Starting phenix.real_space_refine on Mon Sep 30 04:22:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5a_33614/09_2024/7y5a_33614.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5a_33614/09_2024/7y5a_33614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5a_33614/09_2024/7y5a_33614.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5a_33614/09_2024/7y5a_33614.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5a_33614/09_2024/7y5a_33614.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5a_33614/09_2024/7y5a_33614.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.002 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: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 74 5.16 5 C 15085 2.51 5 N 4198 2.21 5 O 4600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23975 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3766 Classifications: {'peptide': 500} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 22, 'TRANS': 477} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3713 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 472} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 3643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3643 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 20, 'TRANS': 468} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3495 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 23, 'TRANS': 440} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3486 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 23, 'TRANS': 440} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 64 Chain: "F" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3525 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 23, 'TRANS': 440} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 29 Chain: "G" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2195 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.35, per 1000 atoms: 0.60 Number of scatterers: 23975 At special positions: 0 Unit cell: (129.8, 156.2, 135.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 74 16.00 P 13 15.00 Mg 5 11.99 O 4600 8.00 N 4198 7.00 C 15085 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: 6.61 Conformation dependent library (CDL) restraints added in 2.8 seconds 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5754 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 24 sheets defined 46.3% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'A' and resid 81 through 85 removed outlier: 4.159A pdb=" N LYS A 84 " --> pdb=" O GLU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.988A pdb=" N PHE A 106 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU A 107 " --> pdb=" O ASP A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 107' Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 179 through 189 Processing helix chain 'A' and resid 189 through 196 removed outlier: 4.211A pdb=" N GLY A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 removed outlier: 3.536A pdb=" N ILE A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 262 removed outlier: 3.627A pdb=" N LYS A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Proline residue: A 250 - end of helix removed outlier: 4.104A pdb=" N GLY A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 288 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 300 through 310 removed outlier: 3.878A pdb=" N LEU A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N HIS A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 removed outlier: 3.739A pdb=" N THR A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 377 through 381 removed outlier: 3.599A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 Processing helix chain 'A' and resid 392 through 408 removed outlier: 4.224A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 431 removed outlier: 3.558A pdb=" N LEU A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 454 through 457 Processing helix chain 'A' and resid 464 through 478 removed outlier: 3.569A pdb=" N GLU A 468 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 490 removed outlier: 3.871A pdb=" N ASP A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 511 removed outlier: 3.795A pdb=" N LYS A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 removed outlier: 3.930A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 188 removed outlier: 3.521A pdb=" N VAL B 181 " --> pdb=" O GLY B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 195 removed outlier: 3.758A pdb=" N THR B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 227 Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 244 through 247 Processing helix chain 'B' and resid 248 through 262 removed outlier: 3.770A pdb=" N HIS B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 removed outlier: 3.891A pdb=" N LEU B 288 " --> pdb=" O ILE B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 301 through 310 Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 356 through 363 Processing helix chain 'B' and resid 383 through 403 removed outlier: 3.887A pdb=" N GLY B 391 " --> pdb=" O LYS B 387 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.694A pdb=" N ALA B 407 " --> pdb=" O GLU B 404 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA B 408 " --> pdb=" O ALA B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 414 through 432 removed outlier: 4.569A pdb=" N LYS B 432 " --> pdb=" O VAL B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 460 through 479 removed outlier: 3.849A pdb=" N GLN B 465 " --> pdb=" O VAL B 461 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU B 468 " --> pdb=" O VAL B 464 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 490 removed outlier: 3.535A pdb=" N ASP B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 511 removed outlier: 3.987A pdb=" N LYS B 509 " --> pdb=" O ASN B 505 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 158 removed outlier: 3.539A pdb=" N ASP C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA C 158 " --> pdb=" O LYS C 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 153 through 158' Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.953A pdb=" N GLY C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 Processing helix chain 'C' and resid 242 through 262 removed outlier: 3.984A pdb=" N LYS C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) Proline residue: C 250 - end of helix removed outlier: 4.128A pdb=" N ILE C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR C 262 " --> pdb=" O GLN C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 293 through 297 removed outlier: 4.148A pdb=" N ALA C 296 " --> pdb=" O GLY C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 311 Processing helix chain 'C' and resid 339 through 349 removed outlier: 3.731A pdb=" N THR C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.597A pdb=" N ALA C 390 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 408 removed outlier: 3.832A pdb=" N ASP C 396 " --> pdb=" O SER C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 431 removed outlier: 3.551A pdb=" N LEU C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 454 removed outlier: 3.839A pdb=" N GLY C 454 " --> pdb=" O LEU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 478 removed outlier: 3.560A pdb=" N PHE C 467 " --> pdb=" O ASP C 463 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU C 472 " --> pdb=" O GLU C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 490 removed outlier: 3.838A pdb=" N ASP C 484 " --> pdb=" O SER C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 506 Processing helix chain 'C' and resid 507 through 511 removed outlier: 3.521A pdb=" N PHE C 511 " --> pdb=" O LYS C 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 147 Processing helix chain 'D' and resid 165 through 178 removed outlier: 3.647A pdb=" N LEU D 169 " --> pdb=" O GLY D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 207 Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 223 through 228 removed outlier: 3.889A pdb=" N ARG D 227 " --> pdb=" O PRO D 223 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET D 228 " --> pdb=" O PRO D 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 223 through 228' Processing helix chain 'D' and resid 229 through 245 Processing helix chain 'D' and resid 256 through 270 removed outlier: 3.993A pdb=" N THR D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU D 265 " --> pdb=" O GLN D 261 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL D 266 " --> pdb=" O ALA D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.972A pdb=" N GLU D 286 " --> pdb=" O THR D 282 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR D 295 " --> pdb=" O GLN D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 314 removed outlier: 3.850A pdb=" N ASP D 313 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 326 removed outlier: 3.976A pdb=" N ALA D 321 " --> pdb=" O ASP D 317 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR D 322 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 347 through 351 removed outlier: 4.152A pdb=" N SER D 351 " --> pdb=" O PRO D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 390 removed outlier: 3.712A pdb=" N TYR D 366 " --> pdb=" O GLY D 362 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ILE D 388 " --> pdb=" O ASP D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 394 removed outlier: 3.515A pdb=" N LEU D 394 " --> pdb=" O ILE D 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 391 through 394' Processing helix chain 'D' and resid 395 through 412 Processing helix chain 'D' and resid 419 through 424 removed outlier: 3.504A pdb=" N THR D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 445 Processing helix chain 'D' and resid 446 through 450 removed outlier: 4.195A pdb=" N HIS D 449 " --> pdb=" O GLU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 456 removed outlier: 3.521A pdb=" N PHE D 456 " --> pdb=" O GLN D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 470 Processing helix chain 'E' and resid 141 through 146 removed outlier: 3.627A pdb=" N ASP E 145 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU E 146 " --> pdb=" O LYS E 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 141 through 146' Processing helix chain 'E' and resid 165 through 180 removed outlier: 3.532A pdb=" N LEU E 169 " --> pdb=" O GLY E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 208 Processing helix chain 'E' and resid 225 through 246 removed outlier: 3.763A pdb=" N ARG E 229 " --> pdb=" O GLY E 225 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN E 245 " --> pdb=" O PHE E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 271 removed outlier: 4.093A pdb=" N THR E 260 " --> pdb=" O ILE E 256 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN E 261 " --> pdb=" O PHE E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 294 removed outlier: 3.558A pdb=" N GLU E 286 " --> pdb=" O THR E 282 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE E 294 " --> pdb=" O LEU E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 324 Processing helix chain 'E' and resid 357 through 387 removed outlier: 7.664A pdb=" N ASP E 363 " --> pdb=" O ALA E 359 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N GLU E 364 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N HIS E 365 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR E 366 " --> pdb=" O GLY E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 394 Processing helix chain 'E' and resid 395 through 412 Processing helix chain 'E' and resid 416 through 421 Processing helix chain 'E' and resid 431 through 445 removed outlier: 3.576A pdb=" N THR E 435 " --> pdb=" O PRO E 431 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS E 444 " --> pdb=" O ASP E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 450 Processing helix chain 'E' and resid 451 through 456 removed outlier: 3.950A pdb=" N PHE E 455 " --> pdb=" O PRO E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 471 Processing helix chain 'F' and resid 141 through 147 Processing helix chain 'F' and resid 165 through 179 removed outlier: 4.160A pdb=" N ARG F 179 " --> pdb=" O ASN F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 206 removed outlier: 3.852A pdb=" N GLY F 197 " --> pdb=" O ARG F 193 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP F 206 " --> pdb=" O VAL F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 228 removed outlier: 3.723A pdb=" N MET F 228 " --> pdb=" O GLY F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 244 Processing helix chain 'F' and resid 255 through 271 removed outlier: 3.856A pdb=" N PHE F 259 " --> pdb=" O ASN F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 292 removed outlier: 3.534A pdb=" N GLU F 286 " --> pdb=" O THR F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 314 Processing helix chain 'F' and resid 317 through 324 removed outlier: 3.936A pdb=" N THR F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 327 No H-bonds generated for 'chain 'F' and resid 325 through 327' Processing helix chain 'F' and resid 334 through 341 Processing helix chain 'F' and resid 347 through 351 removed outlier: 3.640A pdb=" N SER F 351 " --> pdb=" O PRO F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 389 removed outlier: 3.901A pdb=" N TYR F 366 " --> pdb=" O GLY F 362 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG F 367 " --> pdb=" O ASP F 363 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL F 368 " --> pdb=" O GLU F 364 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 412 Processing helix chain 'F' and resid 418 through 422 removed outlier: 4.321A pdb=" N GLN F 421 " --> pdb=" O ALA F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 445 Processing helix chain 'F' and resid 451 through 455 removed outlier: 3.551A pdb=" N ALA F 454 " --> pdb=" O PRO F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 470 removed outlier: 3.872A pdb=" N GLU F 469 " --> pdb=" O ALA F 465 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER F 470 " --> pdb=" O LYS F 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 61 removed outlier: 3.838A pdb=" N ALA G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) Proline residue: G 45 - end of helix removed outlier: 4.392A pdb=" N ALA G 60 " --> pdb=" O GLU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 69 Processing helix chain 'G' and resid 91 through 111 removed outlier: 3.836A pdb=" N VAL G 96 " --> pdb=" O TYR G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 130 removed outlier: 3.738A pdb=" N LEU G 124 " --> pdb=" O GLY G 120 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE G 129 " --> pdb=" O GLY G 125 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG G 130 " --> pdb=" O TYR G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 163 removed outlier: 3.695A pdb=" N ALA G 150 " --> pdb=" O THR G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 302 removed outlier: 4.005A pdb=" N LEU G 231 " --> pdb=" O ASP G 227 " (cutoff:3.500A) Proline residue: G 237 - end of helix removed outlier: 4.581A pdb=" N ASP G 272 " --> pdb=" O ASP G 268 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU G 273 " --> pdb=" O ASN G 269 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 37 removed outlier: 3.598A pdb=" N THR A 33 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 45 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N HIS A 43 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA A 37 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLY A 75 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 67 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 66 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLU A 54 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU A 55 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 102 Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.518A pdb=" N ALA A 236 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 325 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE A 271 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 331 removed outlier: 3.619A pdb=" N LEU A 355 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 540 removed outlier: 6.435A pdb=" N VAL A 538 " --> pdb=" O GLU G 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 36 through 37 removed outlier: 3.810A pdb=" N ASP B 36 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS B 43 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLY B 75 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 67 " --> pdb=" O GLY B 75 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 101 removed outlier: 3.666A pdb=" N ARG B 130 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 111 Processing sheet with id=AA9, first strand: chain 'B' and resid 329 through 331 removed outlier: 8.524A pdb=" N ILE B 330 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE B 170 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 31 through 37 removed outlier: 3.693A pdb=" N THR C 33 " --> pdb=" O GLU C 45 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N HIS C 43 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ALA C 37 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN C 68 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL C 77 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ALA C 66 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA C 66 " --> pdb=" O GLU C 54 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU C 54 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU C 55 " --> pdb=" O THR C 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 99 through 102 Processing sheet with id=AB3, first strand: chain 'C' and resid 109 through 111 removed outlier: 6.373A pdb=" N ARG C 109 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ALA C 236 " --> pdb=" O ARG C 109 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL C 111 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N THR C 233 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N CYS C 204 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N VAL C 235 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TYR C 206 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ALA C 237 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ALA C 208 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 207 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR C 325 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE C 271 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE C 170 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 11 through 16 removed outlier: 6.832A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ILE D 15 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE D 65 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL D 53 " --> pdb=" O ILE D 65 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 88 through 89 removed outlier: 3.810A pdb=" N VAL D 88 " --> pdb=" O TRP D 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP D 118 " --> pdb=" O VAL D 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 98 through 99 removed outlier: 3.816A pdb=" N PHE D 217 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N SER D 185 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N VAL D 216 " --> pdb=" O SER D 185 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N PHE D 187 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N GLY D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLY D 189 " --> pdb=" O GLY D 218 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP D 254 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL D 190 " --> pdb=" O ASP D 254 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE D 156 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.697A pdb=" N ASP E 21 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LEU E 61 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE E 65 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL E 53 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLU E 39 " --> pdb=" O GLU E 78 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU E 78 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL E 79 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY E 10 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 87 through 90 removed outlier: 3.898A pdb=" N GLU E 116 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 98 through 99 removed outlier: 6.667A pdb=" N PHE E 99 " --> pdb=" O PHE E 217 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLN E 219 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY E 191 " --> pdb=" O GLY E 218 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR E 184 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE E 252 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL E 186 " --> pdb=" O PHE E 252 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL E 249 " --> pdb=" O SER E 301 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR E 303 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA E 307 " --> pdb=" O ILE E 253 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 98 through 99 removed outlier: 6.667A pdb=" N PHE E 99 " --> pdb=" O PHE E 217 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLN E 219 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY E 191 " --> pdb=" O GLY E 218 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR E 184 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE E 252 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL E 186 " --> pdb=" O PHE E 252 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL E 249 " --> pdb=" O SER E 301 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR E 303 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA E 307 " --> pdb=" O ILE E 253 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE E 159 " --> pdb=" O THR E 331 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 136 through 137 removed outlier: 4.101A pdb=" N TYR E 150 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 15 removed outlier: 6.974A pdb=" N ASP F 21 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU F 61 " --> pdb=" O HIS F 56 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N HIS F 56 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG F 63 " --> pdb=" O ALA F 54 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS F 47 " --> pdb=" O ILE F 40 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLU F 39 " --> pdb=" O GLU F 78 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLU F 78 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL F 79 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY F 10 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 87 through 89 Processing sheet with id=AC5, first strand: chain 'F' and resid 98 through 99 removed outlier: 6.571A pdb=" N PHE F 99 " --> pdb=" O PHE F 217 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N GLN F 219 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA F 214 " --> pdb=" O SER F 185 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE F 187 " --> pdb=" O ALA F 214 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL F 216 " --> pdb=" O PHE F 187 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR F 184 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N PHE F 252 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL F 186 " --> pdb=" O PHE F 252 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N ASP F 254 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ALA F 188 " --> pdb=" O ASP F 254 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE F 156 " --> pdb=" O GLN F 306 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL F 308 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU F 158 " --> pdb=" O VAL F 308 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA F 329 " --> pdb=" O LYS F 155 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA F 157 " --> pdb=" O ALA F 329 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR F 331 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER F 352 " --> pdb=" O THR F 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 136 through 138 removed outlier: 10.624A pdb=" N GLU G 136 " --> pdb=" O PRO G 114 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU G 116 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N TRP G 138 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL G 118 " --> pdb=" O TRP G 138 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N HIS G 184 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY G 78 " --> pdb=" O HIS G 184 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL G 186 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU G 80 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N THR G 188 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 9.361A pdb=" N VAL G 82 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 12.314A pdb=" N PHE G 190 " --> pdb=" O VAL G 82 " (cutoff:3.500A) 1096 hydrogen bonds defined for protein. 3135 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.83 Time building geometry restraints manager: 7.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8159 1.34 - 1.46: 4843 1.46 - 1.58: 11226 1.58 - 1.70: 19 1.70 - 1.81: 130 Bond restraints: 24377 Sorted by residual: bond pdb=" CA HIS D 326 " pdb=" C HIS D 326 " ideal model delta sigma weight residual 1.526 1.510 0.016 1.20e-02 6.94e+03 1.83e+00 bond pdb=" N SER D 119 " pdb=" CA SER D 119 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.55e+00 bond pdb=" CA SER C 437 " pdb=" CB SER C 437 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.22e+00 bond pdb=" C PHE F 343 " pdb=" N PRO F 344 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.36e-02 5.41e+03 1.16e+00 bond pdb=" CA VAL D 277 " pdb=" C VAL D 277 " ideal model delta sigma weight residual 1.523 1.536 -0.013 1.27e-02 6.20e+03 1.12e+00 ... (remaining 24372 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 32514 1.94 - 3.88: 477 3.88 - 5.82: 70 5.82 - 7.77: 10 7.77 - 9.71: 4 Bond angle restraints: 33075 Sorted by residual: angle pdb=" N TRP D 118 " pdb=" CA TRP D 118 " pdb=" C TRP D 118 " ideal model delta sigma weight residual 108.34 114.95 -6.61 1.31e+00 5.83e-01 2.55e+01 angle pdb=" C PHE C 340 " pdb=" N ILE C 341 " pdb=" CA ILE C 341 " ideal model delta sigma weight residual 120.33 123.34 -3.01 8.00e-01 1.56e+00 1.41e+01 angle pdb=" N ILE D 120 " pdb=" CA ILE D 120 " pdb=" C ILE D 120 " ideal model delta sigma weight residual 113.53 110.13 3.40 9.80e-01 1.04e+00 1.20e+01 angle pdb=" CB MET E 67 " pdb=" CG MET E 67 " pdb=" SD MET E 67 " ideal model delta sigma weight residual 112.70 122.41 -9.71 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C PHE A 340 " pdb=" N ILE A 341 " pdb=" CA ILE A 341 " ideal model delta sigma weight residual 120.33 122.92 -2.59 8.00e-01 1.56e+00 1.05e+01 ... (remaining 33070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 13252 17.84 - 35.69: 1162 35.69 - 53.53: 238 53.53 - 71.37: 61 71.37 - 89.22: 38 Dihedral angle restraints: 14751 sinusoidal: 5790 harmonic: 8961 Sorted by residual: dihedral pdb=" CA ARG E 258 " pdb=" C ARG E 258 " pdb=" N PHE E 259 " pdb=" CA PHE E 259 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA GLY D 263 " pdb=" C GLY D 263 " pdb=" N SER D 264 " pdb=" CA SER D 264 " ideal model delta harmonic sigma weight residual 180.00 -162.02 -17.98 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ILE B 383 " pdb=" C ILE B 383 " pdb=" N LYS B 384 " pdb=" CA LYS B 384 " ideal model delta harmonic sigma weight residual -180.00 -163.15 -16.85 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 14748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2579 0.034 - 0.067: 840 0.067 - 0.101: 284 0.101 - 0.135: 124 0.135 - 0.168: 4 Chirality restraints: 3831 Sorted by residual: chirality pdb=" CA TRP D 118 " pdb=" N TRP D 118 " pdb=" C TRP D 118 " pdb=" CB TRP D 118 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CB VAL B 102 " pdb=" CA VAL B 102 " pdb=" CG1 VAL B 102 " pdb=" CG2 VAL B 102 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CG LEU D 146 " pdb=" CB LEU D 146 " pdb=" CD1 LEU D 146 " pdb=" CD2 LEU D 146 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.40e-01 ... (remaining 3828 not shown) Planarity restraints: 4320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 310 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.20e+00 pdb=" N PRO E 311 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO E 311 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 311 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 430 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.33e+00 pdb=" N PRO D 431 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 431 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 431 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 430 " 0.029 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO E 431 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 431 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 431 " 0.025 5.00e-02 4.00e+02 ... (remaining 4317 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 208 2.57 - 3.15: 19995 3.15 - 3.73: 37296 3.73 - 4.32: 46952 4.32 - 4.90: 78930 Nonbonded interactions: 183381 Sorted by model distance: nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.986 2.170 nonbonded pdb=" O1A ATP B 600 " pdb="MG MG B 601 " model vdw 2.014 2.170 nonbonded pdb=" O2B ATP B 600 " pdb="MG MG B 601 " model vdw 2.026 2.170 nonbonded pdb=" O1G ATP B 600 " pdb="MG MG B 601 " model vdw 2.059 2.170 nonbonded pdb=" O3B ADP F 600 " pdb="MG MG F 601 " model vdw 2.074 2.170 ... (remaining 183376 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 29 and (name N or name CA or name C or name O or name CB \ )) or resid 30 through 44 or (resid 45 and (name N or name CA or name C or name \ O or name CB )) or resid 46 through 132 or (resid 133 and (name N or name CA or \ name C or name O or name CB )) or resid 134 through 355 or (resid 356 and (name \ N or name CA or name C or name O or name CB )) or resid 357 or (resid 358 and (n \ ame N or name CA or name C or name O or name CB )) or resid 359 through 400 or ( \ resid 401 through 402 and (name N or name CA or name C or name O or name CB )) o \ r resid 403 through 410 or resid 414 through 416 or (resid 417 through 419 and ( \ name N or name CA or name C or name O or name CB )) or resid 420 through 461 or \ (resid 462 through 463 and (name N or name CA or name C or name O or name CB )) \ or resid 464 through 467 or (resid 468 and (name N or name CA or name C or name \ O or name CB )) or resid 469 or (resid 470 and (name N or name CA or name C or n \ ame O or name CB )) or resid 471 through 475 or (resid 476 through 477 and (name \ N or name CA or name C or name O or name CB )) or resid 478 through 494 or (res \ id 495 through 499 and (name N or name CA or name C or name O or name CB )) or r \ esid 500 through 505 or (resid 506 and (name N or name CA or name C or name O or \ name CB )) or resid 507 through 515 or resid 537 through 538 or resid 540 or re \ sid 600 through 601)) selection = (chain 'B' and ((resid 29 and (name N or name CA or name C or name O or name CB \ )) or resid 30 through 44 or (resid 45 and (name N or name CA or name C or name \ O or name CB )) or resid 46 through 132 or (resid 133 and (name N or name CA or \ name C or name O or name CB )) or resid 134 through 190 or (resid 191 through 19 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 193 through \ 316 or (resid 317 and (name N or name CA or name C or name O or name CB )) or re \ sid 318 through 355 or (resid 356 and (name N or name CA or name C or name O or \ name CB )) or resid 357 or (resid 358 and (name N or name CA or name C or name O \ or name CB )) or resid 359 through 401 or (resid 402 and (name N or name CA or \ name C or name O or name CB )) or resid 403 through 410 or resid 414 through 416 \ or (resid 417 through 419 and (name N or name CA or name C or name O or name CB \ )) or resid 420 through 456 or (resid 457 and (name N or name CA or name C or n \ ame O or name CB )) or resid 458 through 467 or (resid 468 and (name N or name C \ A or name C or name O or name CB )) or resid 469 through 475 or (resid 476 throu \ gh 477 and (name N or name CA or name C or name O or name CB )) or resid 478 thr \ ough 493 or (resid 494 through 499 and (name N or name CA or name C or name O or \ name CB )) or resid 500 through 505 or (resid 506 and (name N or name CA or nam \ e C or name O or name CB )) or resid 507 through 514 or (resid 515 and (name N o \ r name CA or name C or name O or name CB )) or resid 518 through 520 or resid 60 \ 0 through 601)) selection = (chain 'C' and (resid 29 through 190 or (resid 191 through 192 and (name N or na \ me CA or name C or name O or name CB )) or resid 193 through 316 or (resid 317 a \ nd (name N or name CA or name C or name O or name CB )) or resid 318 through 400 \ or (resid 401 through 402 and (name N or name CA or name C or name O or name CB \ )) or resid 403 through 456 or (resid 457 and (name N or name CA or name C or n \ ame O or name CB )) or resid 458 through 469 or (resid 470 and (name N or name C \ A or name C or name O or name CB )) or resid 471 through 493 or (resid 494 throu \ gh 499 and (name N or name CA or name C or name O or name CB )) or resid 500 thr \ ough 515 or resid 518 through 520 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 103 or (resid 104 through 105 and (name N or nam \ e CA or name C or name O or name CB )) or resid 106 or (resid 107 through 108 an \ d (name N or name CA or name C or name O or name CB )) or resid 109 through 113 \ or (resid 114 and (name N or name CA or name C or name O or name CB )) or resid \ 115 through 198 or (resid 199 and (name N or name CA or name C or name O or name \ CB )) or resid 200 through 202 or (resid 203 and (name N or name CA or name C o \ r name O or name CB )) or resid 204 through 205 or (resid 206 through 207 and (n \ ame N or name CA or name C or name O or name CB )) or resid 208 through 285 or ( \ resid 286 and (name N or name CA or name C or name O or name CB )) or resid 287 \ through 362 or (resid 363 through 364 and (name N or name CA or name C or name O \ or name CB )) or resid 365 through 369 or (resid 370 through 371 and (name N or \ name CA or name C or name O or name CB )) or resid 372 through 380 or (resid 38 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 382 through \ 391 or (resid 392 through 393 and (name N or name CA or name C or name O or name \ CB )) or resid 394 through 402 or (resid 403 and (name N or name CA or name C o \ r name O or name CB )) or resid 404 through 424 or (resid 425 and (name N or nam \ e CA or name C or name O or name CB )) or resid 426 through 471)) selection = (chain 'E' and (resid 8 through 104 or (resid 105 and (name N or name CA or name \ C or name O or name CB )) or resid 106 through 137 or (resid 138 and (name N or \ name CA or name C or name O or name CB )) or resid 139 through 220 or (resid 22 \ 1 through 222 and (name N or name CA or name C or name O or name CB )) or resid \ 223 through 285 or (resid 286 and (name N or name CA or name C or name O or name \ CB )) or resid 287 through 288 or (resid 289 and (name N or name CA or name C o \ r name O or name CB )) or resid 290 through 291 or (resid 292 and (name N or nam \ e CA or name C or name O or name CB )) or resid 293 through 370 or (resid 371 an \ d (name N or name CA or name C or name O or name CB )) or resid 372 through 395 \ or (resid 396 through 398 and (name N or name CA or name C or name O or name CB \ )) or resid 399 through 461 or (resid 462 through 463 and (name N or name CA or \ name C or name O or name CB )) or resid 464 through 465 or (resid 466 and (name \ N or name CA or name C or name O or name CB )) or resid 467 through 471)) selection = (chain 'F' and (resid 8 through 103 or (resid 104 through 105 and (name N or nam \ e CA or name C or name O or name CB )) or resid 106 through 107 or (resid 108 an \ d (name N or name CA or name C or name O or name CB )) or resid 109 through 113 \ or (resid 114 and (name N or name CA or name C or name O or name CB )) or resid \ 115 through 134 or (resid 135 and (name N or name CA or name C or name O or name \ CB )) or resid 136 through 137 or (resid 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 198 or (resid 199 and (name N or nam \ e CA or name C or name O or name CB )) or resid 200 through 202 or (resid 203 an \ d (name N or name CA or name C or name O or name CB )) or resid 204 through 205 \ or (resid 206 through 207 and (name N or name CA or name C or name O or name CB \ )) or resid 208 through 220 or (resid 221 through 222 and (name N or name CA or \ name C or name O or name CB )) or resid 223 through 291 or (resid 292 and (name \ N or name CA or name C or name O or name CB )) or resid 293 through 369 or (resi \ d 370 through 371 and (name N or name CA or name C or name O or name CB )) or re \ sid 372 through 380 or (resid 381 and (name N or name CA or name C or name O or \ name CB )) or resid 382 through 383 or (resid 384 and (name N or name CA or name \ C or name O or name CB )) or resid 385 through 391 or (resid 392 through 393 an \ d (name N or name CA or name C or name O or name CB )) or resid 394 through 395 \ or (resid 396 through 398 and (name N or name CA or name C or name O or name CB \ )) or resid 399 through 402 or (resid 403 and (name N or name CA or name C or na \ me O or name CB )) or resid 404 through 432 or (resid 433 and (name N or name CA \ or name C or name O or name CB )) or resid 434 through 461 or (resid 462 throug \ h 463 and (name N or name CA or name C or name O or name CB )) or resid 464 thro \ ugh 465 or (resid 466 and (name N or name CA or name C or name O or name CB )) o \ r resid 467 through 471)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.900 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 52.250 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24377 Z= 0.169 Angle : 0.595 9.708 33075 Z= 0.322 Chirality : 0.041 0.168 3831 Planarity : 0.004 0.062 4320 Dihedral : 15.011 89.218 8997 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.04 % Allowed : 0.20 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.15), residues: 3142 helix: 1.55 (0.15), residues: 1218 sheet: 0.71 (0.25), residues: 401 loop : -0.86 (0.16), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 138 HIS 0.004 0.001 HIS D 117 PHE 0.017 0.001 PHE D 439 TYR 0.010 0.001 TYR C 231 ARG 0.006 0.000 ARG F 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 2.939 Fit side-chains revert: symmetry clash REVERT: C 261 MET cc_start: 0.7828 (mmm) cc_final: 0.7372 (tpt) REVERT: D 255 ASN cc_start: 0.8213 (t0) cc_final: 0.7732 (t0) REVERT: D 273 MET cc_start: 0.8918 (mmm) cc_final: 0.8643 (mtt) REVERT: D 309 TYR cc_start: 0.8124 (t80) cc_final: 0.7908 (t80) REVERT: D 323 THR cc_start: 0.8902 (p) cc_final: 0.8691 (p) REVERT: E 343 PHE cc_start: 0.8609 (t80) cc_final: 0.8347 (t80) REVERT: F 365 HIS cc_start: 0.7228 (m90) cc_final: 0.6822 (m170) REVERT: G 53 MET cc_start: 0.8716 (ppp) cc_final: 0.8493 (ppp) outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.3160 time to fit residues: 64.6648 Evaluate side-chains 100 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 0.5980 chunk 237 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 160 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 chunk 246 optimal weight: 0.0770 chunk 95 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 285 optimal weight: 3.9990 overall best weight: 1.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 GLN ** C 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 HIS ** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.0741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24377 Z= 0.183 Angle : 0.539 7.512 33075 Z= 0.279 Chirality : 0.041 0.146 3831 Planarity : 0.004 0.048 4320 Dihedral : 7.464 87.850 3520 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.28 % Allowed : 5.77 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.15), residues: 3142 helix: 1.71 (0.15), residues: 1251 sheet: 0.66 (0.24), residues: 421 loop : -0.87 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 118 HIS 0.003 0.001 HIS C 474 PHE 0.012 0.001 PHE D 259 TYR 0.019 0.001 TYR E 366 ARG 0.003 0.000 ARG E 258 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 2.552 Fit side-chains REVERT: A 300 ASP cc_start: 0.7045 (t0) cc_final: 0.6790 (t0) REVERT: C 261 MET cc_start: 0.8391 (mmm) cc_final: 0.7948 (tpt) REVERT: D 255 ASN cc_start: 0.8006 (t0) cc_final: 0.7523 (t0) REVERT: D 309 TYR cc_start: 0.8156 (t80) cc_final: 0.7922 (t80) REVERT: E 343 PHE cc_start: 0.8536 (t80) cc_final: 0.8261 (t80) REVERT: G 53 MET cc_start: 0.8799 (ppp) cc_final: 0.8555 (ppp) REVERT: G 206 MET cc_start: 0.6852 (ppp) cc_final: 0.6576 (ppp) outliers start: 7 outliers final: 3 residues processed: 112 average time/residue: 0.3192 time to fit residues: 61.4159 Evaluate side-chains 104 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain F residue 305 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 158 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 237 optimal weight: 3.9990 chunk 194 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 285 optimal weight: 0.5980 chunk 308 optimal weight: 5.9990 chunk 254 optimal weight: 5.9990 chunk 283 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 229 optimal weight: 7.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 GLN B 43 HIS ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 24377 Z= 0.420 Angle : 0.672 8.037 33075 Z= 0.354 Chirality : 0.044 0.188 3831 Planarity : 0.005 0.056 4320 Dihedral : 7.497 85.980 3520 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.69 % Allowed : 11.38 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.15), residues: 3142 helix: 1.33 (0.15), residues: 1250 sheet: 0.53 (0.24), residues: 426 loop : -1.04 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 118 HIS 0.009 0.002 HIS E 56 PHE 0.021 0.002 PHE B 340 TYR 0.020 0.002 TYR C 231 ARG 0.006 0.001 ARG F 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 2.726 Fit side-chains REVERT: A 300 ASP cc_start: 0.7588 (t0) cc_final: 0.7359 (t0) REVERT: C 261 MET cc_start: 0.8530 (mmm) cc_final: 0.7538 (tpt) REVERT: D 255 ASN cc_start: 0.8046 (t0) cc_final: 0.7565 (t0) REVERT: D 287 MET cc_start: 0.8880 (ttp) cc_final: 0.8619 (ttm) REVERT: D 309 TYR cc_start: 0.8386 (t80) cc_final: 0.8158 (t80) REVERT: E 255 ASN cc_start: 0.6815 (t0) cc_final: 0.6270 (t0) REVERT: G 53 MET cc_start: 0.8736 (ppp) cc_final: 0.8463 (ppp) outliers start: 17 outliers final: 10 residues processed: 113 average time/residue: 0.3018 time to fit residues: 59.2773 Evaluate side-chains 108 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 217 PHE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 343 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 282 optimal weight: 7.9990 chunk 214 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 286 optimal weight: 1.9990 chunk 303 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 271 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN A 382 GLN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 24377 Z= 0.252 Angle : 0.567 8.170 33075 Z= 0.295 Chirality : 0.042 0.151 3831 Planarity : 0.004 0.062 4320 Dihedral : 7.195 86.909 3520 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.61 % Allowed : 12.91 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.15), residues: 3142 helix: 1.53 (0.15), residues: 1258 sheet: 0.58 (0.24), residues: 427 loop : -1.05 (0.16), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 118 HIS 0.004 0.001 HIS A 455 PHE 0.013 0.001 PHE B 340 TYR 0.021 0.001 TYR E 366 ARG 0.003 0.000 ARG E 258 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 102 time to evaluate : 2.892 Fit side-chains REVERT: A 300 ASP cc_start: 0.7533 (t0) cc_final: 0.7248 (t0) REVERT: B 431 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8900 (mm) REVERT: C 261 MET cc_start: 0.8523 (mmm) cc_final: 0.7725 (tpt) REVERT: C 324 MET cc_start: 0.8280 (mmm) cc_final: 0.7899 (tpp) REVERT: D 255 ASN cc_start: 0.8114 (t0) cc_final: 0.7713 (t0) REVERT: D 273 MET cc_start: 0.8989 (mmm) cc_final: 0.8784 (mtt) REVERT: D 287 MET cc_start: 0.8865 (ttp) cc_final: 0.8608 (ttm) REVERT: D 309 TYR cc_start: 0.8342 (t80) cc_final: 0.8086 (t80) REVERT: E 255 ASN cc_start: 0.6881 (t0) cc_final: 0.6266 (t0) REVERT: F 32 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.9007 (tt) REVERT: G 53 MET cc_start: 0.8733 (ppp) cc_final: 0.8475 (ppp) REVERT: G 206 MET cc_start: 0.7121 (ppp) cc_final: 0.6828 (ppp) outliers start: 40 outliers final: 25 residues processed: 136 average time/residue: 0.2973 time to fit residues: 70.4961 Evaluate side-chains 124 residues out of total 2561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 479 HIS Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 217 PHE Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 415 ASN Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain G residue 103 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.2088 > 50: distance: 20 - 40: 14.806 distance: 36 - 40: 18.379 distance: 40 - 41: 21.888 distance: 41 - 42: 13.796 distance: 41 - 44: 9.849 distance: 42 - 43: 28.552 distance: 42 - 48: 23.643 distance: 44 - 45: 12.657 distance: 45 - 46: 4.221 distance: 45 - 47: 3.016 distance: 48 - 49: 16.557 distance: 49 - 50: 7.613 distance: 49 - 52: 10.032 distance: 50 - 51: 14.462 distance: 50 - 59: 14.223 distance: 52 - 53: 15.283 distance: 53 - 54: 7.017 distance: 54 - 55: 8.795 distance: 55 - 56: 4.148 distance: 56 - 57: 3.785 distance: 56 - 58: 3.382 distance: 59 - 60: 21.348 distance: 60 - 61: 23.743 distance: 60 - 63: 7.780 distance: 61 - 62: 26.952 distance: 61 - 70: 21.699 distance: 63 - 64: 7.534 distance: 64 - 65: 12.314 distance: 65 - 66: 3.417 distance: 66 - 67: 7.887 distance: 67 - 68: 7.692 distance: 67 - 69: 7.098 distance: 70 - 71: 19.344 distance: 70 - 76: 4.367 distance: 71 - 72: 9.745 distance: 71 - 74: 26.239 distance: 72 - 73: 20.076 distance: 72 - 77: 21.520 distance: 74 - 75: 12.407 distance: 75 - 76: 24.474 distance: 77 - 78: 6.012 distance: 77 - 83: 14.671 distance: 78 - 79: 14.567 distance: 78 - 81: 22.711 distance: 79 - 80: 18.079 distance: 79 - 84: 23.095 distance: 81 - 82: 14.901 distance: 82 - 83: 16.575 distance: 84 - 85: 25.676 distance: 85 - 86: 16.901 distance: 86 - 87: 22.450 distance: 86 - 88: 22.572 distance: 88 - 89: 16.174 distance: 89 - 90: 8.843 distance: 89 - 92: 31.281 distance: 90 - 91: 23.401 distance: 90 - 99: 7.718 distance: 91 - 113: 23.232 distance: 92 - 93: 10.167 distance: 93 - 94: 16.968 distance: 94 - 95: 6.817 distance: 95 - 96: 5.077 distance: 96 - 97: 10.820 distance: 96 - 98: 17.667 distance: 99 - 100: 7.445 distance: 100 - 101: 4.201 distance: 100 - 103: 9.439 distance: 101 - 102: 27.137 distance: 103 - 104: 17.422 distance: 104 - 105: 12.274 distance: 105 - 106: 3.821 distance: 105 - 107: 6.468 distance: 108 - 109: 4.968 distance: 109 - 110: 15.620 distance: 109 - 112: 23.203 distance: 110 - 111: 16.268 distance: 110 - 113: 16.067 distance: 113 - 114: 6.460 distance: 114 - 115: 4.089 distance: 114 - 117: 13.770 distance: 115 - 116: 20.600 distance: 115 - 124: 3.569 distance: 117 - 118: 8.288 distance: 118 - 120: 4.857 distance: 119 - 121: 6.773 distance: 120 - 122: 5.964 distance: 121 - 123: 3.080