERT: I 162 MET cc_start: 0.5330 (mmm) cc_final: 0.5018 (mmm) REVERT: I 207 ARG cc_start: 0.4931 (mmt180) cc_final: 0.4472 (mtp85) outliers start: 134 outliers final: 61 residues processed: 409 average time/residue: 0.8439 time to fit residues: 406.7585 Evaluate side-chains 397 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 311 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 613 ASN Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 451 ARG Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 69 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 170 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 416 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 356 optimal weight: 0.8980 chunk 349 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 98 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN C1236 ASN D 667 GLN D 897 HIS F 128 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.214211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.135790 restraints weight = 42221.599| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.33 r_work: 0.3405 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36167 Z= 0.128 Angle : 0.553 11.449 49402 Z= 0.293 Chirality : 0.041 0.319 5634 Planarity : 0.004 0.050 6004 Dihedral : 18.678 174.411 6034 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.21 % Favored : 96.77 % Rotamer: Outliers : 3.23 % Allowed : 21.41 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.13), residues: 4143 helix: 1.37 (0.13), residues: 1744 sheet: -0.66 (0.23), residues: 491 loop : -0.76 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1231 TYR 0.015 0.001 TYR D 631 PHE 0.021 0.001 PHE F 316 TRP 0.013 0.001 TRP C 183 HIS 0.009 0.001 HIS I 119 Details of bonding type rmsd covalent geometry : bond 0.00293 (36167) covalent geometry : angle 0.55324 (49402) hydrogen bonds : bond 0.03664 ( 1609) hydrogen bonds : angle 4.46813 ( 4501) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8286 Ramachandran restraints generated. 4143 Oldfield, 0 Emsley, 4143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8286 Ramachandran restraints generated. 4143 Oldfield, 0 Emsley, 4143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 326 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7250 (mtp85) REVERT: A 25 LYS cc_start: 0.8477 (mmtt) cc_final: 0.8217 (mtpp) REVERT: B 58 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7620 (mt-10) REVERT: B 60 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6993 (mt-10) REVERT: B 65 LEU cc_start: 0.8089 (mm) cc_final: 0.7361 (pt) REVERT: B 145 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7838 (ttpp) REVERT: B 214 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: C 20 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7010 (pp30) REVERT: C 41 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7173 (mt0) REVERT: C 160 ASP cc_start: 0.6850 (t70) cc_final: 0.6344 (t0) REVERT: C 202 ARG cc_start: 0.7159 (mtm110) cc_final: 0.6750 (mtp180) REVERT: C 365 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7791 (mm-30) REVERT: C 441 GLU cc_start: 0.7500 (pm20) cc_final: 0.7125 (pm20) REVERT: C 542 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.6844 (tpt170) REVERT: C 546 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7632 (mm-30) REVERT: C 601 ASP cc_start: 0.7403 (p0) cc_final: 0.7180 (p0) REVERT: C 738 GLU cc_start: 0.7839 (tp30) cc_final: 0.7376 (mt-10) REVERT: C 968 GLU cc_start: 0.3508 (mm-30) cc_final: 0.2782 (pp20) REVERT: C 1026 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7039 (mp0) REVERT: C 1233 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8751 (mt) REVERT: D 18 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7520 (m-30) REVERT: D 69 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7961 (mt-10) REVERT: D 129 ASP cc_start: 0.7495 (t70) cc_final: 0.7078 (t0) REVERT: D 151 MET cc_start: 0.3472 (OUTLIER) cc_final: 0.3173 (tmt) REVERT: D 218 THR cc_start: 0.8012 (m) cc_final: 0.7792 (p) REVERT: D 414 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7871 (tp30) REVERT: D 416 ILE cc_start: 0.8294 (tt) cc_final: 0.7990 (pp) REVERT: D 648 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: D 785 ASP cc_start: 0.7559 (t70) cc_final: 0.7009 (m-30) REVERT: D 805 GLN cc_start: 0.7791 (tp40) cc_final: 0.7299 (tm-30) REVERT: D 867 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7162 (tm-30) REVERT: D 1095 MET cc_start: 0.3050 (tpt) cc_final: 0.1466 (ttm) REVERT: D 1138 LEU cc_start: 0.7313 (tp) cc_final: 0.6779 (mt) REVERT: D 1298 VAL cc_start: 0.4604 (OUTLIER) cc_final: 0.4393 (m) REVERT: D 1370 MET cc_start: 0.6446 (mpp) cc_final: 0.5761 (mpm) REVERT: E 47 THR cc_start: 0.7762 (OUTLIER) cc_final: 0.7317 (p) REVERT: E 56 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6891 (mp0) REVERT: F 297 MET cc_start: 0.0679 (OUTLIER) cc_final: 0.0468 (mtm) REVERT: F 413 MET cc_start: 0.7631 (mtm) cc_final: 0.7383 (mtp) REVERT: F 437 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7436 (tm-30) REVERT: F 451 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8120 (ttp80) REVERT: F 474 MET cc_start: 0.7456 (mtp) cc_final: 0.7102 (mmt) REVERT: F 606 VAL cc_start: 0.4607 (p) cc_final: 0.4381 (t) REVERT: H 162 MET cc_start: 0.4272 (mtp) cc_final: 0.3812 (tpp) REVERT: I 66 MET cc_start: 0.0340 (OUTLIER) cc_final: 0.0132 (tpp) REVERT: I 69 GLU cc_start: 0.1352 (OUTLIER) cc_final: 0.0859 (pt0) REVERT: I 162 MET cc_start: 0.5289 (mmm) cc_final: 0.5008 (mmm) REVERT: I 207 ARG cc_start: 0.4935 (mmt180) cc_final: 0.4440 (tpt90) REVERT: I 210 ARG cc_start: 0.4076 (mmt90) cc_final: 0.3373 (ttt90) outliers start: 115 outliers final: 45 residues processed: 403 average time/residue: 0.7510 time to fit residues: 359.3329 Evaluate side-chains 373 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 310 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain F residue 451 ARG Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 66 MET Chi-restraints excluded: chain I residue 69 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 323 optimal weight: 3.9990 chunk 357 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 272 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 219 optimal weight: 0.9990 chunk 341 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN C1136 GLN C1236 ASN D 186 GLN D 477 GLN D 667 GLN D 897 HIS F 128 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.210261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.130253 restraints weight = 41877.490| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.25 r_work: 0.3350 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 36167 Z= 0.224 Angle : 0.640 11.029 49402 Z= 0.335 Chirality : 0.044 0.234 5634 Planarity : 0.005 0.055 6004 Dihedral : 18.748 173.666 6034 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.81 % Favored : 96.16 % Rotamer: Outliers : 3.15 % Allowed : 21.80 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.13), residues: 4143 helix: 1.14 (0.12), residues: 1737 sheet: -0.76 (0.23), residues: 507 loop : -0.80 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1156 TYR 0.021 0.002 TYR C1229 PHE 0.030 0.002 PHE C 337 TRP 0.027 0.002 TRP C 183 HIS 0.012 0.002 HIS C 526 Details of bonding type rmsd covalent geometry : bond 0.00546 (36167) covalent geometry : angle 0.64030 (49402) hydrogen bonds : bond 0.04520 ( 1609) hydrogen bonds : angle 4.66019 ( 4501) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8286 Ramachandran restraints generated. 4143 Oldfield, 0 Emsley, 4143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8286 Ramachandran restraints generated. 4143 Oldfield, 0 Emsley, 4143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 303 time to evaluate : 1.204 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 12 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7292 (mtp85) REVERT: A 25 LYS cc_start: 0.8502 (mmtt) cc_final: 0.8168 (mtpp) REVERT: B 58 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7624 (mt-10) REVERT: B 65 LEU cc_start: 0.8097 (mm) cc_final: 0.7341 (pt) REVERT: B 145 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7836 (ttpp) REVERT: C 20 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.6954 (pp30) REVERT: C 41 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7656 (mt0) REVERT: C 160 ASP cc_start: 0.6946 (t70) cc_final: 0.6434 (t0) REVERT: C 202 ARG cc_start: 0.7203 (mtm110) cc_final: 0.6807 (mtp180) REVERT: C 441 GLU cc_start: 0.7561 (pm20) cc_final: 0.7178 (pm20) REVERT: C 546 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7673 (mm-30) REVERT: C 738 GLU cc_start: 0.7921 (tp30) cc_final: 0.7390 (mt-10) REVERT: C 951 MET cc_start: 0.7486 (ttp) cc_final: 0.6588 (tmm) REVERT: C 968 GLU cc_start: 0.3806 (mm-30) cc_final: 0.2979 (pp20) REVERT: C 1026 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6966 (mp0) REVERT: C 1136 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7681 (mt0) REVERT: C 1171 ARG cc_start: 0.8178 (ttp-110) cc_final: 0.7956 (ttp-170) REVERT: C 1233 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8698 (mt) REVERT: D 69 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8038 (mt-10) REVERT: D 129 ASP cc_start: 0.7632 (t70) cc_final: 0.7136 (t0) REVERT: D 151 MET cc_start: 0.3865 (OUTLIER) cc_final: 0.3436 (tmt) REVERT: D 218 THR cc_start: 0.8073 (m) cc_final: 0.7855 (p) REVERT: D 414 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7889 (tp30) REVERT: D 648 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: D 785 ASP cc_start: 0.7622 (t70) cc_final: 0.7373 (t70) REVERT: D 805 GLN cc_start: 0.7935 (tp40) cc_final: 0.7362 (tt0) REVERT: D 867 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7160 (tm-30) REVERT: D 1095 MET cc_start: 0.2695 (tpt) cc_final: 0.1057 (ttm) REVERT: D 1138 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6769 (mt) REVERT: D 1278 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6782 (pm20) REVERT: D 1298 VAL cc_start: 0.4543 (OUTLIER) cc_final: 0.4323 (m) REVERT: D 1370 MET cc_start: 0.6433 (OUTLIER) cc_final: 0.5805 (mpm) REVERT: E 47 THR cc_start: 0.7918 (OUTLIER) cc_final: 0.7363 (p) REVERT: E 56 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6966 (mp0) REVERT: F 297 MET cc_start: 0.0660 (OUTLIER) cc_final: 0.0382 (mtm) REVERT: F 413 MET cc_start: 0.7613 (mtm) cc_final: 0.7308 (mtp) REVERT: F 437 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: F 451 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8476 (tmm160) REVERT: F 474 MET cc_start: 0.7421 (mtp) cc_final: 0.7129 (mmt) REVERT: H 162 MET cc_start: 0.4222 (mtp) cc_final: 0.4006 (ttp) REVERT: I 69 GLU cc_start: 0.1399 (OUTLIER) cc_final: 0.0825 (pt0) REVERT: I 140 LEU cc_start: 0.4512 (OUTLIER) cc_final: 0.4306 (mp) REVERT: I 162 MET cc_start: 0.5290 (mmm) cc_final: 0.5008 (mmm) outliers start: 112 outliers final: 58 residues processed: 382 average time/residue: 0.6527 time to fit residues: 297.2403 Evaluate side-chains 372 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 295 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 625 GLU Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1252 SER Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain D residue 1278 GLU Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain F residue 451 ARG Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 43 ASN Chi-restraints excluded: chain I residue 66 MET Chi-restraints excluded: chain I residue 69 GLU Chi-restraints excluded: chain I residue 140 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 9 optimal weight: 7.9990 chunk 327 optimal weight: 0.7980 chunk 221 optimal weight: 6.9990 chunk 395 optimal weight: 6.9990 chunk 206 optimal weight: 0.9980 chunk 344 optimal weight: 30.0000 chunk 401 optimal weight: 5.9990 chunk 276 optimal weight: 2.9990 chunk 189 optimal weight: 0.5980 chunk 338 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 GLN C1136 GLN C1236 ASN D 667 GLN D 897 HIS F 128 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.210872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.130640 restraints weight = 42249.480| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.32 r_work: 0.3363 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 36167 Z= 0.194 Angle : 0.619 17.139 49402 Z= 0.323 Chirality : 0.043 0.187 5634 Planarity : 0.005 0.053 6004 Dihedral : 18.703 174.241 6034 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.38 % Favored : 96.60 % Rotamer: Outliers : 2.93 % Allowed : 22.05 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.13), residues: 4143 helix: 1.14 (0.12), residues: 1738 sheet: -0.67 (0.23), residues: 483 loop : -0.80 (0.14), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 133 TYR 0.023 0.002 TYR D 144 PHE 0.026 0.002 PHE C 337 TRP 0.028 0.001 TRP C 183 HIS 0.010 0.001 HIS C 526 Details of bonding type rmsd covalent geometry : bond 0.00472 (36167) covalent geometry : angle 0.61876 (49402) hydrogen bonds : bond 0.04221 ( 1609) hydrogen bonds : angle 4.61050 ( 4501) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8286 Ramachandran restraints generated. 4143 Oldfield, 0 Emsley, 4143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8286 Ramachandran restraints generated. 4143 Oldfield, 0 Emsley, 4143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 304 time to evaluate : 1.334 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 12 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7248 (mtp85) REVERT: A 25 LYS cc_start: 0.8435 (mmtt) cc_final: 0.8131 (mtpp) REVERT: A 204 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: B 65 LEU cc_start: 0.8126 (mm) cc_final: 0.7392 (pt) REVERT: C 20 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.6967 (pp30) REVERT: C 41 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7664 (mt0) REVERT: C 160 ASP cc_start: 0.6942 (t70) cc_final: 0.6459 (t0) REVERT: C 180 ARG cc_start: 0.7939 (ttm170) cc_final: 0.7656 (ttp80) REVERT: C 202 ARG cc_start: 0.7162 (mtm110) cc_final: 0.6770 (mtp180) REVERT: C 284 LEU cc_start: 0.6047 (OUTLIER) cc_final: 0.5718 (tp) REVERT: C 300 ASP cc_start: 0.7250 (OUTLIER) cc_final: 0.6992 (m-30) REVERT: C 441 GLU cc_start: 0.7533 (pm20) cc_final: 0.7130 (pm20) REVERT: C 492 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7739 (ptt) REVERT: C 546 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7664 (mm-30) REVERT: C 601 ASP cc_start: 0.7647 (p0) cc_final: 0.7380 (p0) REVERT: C 738 GLU cc_start: 0.7833 (tp30) cc_final: 0.7352 (mt-10) REVERT: C 951 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.7073 (mtp) REVERT: C 968 GLU cc_start: 0.3568 (mm-30) cc_final: 0.2818 (pp20) REVERT: C 1026 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6985 (mp0) REVERT: C 1171 ARG cc_start: 0.8139 (ttp-110) cc_final: 0.7923 (ttp-170) REVERT: C 1233 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8707 (mt) REVERT: D 18 ASP cc_start: 0.7887 (m-30) cc_final: 0.7400 (m-30) REVERT: D 69 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8013 (mt-10) REVERT: D 129 ASP cc_start: 0.7585 (t70) cc_final: 0.7128 (t0) REVERT: D 151 MET cc_start: 0.3861 (OUTLIER) cc_final: 0.3456 (tmt) REVERT: D 218 THR cc_start: 0.8045 (m) cc_final: 0.7827 (p) REVERT: D 414 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7877 (tp30) REVERT: D 453 VAL cc_start: 0.8863 (OUTLIER) cc_final: 0.8645 (m) REVERT: D 648 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: D 785 ASP cc_start: 0.7591 (t70) cc_final: 0.7355 (t70) REVERT: D 805 GLN cc_start: 0.7912 (tp40) cc_final: 0.7318 (tt0) REVERT: D 867 GLN cc_start: 0.8092 (mm-40) cc_final: 0.7141 (tm-30) REVERT: D 1095 MET cc_start: 0.2584 (tpt) cc_final: 0.0904 (ttm) REVERT: D 1138 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6760 (mt) REVERT: D 1278 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6775 (pm20) REVERT: D 1298 VAL cc_start: 0.4355 (OUTLIER) cc_final: 0.4102 (m) REVERT: D 1370 MET cc_start: 0.6444 (mpp) cc_final: 0.5817 (mpm) REVERT: E 47 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7372 (p) REVERT: E 56 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6942 (mp0) REVERT: F 297 MET cc_start: 0.0734 (OUTLIER) cc_final: 0.0458 (mtm) REVERT: F 413 MET cc_start: 0.7598 (mtm) cc_final: 0.7309 (mtp) REVERT: F 437 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7412 (tm-30) REVERT: F 451 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8244 (tmm160) REVERT: F 474 MET cc_start: 0.7363 (mtp) cc_final: 0.7108 (mmt) REVERT: I 69 GLU cc_start: 0.1459 (OUTLIER) cc_final: 0.0960 (pt0) REVERT: I 207 ARG cc_start: 0.4936 (mmt180) cc_final: 0.4454 (tpt-90) outliers start: 104 outliers final: 58 residues processed: 378 average time/residue: 0.7529 time to fit residues: 337.4574 Evaluate side-chains 378 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 299 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 625 GLU Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1252 SER Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain D residue 1278 GLU Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain F residue 451 ARG Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 43 ASN Chi-restraints excluded: chain I residue 69 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 165 optimal weight: 0.5980 chunk 199 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 282 optimal weight: 4.9990 chunk 319 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 273 optimal weight: 0.0570 chunk 295 optimal weight: 8.9990 chunk 297 optimal weight: 4.9990 chunk 402 optimal weight: 20.0000 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN ** C1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN D 186 GLN D 667 GLN D 897 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.214110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.137148 restraints weight = 42094.656| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.73 r_work: 0.3418 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36167 Z= 0.126 Angle : 0.563 15.576 49402 Z= 0.293 Chirality : 0.041 0.153 5634 Planarity : 0.004 0.052 6004 Dihedral : 18.556 174.768 6031 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.57 % Favored : 96.40 % Rotamer: Outliers : 2.22 % Allowed : 22.95 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.13), residues: 4143 helix: 1.39 (0.13), residues: 1752 sheet: -0.35 (0.24), residues: 460 loop : -0.69 (0.14), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 200 TYR 0.023 0.001 TYR D 144 PHE 0.020 0.001 PHE F 316 TRP 0.018 0.001 TRP C 183 HIS 0.009 0.001 HIS I 119 Details of bonding type rmsd covalent geometry : bond 0.00292 (36167) covalent geometry : angle 0.56313 (49402) hydrogen bonds : bond 0.03587 ( 1609) hydrogen bonds : angle 4.41059 ( 4501) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19752.17 seconds wall clock time: 334 minutes 58.66 seconds (20098.66 seconds total)