Starting phenix.real_space_refine on Mon Jul 6 12:23:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jo2_36453/07_2026/8jo2_36453_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jo2_36453/07_2026/8jo2_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jo2_36453/07_2026/8jo2_36453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jo2_36453/07_2026/8jo2_36453.map" model { file = "/net/cci-nas-00/data/ceres_data/8jo2_36453/07_2026/8jo2_36453_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jo2_36453/07_2026/8jo2_36453_neut.cif" } 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-dev-6108/lib/python3.11/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: 6.29, per 1000 atoms: 0.18 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: 2.39 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 3.56 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: 7.39 Time building geometry restraints manager: 3.26 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: 46901 2.35 - 4.70: 2298 4.70 - 7.04: 168 7.04 - 9.39: 26 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=" C PRO A 52 " pdb=" CA PRO A 52 " pdb=" CB PRO A 52 " ideal model delta sigma weight residual 110.85 102.27 8.58 1.41e+00 5.03e-01 3.70e+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: 5065 0.103 - 0.206: 515 0.206 - 0.309: 47 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: 6.750 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: 0.030 Extract box with map and model: 0.740 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 30.760 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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= 0.569 Angle : 1.063 11.740 49402 Z= 0.703 Chirality : 0.065 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 are 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/Z covalent geometry : bond 0.01060 / 0.57 (36167) covalent geometry : angle 1.06350 / 0.70 (49402) hydrogen bonds : bond 0.15248 / 16.85 ( 1609) hydrogen bonds : angle 7.39701 / 9.38 ( 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 : 1.144 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: 0.8648 (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: 0.7555 time to fit residues: 649.1386 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 : 1.286 ------------------------------------------------------------------------------- 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... A 75 GLN A 84 ASN A 137 ASN B 18 GLN B 227 GLN C 604 HIS C 658 GLN C 659 GLN C1038 GLN C1134 GLN C1209 GLN C1220 GLN C1236 ASN D 45 ASN D 157 GLN D 164 GLN D 232 ASN D 294 ASN D 545 HIS D 667 GLN D 929 GLN E 15 ASN E 61 ASN F 128 ASN F 129 GLN F 271 ASN F 309 ASN ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 GLN F 437 GLN F 472 GLN F 600 HIS I 193 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.217373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.141823 restraints weight = 43457.219| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.58 r_work: 0.3504 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 36167 Z= 0.167 Angle : 0.686 9.593 49402 Z= 0.369 Chirality : 0.047 0.285 5634 Planarity : 0.005 0.046 6004 Dihedral : 19.637 178.041 6059 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.90 % Allowed : 13.87 % Favored : 83.23 % 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 are not related in a simple way. whole: -1.06 (0.13), residues: 4143 helix: 0.32 (0.12), residues: 1717 sheet: -1.30 (0.22), residues: 483 loop : -1.45 (0.13), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C1301 TYR 0.023 0.002 TYR H 25 PHE 0.033 0.002 PHE H 62 TRP 0.008 0.001 TRP F 434 HIS 0.007 0.001 HIS C1116 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (36167) covalent geometry : angle 0.68614 / 0.37 (49402) hydrogen bonds : bond 0.05315 / 5.72 ( 1609) hydrogen bonds : angle 5.45310 / 6.90 ( 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 480 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 377 time to evaluate : 1.293 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: 0.7402 (ttp80) cc_final: 0.6993 (tpp-160) REVERT: A 122 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: A 183 ILE cc_start: 0.8213 (tt) cc_final: 0.7921 (mt) REVERT: A 219 ARG cc_start: 0.8493 (mtt-85) cc_final: 0.7404 (mmp-170) REVERT: B 17 GLU cc_start: 0.7573 (tt0) cc_final: 0.6107 (mp0) REVERT: B 65 LEU cc_start: 0.7775 (mm) cc_final: 0.7222 (pt) REVERT: C 37 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7701 (mtmm) REVERT: C 340 ASP cc_start: 0.7597 (t0) cc_final: 0.7149 (t0) REVERT: C 403 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7787 (ttp) REVERT: C 492 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7950 (ptt) REVERT: C 542 ARG cc_start: 0.7860 (mtm-85) cc_final: 0.6785 (tmm-80) REVERT: C 641 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7130 (mt-10) REVERT: C 876 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8073 (mm-30) REVERT: C 947 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7127 (tt0) REVERT: C 1040 ASP cc_start: 0.5951 (m-30) cc_final: 0.5569 (m-30) REVERT: C 1230 MET cc_start: 0.8929 (ttm) cc_final: 0.8679 (ttp) REVERT: C 1233 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8663 (mt) REVERT: D 69 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7818 (mt-10) REVERT: D 77 ARG cc_start: 0.7062 (mtm110) cc_final: 0.6456 (mtm110) REVERT: D 81 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.6985 (ptp90) REVERT: D 200 GLN cc_start: 0.6995 (OUTLIER) cc_final: 0.6539 (mp10) REVERT: D 418 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8453 (mt-10) REVERT: D 725 MET cc_start: 0.8857 (mtt) cc_final: 0.8556 (mtm) REVERT: D 736 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.7759 (mt0) REVERT: D 812 ASP cc_start: 0.8328 (m-30) cc_final: 0.8052 (t0) REVERT: D 867 GLN cc_start: 0.8102 (mm110) cc_final: 0.7008 (tm-30) REVERT: D 1188 GLU cc_start: 0.6663 (tt0) cc_final: 0.6404 (mp0) REVERT: E 35 LYS cc_start: 0.7884 (ptpt) cc_final: 0.7658 (ptpp) REVERT: E 47 THR cc_start: 0.8030 (m) cc_final: 0.7353 (p) REVERT: E 56 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7026 (mp0) REVERT: F 100 MET cc_start: 0.7727 (mtt) cc_final: 0.7409 (mtp) REVERT: F 322 MET cc_start: 0.1605 (tpt) cc_final: 0.0863 (mtm) REVERT: F 451 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7707 (ttp80) REVERT: F 526 THR cc_start: 0.8036 (OUTLIER) cc_final: 0.7755 (p) REVERT: F 591 GLU cc_start: 0.5421 (OUTLIER) cc_final: 0.5159 (pt0) REVERT: H 18 LEU cc_start: 0.2886 (mm) cc_final: 0.2558 (tp) REVERT: H 162 MET cc_start: 0.4977 (mtp) cc_final: 0.4489 (mtp) REVERT: I 71 MET cc_start: -0.0446 (tmm) cc_final: -0.0703 (tpp) REVERT: I 210 ARG cc_start: 0.3948 (mmm160) cc_final: 0.2965 (mmm-85) outliers start: 103 outliers final: 30 residues processed: 443 average time/residue: 0.7778 time to fit residues: 403.2315 Evaluate side-chains 384 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 339 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 876 GLU Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 892 GLU 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 81 ARG Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 684 ASP Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1148 ARG Chi-restraints excluded: chain D residue 1152 GLU Chi-restraints excluded: chain D residue 1177 ILE 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 485 GLU Chi-restraints excluded: chain F residue 526 THR Chi-restraints excluded: chain F residue 539 SER Chi-restraints excluded: chain F residue 548 LEU Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 591 GLU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 66 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 308 optimal weight: 9.9990 chunk 193 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 417 optimal weight: 4.9990 chunk 300 optimal weight: 9.9990 chunk 187 optimal weight: 0.1980 chunk 216 optimal weight: 0.5980 chunk 137 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 248 optimal weight: 0.0770 chunk 170 optimal weight: 1.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN B 75 GLN C 518 ASN C 618 GLN C 658 GLN C1038 GLN C1236 ASN D 545 HIS D 667 GLN D 805 GLN D 897 HIS E 15 ASN E 61 ASN F 128 ASN F 271 ASN F 362 ASN F 383 ASN F 469 GLN F 589 GLN I 120 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.217279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.143002 restraints weight = 43145.815| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.71 r_work: 0.3510 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36167 Z= 0.129 Angle : 0.597 9.828 49402 Z= 0.321 Chirality : 0.044 0.258 5634 Planarity : 0.004 0.044 6004 Dihedral : 19.516 179.899 6044 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.67 % Allowed : 16.93 % 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 are not related in a simple way. whole: -0.53 (0.13), residues: 4143 helix: 0.81 (0.12), residues: 1729 sheet: -1.14 (0.23), residues: 485 loop : -1.19 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1301 TYR 0.019 0.001 TYR H 25 PHE 0.024 0.002 PHE H 62 TRP 0.008 0.001 TRP C 183 HIS 0.008 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (36167) covalent geometry : angle 0.59662 / 0.32 (49402) hydrogen bonds : bond 0.04394 / 4.71 ( 1609) hydrogen bonds : angle 4.99649 / 6.32 ( 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 456 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 361 time to evaluate : 0.963 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 122 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: B 17 GLU cc_start: 0.7629 (tt0) cc_final: 0.6164 (mp0) REVERT: B 65 LEU cc_start: 0.7779 (mm) cc_final: 0.7225 (pt) REVERT: C 20 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.6672 (pp30) REVERT: C 41 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7489 (mt0) REVERT: C 160 ASP cc_start: 0.6606 (t70) cc_final: 0.6299 (t0) REVERT: C 183 TRP cc_start: 0.8162 (m-10) cc_final: 0.7939 (m-10) REVERT: C 340 ASP cc_start: 0.7487 (t0) cc_final: 0.7075 (t0) REVERT: C 403 MET cc_start: 0.8109 (tmm) cc_final: 0.7897 (ttp) REVERT: C 407 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6688 (mtm-85) REVERT: C 492 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.8022 (ptt) REVERT: C 542 ARG cc_start: 0.7882 (mtm-85) cc_final: 0.6899 (tmm-80) REVERT: C 641 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7071 (mt-10) REVERT: C 947 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7066 (tt0) REVERT: C 951 MET cc_start: 0.7117 (mtm) cc_final: 0.6606 (tmm) REVERT: C 1040 ASP cc_start: 0.5942 (m-30) cc_final: 0.5605 (m-30) REVERT: C 1230 MET cc_start: 0.8887 (ttm) cc_final: 0.8642 (ttp) REVERT: C 1233 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8664 (mt) REVERT: D 69 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7742 (mt-10) REVERT: D 164 GLN cc_start: 0.6775 (tt0) cc_final: 0.5865 (mp10) REVERT: D 200 GLN cc_start: 0.6999 (tp40) cc_final: 0.6544 (mp10) REVERT: D 596 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8394 (mp) REVERT: D 648 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: D 695 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7427 (tptm) REVERT: D 725 MET cc_start: 0.8938 (mtt) cc_final: 0.8669 (mtm) REVERT: D 736 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.7726 (mt0) REVERT: D 785 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7315 (t70) REVERT: D 812 ASP cc_start: 0.8286 (m-30) cc_final: 0.8059 (t0) REVERT: D 867 GLN cc_start: 0.8045 (mm110) cc_final: 0.7007 (tm-30) REVERT: D 1342 ASP cc_start: 0.8526 (p0) cc_final: 0.7793 (p0) REVERT: D 1369 ARG cc_start: 0.5337 (mtm110) cc_final: 0.4855 (mtp-110) REVERT: E 47 THR cc_start: 0.7942 (m) cc_final: 0.7356 (p) REVERT: E 56 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6935 (mp0) REVERT: F 100 MET cc_start: 0.7672 (mtt) cc_final: 0.7283 (mtt) REVERT: F 322 MET cc_start: 0.1808 (tpt) cc_final: 0.0780 (mmm) REVERT: F 413 MET cc_start: 0.7624 (mtm) cc_final: 0.7359 (mtp) REVERT: F 451 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7910 (mtp-110) REVERT: F 526 THR cc_start: 0.8066 (OUTLIER) cc_final: 0.7798 (p) REVERT: F 567 MET cc_start: 0.6464 (tpt) cc_final: 0.6254 (tpt) REVERT: H 162 MET cc_start: 0.5040 (mtp) cc_final: 0.4646 (mtp) REVERT: I 162 MET cc_start: 0.5083 (mmm) cc_final: 0.4771 (mmt) REVERT: I 171 ARG cc_start: 0.4421 (ttt180) cc_final: 0.4150 (ttt90) outliers start: 95 outliers final: 32 residues processed: 425 average time/residue: 0.7630 time to fit residues: 381.0001 Evaluate side-chains 362 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 315 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 407 ARG Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 503 LYS Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 892 GLU Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 596 LEU 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 685 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 785 ASP 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 1152 GLU Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1244 GLN 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 485 GLU Chi-restraints excluded: chain F residue 526 THR Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 66 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 68 optimal weight: 0.8980 chunk 212 optimal weight: 0.7980 chunk 332 optimal weight: 0.9980 chunk 181 optimal weight: 0.5980 chunk 401 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 331 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN C 568 ASN C1236 ASN D 341 ASN D 667 GLN D 777 HIS E 15 ASN E 61 ASN F 128 ASN F 357 GLN F 589 GLN I 170 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.216570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.138108 restraints weight = 42837.267| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.23 r_work: 0.3464 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36167 Z= 0.136 Angle : 0.586 10.438 49402 Z= 0.314 Chirality : 0.044 0.361 5634 Planarity : 0.004 0.055 6004 Dihedral : 19.419 179.729 6042 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.60 % Allowed : 17.61 % Favored : 78.79 % 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 are not related in a simple way. whole: -0.26 (0.13), residues: 4143 helix: 1.03 (0.12), residues: 1734 sheet: -1.01 (0.23), residues: 495 loop : -1.04 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1246 TYR 0.021 0.001 TYR D 144 PHE 0.023 0.002 PHE H 62 TRP 0.007 0.001 TRP D1020 HIS 0.014 0.001 HIS I 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (36167) covalent geometry : angle 0.58633 / 0.31 (49402) hydrogen bonds : bond 0.04156 / 4.45 ( 1609) hydrogen bonds : angle 4.77209 / 6.01 ( 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: 128 poor density : 352 time to evaluate : 0.995 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 205 MET cc_start: 0.8266 (mtp) cc_final: 0.8051 (ttm) REVERT: B 17 GLU cc_start: 0.7642 (tt0) cc_final: 0.6204 (mp0) REVERT: B 65 LEU cc_start: 0.7823 (mm) cc_final: 0.7263 (pt) REVERT: B 205 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.6828 (tpt) REVERT: B 214 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: C 20 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.6706 (pp30) REVERT: C 41 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7454 (mt0) REVERT: C 160 ASP cc_start: 0.6595 (t70) cc_final: 0.6332 (t0) REVERT: C 340 ASP cc_start: 0.7468 (t0) cc_final: 0.7034 (t0) REVERT: C 407 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6898 (mtm-85) REVERT: C 492 MET cc_start: 0.8239 (ptm) cc_final: 0.7971 (ptt) REVERT: C 542 ARG cc_start: 0.7774 (mtm-85) cc_final: 0.6879 (tmm-80) REVERT: C 820 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7777 (pt0) REVERT: C 876 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8058 (mm-30) REVERT: C 947 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7103 (tt0) REVERT: C 951 MET cc_start: 0.7166 (mtm) cc_final: 0.6626 (tmm) REVERT: C 1040 ASP cc_start: 0.6209 (m-30) cc_final: 0.5872 (m-30) REVERT: C 1230 MET cc_start: 0.8957 (ttm) cc_final: 0.8714 (ttp) REVERT: C 1233 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8709 (mt) REVERT: D 69 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7750 (mt-10) REVERT: D 136 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7625 (mt-10) REVERT: D 164 GLN cc_start: 0.6784 (tt0) cc_final: 0.5898 (mp10) REVERT: D 200 GLN cc_start: 0.7054 (tp40) cc_final: 0.6542 (mp10) REVERT: D 414 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7782 (tp30) REVERT: D 648 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: D 725 MET cc_start: 0.9035 (mtt) cc_final: 0.8779 (mtt) REVERT: D 736 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.7849 (mt0) REVERT: D 743 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8608 (ptp) REVERT: D 785 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.6989 (m-30) REVERT: D 805 GLN cc_start: 0.7644 (tp40) cc_final: 0.6995 (tt0) REVERT: D 812 ASP cc_start: 0.8336 (m-30) cc_final: 0.8108 (t0) REVERT: D 867 GLN cc_start: 0.8088 (mm110) cc_final: 0.7040 (tm-30) REVERT: D 1152 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6278 (tm-30) REVERT: D 1369 ARG cc_start: 0.5190 (mtm110) cc_final: 0.4649 (mtp-110) REVERT: E 47 THR cc_start: 0.7787 (OUTLIER) cc_final: 0.7227 (p) REVERT: E 56 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6857 (mp0) REVERT: F 100 MET cc_start: 0.7683 (mtt) cc_final: 0.7331 (mtt) REVERT: F 322 MET cc_start: 0.1585 (tpt) cc_final: 0.0603 (mmm) REVERT: F 413 MET cc_start: 0.7656 (mtm) cc_final: 0.7379 (mtp) REVERT: F 451 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7839 (mtp-110) REVERT: F 526 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7791 (p) REVERT: F 567 MET cc_start: 0.6600 (tpt) cc_final: 0.6339 (tpt) REVERT: F 569 THR cc_start: 0.7793 (OUTLIER) cc_final: 0.7570 (t) REVERT: F 606 VAL cc_start: 0.4695 (p) cc_final: 0.4415 (t) REVERT: H 162 MET cc_start: 0.5017 (mtp) cc_final: 0.4734 (mtp) REVERT: I 162 MET cc_start: 0.5120 (mmm) cc_final: 0.4789 (mmm) REVERT: I 171 ARG cc_start: 0.4491 (ttt180) cc_final: 0.4239 (ttt90) REVERT: I 207 ARG cc_start: 0.4485 (mmt180) cc_final: 0.4267 (mtp85) outliers start: 128 outliers final: 38 residues processed: 433 average time/residue: 0.7306 time to fit residues: 373.6561 Evaluate side-chains 376 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 319 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain B residue 205 MET 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 407 ARG Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 503 LYS Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 820 GLU Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 876 GLU Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 892 GLU Chi-restraints excluded: chain C residue 943 LYS Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 118 LYS 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 393 THR Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 556 GLU 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 684 ASP Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 785 ASP 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 1152 GLU Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 451 ARG Chi-restraints excluded: chain F residue 463 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 85 optimal weight: 7.9990 chunk 389 optimal weight: 7.9990 chunk 105 optimal weight: 0.0070 chunk 51 optimal weight: 1.9990 chunk 340 optimal weight: 20.0000 chunk 385 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 285 optimal weight: 8.9990 chunk 338 optimal weight: 9.9990 chunk 52 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 overall best weight: 1.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN A 186 ASN C 760 ASN C1236 ASN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 ASN D 489 ASN D 667 GLN D 897 HIS D1259 GLN E 61 ASN F 128 ASN I 196 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.214368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.135300 restraints weight = 42315.618| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.21 r_work: 0.3421 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 36167 Z= 0.166 Angle : 0.606 13.486 49402 Z= 0.321 Chirality : 0.045 0.272 5634 Planarity : 0.004 0.050 6004 Dihedral : 19.362 179.844 6042 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.71 % Allowed : 18.65 % Favored : 77.64 % 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 are not related in a simple way. whole: -0.16 (0.13), residues: 4143 helix: 1.14 (0.13), residues: 1734 sheet: -1.01 (0.23), residues: 488 loop : -1.00 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 139 TYR 0.018 0.002 TYR D 631 PHE 0.024 0.002 PHE C 337 TRP 0.018 0.001 TRP C 183 HIS 0.011 0.001 HIS I 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (36167) covalent geometry : angle 0.60624 / 0.32 (49402) hydrogen bonds : bond 0.04285 / 4.61 ( 1609) hydrogen bonds : angle 4.72528 / 6.02 ( 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 478 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 346 time to evaluate : 1.244 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 215 GLU cc_start: 0.8299 (tt0) cc_final: 0.8059 (tm-30) REVERT: B 17 GLU cc_start: 0.7778 (tt0) cc_final: 0.6252 (mp0) REVERT: B 62 ASP cc_start: 0.5003 (p0) cc_final: 0.4760 (m-30) REVERT: B 65 LEU cc_start: 0.8002 (mm) cc_final: 0.7385 (pt) REVERT: B 205 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.6934 (tpt) REVERT: B 214 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: C 20 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.6817 (pp30) REVERT: C 37 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7817 (mtmm) REVERT: C 41 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7413 (mt0) REVERT: C 160 ASP cc_start: 0.6688 (t70) cc_final: 0.6322 (t0) REVERT: C 183 TRP cc_start: 0.8470 (m-10) cc_final: 0.8257 (m-10) REVERT: C 300 ASP cc_start: 0.7281 (OUTLIER) cc_final: 0.6816 (m-30) REVERT: C 340 ASP cc_start: 0.7338 (t0) cc_final: 0.6907 (t0) REVERT: C 407 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7193 (mtm-85) REVERT: C 441 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7235 (pm20) REVERT: C 492 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7929 (ptt) REVERT: C 518 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.8350 (m110) REVERT: C 542 ARG cc_start: 0.7806 (mtm-85) cc_final: 0.6979 (tmm-80) REVERT: C 947 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7120 (tt0) REVERT: C 951 MET cc_start: 0.7030 (mtm) cc_final: 0.6552 (tmm) REVERT: C 968 GLU cc_start: 0.4233 (mm-30) cc_final: 0.3336 (tp30) REVERT: C 1040 ASP cc_start: 0.6306 (m-30) cc_final: 0.5993 (m-30) REVERT: C 1230 MET cc_start: 0.8981 (ttm) cc_final: 0.8769 (ttp) REVERT: C 1233 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8755 (mt) REVERT: D 69 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7959 (mt-10) REVERT: D 136 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7742 (mt-10) REVERT: D 200 GLN cc_start: 0.6787 (tp40) cc_final: 0.6563 (mp10) REVERT: D 322 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7698 (ptm160) REVERT: D 414 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7791 (tp30) REVERT: D 453 VAL cc_start: 0.8927 (OUTLIER) cc_final: 0.8652 (m) REVERT: D 648 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: D 736 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.7939 (mt0) REVERT: D 743 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8669 (ptp) REVERT: D 785 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.6981 (m-30) REVERT: D 805 GLN cc_start: 0.7723 (tp40) cc_final: 0.7039 (tt0) REVERT: D 812 ASP cc_start: 0.8379 (m-30) cc_final: 0.8147 (t70) REVERT: D 1152 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6408 (tm-30) REVERT: D 1369 ARG cc_start: 0.5351 (mtm110) cc_final: 0.4772 (mtp180) REVERT: D 1370 MET cc_start: 0.6888 (tpp) cc_final: 0.6476 (mpp) REVERT: E 47 THR cc_start: 0.7976 (m) cc_final: 0.7186 (p) REVERT: E 56 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6902 (mp0) REVERT: F 100 MET cc_start: 0.7682 (mtt) cc_final: 0.7361 (mtt) REVERT: F 322 MET cc_start: 0.1616 (tpt) cc_final: 0.0652 (mmm) REVERT: F 365 MET cc_start: 0.7026 (tpt) cc_final: 0.6805 (tpp) REVERT: F 413 MET cc_start: 0.7674 (mtm) cc_final: 0.7391 (mtp) REVERT: F 451 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7724 (ttp80) REVERT: F 541 ARG cc_start: 0.6446 (OUTLIER) cc_final: 0.5960 (ttp80) REVERT: F 606 VAL cc_start: 0.4680 (p) cc_final: 0.4431 (t) REVERT: H 50 LEU cc_start: 0.3193 (OUTLIER) cc_final: 0.2547 (pt) REVERT: I 171 ARG cc_start: 0.4568 (ttt180) cc_final: 0.4155 (ttt180) REVERT: I 207 ARG cc_start: 0.4496 (mmt180) cc_final: 0.4050 (mtm180) outliers start: 132 outliers final: 49 residues processed: 434 average time/residue: 0.7283 time to fit residues: 374.4441 Evaluate side-chains 395 residues out of total 3559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 323 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 205 MET 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 37 LYS Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 300 ASP 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 441 GLU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 503 LYS Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 609 ILE 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 892 GLU Chi-restraints excluded: chain C residue 943 LYS Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 71 LEU 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 322 ARG Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 393 THR 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 506 VAL Chi-restraints excluded: chain D residue 556 GLU Chi-restraints excluded: chain D residue 571 ASP 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 743 MET Chi-restraints excluded: chain D residue 785 ASP 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 1152 GLU Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain F residue 273 MET Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 451 ARG Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 541 ARG Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain I residue 13 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.9089 > 50: distance: 86 - 103: 16.572 distance: 90 - 112: 21.793 distance: 95 - 119: 22.329 distance: 99 - 103: 14.295 distance: 100 - 127: 30.418 distance: 103 - 104: 18.875 distance: 104 - 105: 58.562 distance: 104 - 107: 40.115 distance: 105 - 106: 31.645 distance: 105 - 112: 40.994 distance: 106 - 136: 42.734 distance: 107 - 108: 22.848 distance: 108 - 109: 16.213 distance: 109 - 110: 8.125 distance: 110 - 111: 13.646 distance: 112 - 113: 42.397 distance: 113 - 114: 42.201 distance: 113 - 116: 16.641 distance: 114 - 115: 35.502 distance: 114 - 119: 44.784 distance: 115 - 144: 47.005 distance: 116 - 117: 38.203 distance: 116 - 118: 32.929 distance: 119 - 120: 24.491 distance: 120 - 121: 24.537 distance: 120 - 123: 19.386 distance: 121 - 122: 28.352 distance: 121 - 127: 34.687 distance: 123 - 124: 11.770 distance: 124 - 125: 22.023 distance: 124 - 126: 18.353 distance: 127 - 128: 17.610 distance: 128 - 129: 44.091 distance: 128 - 131: 25.154 distance: 129 - 130: 27.992 distance: 129 - 136: 38.647 distance: 131 - 132: 20.025 distance: 132 - 133: 30.861 distance: 133 - 134: 16.128 distance: 134 - 135: 17.239 distance: 136 - 137: 33.812 distance: 137 - 138: 33.069 distance: 137 - 140: 16.541 distance: 138 - 139: 22.124 distance: 138 - 144: 36.095 distance: 140 - 141: 46.591 distance: 140 - 142: 48.951 distance: 141 - 143: 43.172 distance: 144 - 145: 11.988 distance: 145 - 146: 45.451 distance: 145 - 148: 44.731 distance: 146 - 147: 25.219 distance: 146 - 149: 43.062 distance: 149 - 150: 52.432 distance: 150 - 151: 42.768 distance: 150 - 153: 3.749 distance: 151 - 152: 24.746 distance: 151 - 158: 8.875 distance: 153 - 154: 32.087 distance: 154 - 155: 26.431 distance: 155 - 156: 25.988 distance: 156 - 157: 8.144 distance: 159 - 160: 51.294 distance: 159 - 162: 45.105 distance: 160 - 161: 39.849 distance: 160 - 167: 39.677 distance: 162 - 163: 10.745 distance: 163 - 164: 29.231 distance: 164 - 165: 16.212 distance: 164 - 166: 12.631 distance: 167 - 168: 21.307 distance: 167 - 173: 42.516 distance: 168 - 169: 37.015 distance: 168 - 171: 11.072 distance: 169 - 170: 36.584 distance: 169 - 174: 25.829 distance: 171 - 172: 49.025 distance: 172 - 173: 40.622 distance: 174 - 175: 13.603 distance: 175 - 176: 40.580 distance: 175 - 178: 31.524 distance: 176 - 177: 12.758 distance: 176 - 182: 23.837 distance: 178 - 179: 16.297 distance: 178 - 180: 24.953 distance: 179 - 181: 42.326