Starting phenix.real_space_refine (version: 1.19rc7) on Tue Jan 5 23:21:12 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi8_4552/01_2021/6qi8_4552_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi8_4552/01_2021/6qi8_4552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi8_4552/01_2021/6qi8_4552.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi8_4552/01_2021/6qi8_4552.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi8_4552/01_2021/6qi8_4552_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi8_4552/01_2021/6qi8_4552_updated.pdb" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 14789 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2423 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 306} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2369 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 10, 'TRANS': 299} Chain breaks: 2 Chain: "C" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2401 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 305} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2287 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 286} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2585 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2562 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.61, per 1000 atoms: 0.51 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 120 or resid 239 through 248 or (resid 274 throu \ gh 276 and (name N or name CA or name C or name O or name CB )) or resid 277 thr \ ough 452 or resid 501)) selection = (chain 'B' and (resid 2 through 120 or resid 239 through 248 or (resid 274 throu \ gh 276 and (name N or name CA or name C or name O or name CB )) or resid 277 thr \ ough 452 or resid 501)) selection = (chain 'C' and (resid 2 through 120 or resid 239 through 248 or resid 274 throug \ h 452 or resid 501)) } ncs_group { reference = (chain 'D' and (resid 23 through 282 or (resid 283 and (name N or name CA or nam \ e C or name O or name CB )) or resid 284 through 453 or resid 501)) selection = (chain 'E' and (resid 23 through 127 or resid 243 through 249 or (resid 270 and \ (name N or name CA or name C or name O or name CB )) or resid 271 through 282 or \ (resid 283 and (name N or name CA or name C or name O or name CB )) or resid 28 \ 4 through 451 or (resid 452 through 453 and (name N or name CA or name C or name \ O or name CB )) or resid 501)) selection = (chain 'F' and (resid 23 through 127 or resid 243 through 249 or resid 270 throu \ gh 451 or (resid 452 through 453 and (name N or name CA or name C or name O or n \ ame CB )) or resid 501)) } Number of scatterers: 14789 At special positions: 0 Unit cell: (135.16, 128.62, 80.66, 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 69 16.00 P 12 15.00 O 2880 8.00 N 2584 7.00 C 9244 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 - 3.50 Amimo acid : False - 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.66 Conformation dependent library (CDL) restraints added in 2.1 seconds 3750 Ramachandran restraints generated. 1875 Oldfield and 0 Emsley and 1875 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3538 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 16 sheets defined 43.0% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 43 through 57 removed outlier: 3.509A pdb=" N VAL A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 85 removed outlier: 3.543A pdb=" N ILE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 108 through 116 removed outlier: 3.574A pdb=" N LEU A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 246 No H-bonds generated for 'chain 'A' and resid 243 through 246' Processing helix chain 'A' and resid 276 through 289 removed outlier: 3.638A pdb=" N LYS A 281 " --> pdb=" O GLY A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 309 through 316 removed outlier: 3.578A pdb=" N THR A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 368 through 381 removed outlier: 4.028A pdb=" N LYS A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN A 373 " --> pdb=" O GLN A 369 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 397 removed outlier: 3.958A pdb=" N HIS A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 417 removed outlier: 3.772A pdb=" N GLN A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N THR A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Proline residue: A 412 - end of helix removed outlier: 3.595A pdb=" N LEU A 416 " --> pdb=" O PRO A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 435 removed outlier: 3.554A pdb=" N GLU A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 454 removed outlier: 3.641A pdb=" N LYS A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 57 removed outlier: 4.315A pdb=" N ALA B 48 " --> pdb=" O ASN B 44 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 51 " --> pdb=" O GLU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 86 removed outlier: 3.849A pdb=" N ALA B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 108 through 116 removed outlier: 3.977A pdb=" N ASN B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 246 removed outlier: 3.774A pdb=" N ASP B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 289 removed outlier: 3.944A pdb=" N LYS B 281 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP B 288 " --> pdb=" O ASN B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 309 through 317 removed outlier: 3.739A pdb=" N THR B 313 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 371 through 380 removed outlier: 3.760A pdb=" N ILE B 375 " --> pdb=" O MET B 371 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 377 " --> pdb=" O GLN B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 394 removed outlier: 3.710A pdb=" N HIS B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 removed outlier: 3.535A pdb=" N LYS B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 400' Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.617A pdb=" N GLN B 408 " --> pdb=" O ARG B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 411 through 419 Processing helix chain 'B' and resid 427 through 436 removed outlier: 4.207A pdb=" N GLU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 451 removed outlier: 3.604A pdb=" N ASP B 449 " --> pdb=" O LYS B 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 18 removed outlier: 3.547A pdb=" N HIS C 18 " --> pdb=" O ILE C 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 15 through 18' Processing helix chain 'C' and resid 44 through 57 removed outlier: 3.523A pdb=" N ALA C 48 " --> pdb=" O ASN C 44 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS C 57 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 82 removed outlier: 3.754A pdb=" N ALA C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 108 through 116 removed outlier: 3.740A pdb=" N VAL C 111 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N MET C 113 " --> pdb=" O GLU C 110 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU C 114 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE C 116 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 removed outlier: 4.022A pdb=" N ALA C 246 " --> pdb=" O ASP C 242 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 242 through 247' Processing helix chain 'C' and resid 274 through 277 No H-bonds generated for 'chain 'C' and resid 274 through 277' Processing helix chain 'C' and resid 280 through 289 removed outlier: 3.984A pdb=" N LYS C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP C 288 " --> pdb=" O ASN C 284 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 309 through 317 removed outlier: 3.868A pdb=" N THR C 313 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TYR C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 352 through 357 removed outlier: 3.693A pdb=" N ASP C 356 " --> pdb=" O LEU C 352 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ARG C 357 " --> pdb=" O ASP C 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 352 through 357' Processing helix chain 'C' and resid 368 through 382 removed outlier: 3.618A pdb=" N LYS C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN C 373 " --> pdb=" O GLN C 369 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 375 " --> pdb=" O MET C 371 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU C 382 " --> pdb=" O ARG C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 400 removed outlier: 3.769A pdb=" N GLU C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 415 through 419 removed outlier: 3.794A pdb=" N ILE C 419 " --> pdb=" O LEU C 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 415 through 419' Processing helix chain 'C' and resid 427 through 436 removed outlier: 3.535A pdb=" N GLU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 449 removed outlier: 3.604A pdb=" N ALA C 444 " --> pdb=" O ALA C 440 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 446 " --> pdb=" O SER C 442 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 447 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 64 removed outlier: 3.723A pdb=" N ARG D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY D 57 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 92 removed outlier: 3.694A pdb=" N ALA D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN D 92 " --> pdb=" O MET D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 115 through 123 removed outlier: 3.862A pdb=" N LEU D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 248 Processing helix chain 'D' and resid 271 through 286 removed outlier: 3.615A pdb=" N GLN D 275 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE D 276 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN D 277 " --> pdb=" O GLU D 274 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA D 281 " --> pdb=" O ALA D 278 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU D 282 " --> pdb=" O LYS D 279 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TRP D 283 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG D 284 " --> pdb=" O ALA D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 303 No H-bonds generated for 'chain 'D' and resid 301 through 303' Processing helix chain 'D' and resid 306 through 317 removed outlier: 3.612A pdb=" N SER D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU D 317 " --> pdb=" O ASN D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 348 through 353 removed outlier: 3.702A pdb=" N ASP D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ARG D 353 " --> pdb=" O ASP D 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 348 through 353' Processing helix chain 'D' and resid 364 through 377 removed outlier: 3.646A pdb=" N LYS D 368 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE D 370 " --> pdb=" O ASP D 366 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D 376 " --> pdb=" O ARG D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 396 removed outlier: 3.525A pdb=" N THR D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL D 389 " --> pdb=" O ASP D 385 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG D 392 " --> pdb=" O THR D 388 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 393 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 408 No H-bonds generated for 'chain 'D' and resid 405 through 408' Processing helix chain 'D' and resid 412 through 415 No H-bonds generated for 'chain 'D' and resid 412 through 415' Processing helix chain 'D' and resid 423 through 432 removed outlier: 4.824A pdb=" N SER D 431 " --> pdb=" O LYS D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 452 removed outlier: 3.700A pdb=" N THR D 440 " --> pdb=" O GLU D 436 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN D 441 " --> pdb=" O SER D 437 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA D 449 " --> pdb=" O GLU D 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 65 removed outlier: 3.989A pdb=" N ALA E 56 " --> pdb=" O ALA E 52 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 92 removed outlier: 3.554A pdb=" N MET E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 107 No H-bonds generated for 'chain 'E' and resid 105 through 107' Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 244 through 252 removed outlier: 3.781A pdb=" N ASP E 248 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE E 250 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN E 251 " --> pdb=" O ILE E 247 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER E 252 " --> pdb=" O ASP E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 271 through 283 removed outlier: 3.539A pdb=" N ALA E 281 " --> pdb=" O ASN E 277 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 303 No H-bonds generated for 'chain 'E' and resid 301 through 303' Processing helix chain 'E' and resid 306 through 312 removed outlier: 3.532A pdb=" N SER E 310 " --> pdb=" O ILE E 306 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N PHE E 311 " --> pdb=" O GLU E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 345 No H-bonds generated for 'chain 'E' and resid 343 through 345' Processing helix chain 'E' and resid 348 through 353 removed outlier: 3.739A pdb=" N ASP E 352 " --> pdb=" O ILE E 348 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ARG E 353 " --> pdb=" O ASP E 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 348 through 353' Processing helix chain 'E' and resid 364 through 377 removed outlier: 3.632A pdb=" N LYS E 368 " --> pdb=" O GLU E 364 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN E 369 " --> pdb=" O LYS E 365 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS E 375 " --> pdb=" O LEU E 371 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU E 376 " --> pdb=" O ARG E 372 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU E 377 " --> pdb=" O ILE E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 394 removed outlier: 3.537A pdb=" N ARG E 392 " --> pdb=" O THR E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 415 removed outlier: 3.970A pdb=" N ILE E 406 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU E 411 " --> pdb=" O THR E 407 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 432 removed outlier: 3.613A pdb=" N TYR E 430 " --> pdb=" O ILE E 426 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N SER E 431 " --> pdb=" O LYS E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 451 removed outlier: 3.883A pdb=" N MET E 443 " --> pdb=" O SER E 439 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS E 444 " --> pdb=" O THR E 440 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA E 449 " --> pdb=" O GLU E 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 23 No H-bonds generated for 'chain 'F' and resid 21 through 23' Processing helix chain 'F' and resid 50 through 65 removed outlier: 3.744A pdb=" N ARG F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY F 57 " --> pdb=" O ARG F 53 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL F 58 " --> pdb=" O ARG F 54 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG F 64 " --> pdb=" O LEU F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.935A pdb=" N ALA F 87 " --> pdb=" O LYS F 83 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN F 92 " --> pdb=" O MET F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 108 No H-bonds generated for 'chain 'F' and resid 106 through 108' Processing helix chain 'F' and resid 120 through 123 No H-bonds generated for 'chain 'F' and resid 120 through 123' Processing helix chain 'F' and resid 245 through 249 removed outlier: 3.633A pdb=" N VAL F 249 " --> pdb=" O GLU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 263 Processing helix chain 'F' and resid 270 through 279 removed outlier: 3.540A pdb=" N ALA F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 303 No H-bonds generated for 'chain 'F' and resid 301 through 303' Processing helix chain 'F' and resid 306 through 317 removed outlier: 3.663A pdb=" N SER F 310 " --> pdb=" O ILE F 306 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N PHE F 311 " --> pdb=" O GLU F 307 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN F 313 " --> pdb=" O PHE F 309 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU F 317 " --> pdb=" O ASN F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 345 No H-bonds generated for 'chain 'F' and resid 343 through 345' Processing helix chain 'F' and resid 348 through 353 removed outlier: 3.878A pdb=" N ASP F 352 " --> pdb=" O ILE F 348 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ARG F 353 " --> pdb=" O ASP F 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 348 through 353' Processing helix chain 'F' and resid 366 through 376 removed outlier: 3.643A pdb=" N LEU F 371 " --> pdb=" O THR F 367 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG F 372 " --> pdb=" O LYS F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 396 removed outlier: 3.647A pdb=" N THR F 388 " --> pdb=" O GLU F 384 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL F 389 " --> pdb=" O ASP F 385 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG F 392 " --> pdb=" O THR F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 415 removed outlier: 4.112A pdb=" N VAL F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS F 413 " --> pdb=" O ALA F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 432 removed outlier: 3.963A pdb=" N VAL F 429 " --> pdb=" O ASP F 425 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER F 431 " --> pdb=" O LYS F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 451 removed outlier: 3.560A pdb=" N GLU F 445 " --> pdb=" O GLN F 441 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 358 through 363 removed outlier: 6.531A pdb=" N ALA A 65 " --> pdb=" O MET A 359 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE A 361 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 67 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N THR A 363 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA A 69 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE A 329 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N GLY A 70 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N SER A 331 " --> pdb=" O GLY A 70 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 93 through 97 removed outlier: 7.264A pdb=" N VAL A 298 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N MET A 96 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N PHE A 300 " --> pdb=" O MET A 96 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 335 through 337 Processing sheet with id= D, first strand: chain 'B' and resid 358 through 363 removed outlier: 6.289A pdb=" N ALA B 65 " --> pdb=" O MET B 359 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE B 361 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU B 67 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR B 363 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA B 69 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS B 94 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE B 300 " --> pdb=" O CYS B 94 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 335 through 337 Processing sheet with id= F, first strand: chain 'C' and resid 65 through 70 Processing sheet with id= G, first strand: chain 'C' and resid 94 through 97 removed outlier: 6.733A pdb=" N ILE C 326 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL C 301 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE C 328 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 335 through 337 Processing sheet with id= I, first strand: chain 'D' and resid 354 through 358 removed outlier: 6.351A pdb=" N ALA D 72 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL D 357 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU D 74 " --> pdb=" O VAL D 357 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR D 328 " --> pdb=" O ILE D 75 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 102 through 104 removed outlier: 6.531A pdb=" N PHE D 297 " --> pdb=" O ILE D 103 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 332 through 334 Processing sheet with id= L, first strand: chain 'E' and resid 354 through 358 removed outlier: 6.779A pdb=" N ALA E 72 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL E 357 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU E 74 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR E 101 " --> pdb=" O VAL E 295 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 127 through 130 Processing sheet with id= N, first strand: chain 'E' and resid 332 through 334 Processing sheet with id= O, first strand: chain 'F' and resid 354 through 358 removed outlier: 6.834A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR F 328 " --> pdb=" O ILE F 75 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 332 through 334 333 hydrogen bonds defined for protein. 963 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: 4.11 Time building geometry restraints manager: 6.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4978 1.34 - 1.46: 2664 1.46 - 1.58: 7195 1.58 - 1.70: 18 1.70 - 1.81: 120 Bond restraints: 14975 Sorted by residual: bond pdb=" N LYS B 7 " pdb=" CA LYS B 7 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.23e-02 6.61e+03 5.88e+00 bond pdb=" CA THR C 10 " pdb=" CB THR C 10 " ideal model delta sigma weight residual 1.532 1.564 -0.033 1.36e-02 5.41e+03 5.79e+00 bond pdb=" N LYS A 7 " pdb=" CA LYS A 7 " ideal model delta sigma weight residual 1.458 1.488 -0.029 1.23e-02 6.61e+03 5.72e+00 bond pdb=" N LYS C 7 " pdb=" CA LYS C 7 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.56e+00 bond pdb=" N GLU C 342 " pdb=" CA GLU C 342 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.15e-02 7.56e+03 3.59e+00 ... (remaining 14970 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.65: 386 106.65 - 114.27: 9043 114.27 - 121.89: 7697 121.89 - 129.51: 3043 129.51 - 137.12: 63 Bond angle restraints: 20232 Sorted by residual: angle pdb=" N VAL F 249 " pdb=" CA VAL F 249 " pdb=" C VAL F 249 " ideal model delta sigma weight residual 113.53 106.69 6.84 9.80e-01 1.04e+00 4.87e+01 angle pdb=" C VAL A 6 " pdb=" N LYS A 7 " pdb=" CA LYS A 7 " ideal model delta sigma weight residual 120.82 130.86 -10.04 1.50e+00 4.44e-01 4.48e+01 angle pdb=" C VAL B 6 " pdb=" N LYS B 7 " pdb=" CA LYS B 7 " ideal model delta sigma weight residual 120.82 130.84 -10.02 1.50e+00 4.44e-01 4.46e+01 angle pdb=" C ILE E 13 " pdb=" N ARG E 14 " pdb=" CA ARG E 14 " ideal model delta sigma weight residual 121.19 129.37 -8.18 1.59e+00 3.96e-01 2.65e+01 angle pdb=" C GLU D 378 " pdb=" N ASP D 379 " pdb=" CA ASP D 379 " ideal model delta sigma weight residual 121.54 131.27 -9.73 1.91e+00 2.74e-01 2.60e+01 ... (remaining 20227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.36: 8927 33.36 - 66.72: 237 66.72 - 100.08: 37 100.08 - 133.44: 3 133.44 - 166.81: 2 Dihedral angle restraints: 9206 sinusoidal: 3737 harmonic: 5469 Sorted by residual: dihedral pdb=" O2A ADP C 501 " pdb=" O3A ADP C 501 " pdb=" PA ADP C 501 " pdb=" PB ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 106.81 -166.81 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O1B ADP C 501 " pdb=" O3A ADP C 501 " pdb=" PB ADP C 501 " pdb=" PA ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 81.57 -141.57 1 2.00e+01 2.50e-03 4.28e+01 dihedral pdb=" O1B ADP B 501 " pdb=" O3A ADP B 501 " pdb=" PB ADP B 501 " pdb=" PA ADP B 501 " ideal model delta sinusoidal sigma weight residual -60.00 -179.11 119.10 1 2.00e+01 2.50e-03 3.57e+01 ... (remaining 9203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1993 0.063 - 0.125: 336 0.125 - 0.188: 52 0.188 - 0.251: 9 0.251 - 0.313: 5 Chirality restraints: 2395 Sorted by residual: chirality pdb=" CB VAL E 10 " pdb=" CA VAL E 10 " pdb=" CG1 VAL E 10 " pdb=" CG2 VAL E 10 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CB VAL F 10 " pdb=" CA VAL F 10 " pdb=" CG1 VAL F 10 " pdb=" CG2 VAL F 10 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA VAL F 16 " pdb=" N VAL F 16 " pdb=" C VAL F 16 " pdb=" CB VAL F 16 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 2392 not shown) Planarity restraints: 2578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 327 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.67e+00 pdb=" C VAL A 327 " -0.048 2.00e-02 2.50e+03 pdb=" O VAL A 327 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE A 328 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 10 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO E 11 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 11 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 11 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 10 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO F 11 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO F 11 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 11 " 0.038 5.00e-02 4.00e+02 ... (remaining 2575 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 114 2.58 - 3.16: 10795 3.16 - 3.74: 21269 3.74 - 4.32: 29684 4.32 - 4.90: 48379 Nonbonded interactions: 110241 Sorted by model distance: nonbonded pdb=" CB ARG F 14 " pdb=" CG1 VAL F 242 " model vdw 1.999 3.860 nonbonded pdb=" O VAL A 6 " pdb=" OD2 ASP A 242 " model vdw 2.037 3.040 nonbonded pdb=" OG SER E 243 " pdb=" OE1 GLU E 246 " model vdw 2.300 2.440 nonbonded pdb=" O SER E 363 " pdb=" OG1 THR E 367 " model vdw 2.304 2.440 nonbonded pdb=" OG SER E 114 " pdb=" OE1 GLU E 117 " model vdw 2.314 2.440 ... (remaining 110236 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 0 14789 True True No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 69 5.16 5 C 9244 2.51 5 N 2584 2.21 5 O 2880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables 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: 0.660 Set model interpretation parameters: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.190 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.060 Process input model: 40.760 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.350 Internal consistency checks: 0.000 Total: 49.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0212 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.060 14975 Angle : 0.910 10.039 20232 Chirality : 0.052 0.313 2395 Planarity : 0.006 0.068 2578 Dihedral : 16.348 166.805 5668 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer Outliers : 0.19 % 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: -5.84 (0.13), residues: 1875 helix: -4.93 (0.05), residues: 871 sheet: -2.18 (0.33), residues: 199 loop : -2.85 (0.16), residues: 805 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield and 0 Emsley and 1875 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield and 0 Emsley and 1875 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1599 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 3 poor density : 163 time to evaluate : 1.687 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 166 average time/residue: 0.3002 time to fit residues: 52.7466 Evaluate side-chains 109 residues out of total 1599 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 108 time to evaluate : 1.633 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1500 time to fit residues: 2.5559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 147 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN A 429 HIS A 450 GLN ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN B 241 HIS B 380 GLN C 18 HIS C 42 GLN C 85 GLN C 241 HIS C 247 ASN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 GLN E 49 GLN E 251 ASN ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 344 HIS F 41 GLN F 92 GLN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 447 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1685 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.075 14975 Angle : 0.920 11.577 20232 Chirality : 0.051 0.310 2395 Planarity : 0.006 0.078 2578 Dihedral : 10.598 157.420 2111 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.57 % Favored : 92.37 % Rotamer Outliers : 0.44 % 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: -4.48 (0.15), residues: 1875 helix: -3.75 (0.11), residues: 839 sheet: -1.92 (0.34), residues: 187 loop : -2.21 (0.19), residues: 849 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield and 0 Emsley and 1875 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield and 0 Emsley and 1875 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1599 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 7 poor density : 133 time to evaluate : 1.717 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 139 average time/residue: 0.2869 time to fit residues: 42.7755 Evaluate side-chains 110 residues out of total 1599 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 109 time to evaluate : 1.704 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1416 time to fit residues: 2.6805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 184 optimal weight: 0.0980 chunk 152 optimal weight: 2.9990 chunk 169 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 137 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 HIS ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN C 380 GLN ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 HIS E 49 GLN E 251 ASN F 344 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1595 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.051 14975 Angle : 0.667 12.175 20232 Chirality : 0.044 0.184 2395 Planarity : 0.004 0.054 2578 Dihedral : 9.059 122.965 2111 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.76 % Favored : 94.19 % Rotamer Outliers : 0.06 % 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: -3.58 (0.17), residues: 1875 helix: -2.79 (0.14), residues: 844 sheet: -1.46 (0.36), residues: 199 loop : -1.99 (0.19), residues: 832 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield and 0 Emsley and 1875 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield and 0 Emsley and 1875 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1599 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 135 time to evaluate : 1.704 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 136 average time/residue: 0.2673 time to fit residues: 39.2959 Evaluate side-chains 112 residues out of total 1599 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 111 time to evaluate : 1.599 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1394 time to fit residues: 2.6227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 9.9990 chunk 128 optimal weight: 0.3980 chunk 88 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 171 optimal weight: 0.0970 chunk 181 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 ASN ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN E 344 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1794 moved from start: 0.7069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.066 14975 Angle : 0.669 11.668 20232 Chirality : 0.044 0.197 2395 Planarity : 0.004 0.050 2578 Dihedral : 8.742 115.452 2111 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer Outliers : 0.00 % 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: -2.93 (0.18), residues: 1875 helix: -2.22 (0.16), residues: 840 sheet: -1.15 (0.37), residues: 185 loop : -1.68 (0.20), residues: 850 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield and 0 Emsley and 1875 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield and 0 Emsley and 1875 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1599 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.557 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.2972 time to fit residues: 41.9386 Evaluate side-chains 111 residues out of total 1599 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.751 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 92 optimal weight: 0.3980 chunk 163 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN D 422 GLN F 245 HIS F 302 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2685 moved from start: 1.0564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.006 0.072 14975 Angle : 1.090 25.446 20232 Chirality : 0.055 0.277 2395 Planarity : 0.007 0.074 2578 Dihedral : 11.080 152.832 2111 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 26.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.70 (0.17), residues: 1875 helix: -2.77 (0.15), residues: 797 sheet: -1.33 (0.40), residues: 158 loop : -2.30 (0.19), residues: 920 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield and 0 Emsley and 1875 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield and 0 Emsley and 1875 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1599 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 6 poor density : 136 time to evaluate : 1.545 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 142 average time/residue: 0.2858 time to fit residues: 43.6768 Evaluate side-chains 125 residues out of total 1599 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 4 poor density : 121 time to evaluate : 1.641 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1618 time to fit residues: 2.9997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 44 optimal weight: 10.0000 chunk 181 optimal weight: 0.2980 chunk 150 optimal weight: 0.0270 chunk 84 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 60 optimal weight: 0.3980 chunk 95 optimal weight: 4.9990 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 GLN ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 HIS ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN D 313 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2189 moved from start: 1.0088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.037 14975 Angle : 0.693 16.672 20232 Chirality : 0.045 0.169 2395 Planarity : 0.004 0.048 2578 Dihedral : 9.117 122.025 2111 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer Outliers : 0.00 % 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: -2.98 (0.18), residues: 1875 helix: -2.06 (0.16), residues: 846 sheet: -1.09 (0.40), residues: 173 loop : -1.95 (0.20), residues: 856 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield and 0 Emsley and 1875 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield and 0 Emsley and 1875 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1599 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.655 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2716 time to fit residues: 38.3896 Evaluate side-chains 115 residues out of total 1599 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.771 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 102 optimal weight: 0.5980 chunk 153 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 181 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS B 115 ASN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2635 moved from start: 1.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.111 14975 Angle : 0.883 22.697 20232 Chirality : 0.049 0.206 2395 Planarity : 0.005 0.071 2578 Dihedral : 9.962 139.726 2111 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer Outliers : 0.00 % 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: -3.03 (0.18), residues: 1875 helix: -2.14 (0.16), residues: 791 sheet: -1.44 (0.40), residues: 158 loop : -1.91 (0.20), residues: 926 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield and 0 Emsley and 1875 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield and 0 Emsley and 1875 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1599 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.751 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2657 time to fit residues: 39.2941 Evaluate side-chains 118 residues out of total 1599 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.692 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 0.9980 chunk 72 optimal weight: 0.0670 chunk 108 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 142 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 HIS ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2431 moved from start: 1.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.059 14975 Angle : 0.720 18.793 20232 Chirality : 0.045 0.171 2395 Planarity : 0.004 0.050 2578 Dihedral : 9.011 123.991 2111 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer Outliers : 0.00 % 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: -2.77 (0.18), residues: 1875 helix: -1.83 (0.17), residues: 806 sheet: -1.60 (0.38), residues: 172 loop : -1.79 (0.20), residues: 897 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield and 0 Emsley and 1875 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield and 0 Emsley and 1875 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1599 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.684 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.2984 time to fit residues: 45.1748 Evaluate side-chains 124 residues out of total 1599 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.678 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 168 optimal weight: 8.9990 chunk 101 optimal weight: 0.0370 chunk 73 optimal weight: 7.9990 chunk 132 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN E 92 GLN E 277 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2438 moved from start: 1.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.244 14975 Angle : 0.717 16.846 20232 Chirality : 0.045 0.176 2395 Planarity : 0.004 0.078 2578 Dihedral : 8.616 121.665 2111 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer Outliers : 0.00 % 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: -2.51 (0.19), residues: 1875 helix: -1.55 (0.17), residues: 804 sheet: -1.65 (0.37), residues: 172 loop : -1.67 (0.20), residues: 899 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield and 0 Emsley and 1875 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield and 0 Emsley and 1875 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1599 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.718 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2777 time to fit residues: 40.5205 Evaluate side-chains 119 residues out of total 1599 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.664 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 1.9990 chunk 84 optimal weight: 0.0470 chunk 124 optimal weight: 10.0000 chunk 187 optimal weight: 0.8980 chunk 172 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 115 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 158 optimal weight: 0.8980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN B 115 ASN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2369 moved from start: 1.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.111 14975 Angle : 0.685 17.409 20232 Chirality : 0.044 0.168 2395 Planarity : 0.004 0.070 2578 Dihedral : 8.177 118.281 2111 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer Outliers : 0.00 % 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: -2.43 (0.19), residues: 1875 helix: -1.50 (0.17), residues: 830 sheet: -1.59 (0.38), residues: 164 loop : -1.62 (0.21), residues: 881 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield and 0 Emsley and 1875 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield and 0 Emsley and 1875 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1599 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.582 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2661 time to fit residues: 39.9599 Evaluate side-chains 120 residues out of total 1599 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.669 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 149 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 153 optimal weight: 0.6980 chunk 18 optimal weight: 0.0870 chunk 27 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 8 optimal weight: 0.0020 overall best weight: 0.4566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.263771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.245205 restraints weight = 22033.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.249344 restraints weight = 13646.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.252218 restraints weight = 9257.638| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.004 0.450 14975 ANGLE : 0.743 27.495 20232 CHIRALITY : 0.044 0.174 2395 PLANARITY : 0.004 0.076 2578 DIHEDRAL : 8.002 116.481 2111 MIN NONBONDED DISTANCE : 2.118 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 13.20 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 7.15 % FAVORED : 92.85 % ROTAMER OUTLIERS : 0.00 % 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: -2.24 (0.19), RESIDUES: 1875 HELIX: -1.34 (0.17), RESIDUES: 827 SHEET: -1.57 (0.38), RESIDUES: 164 LOOP : -1.49 (0.21), RESIDUES: 884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2239 moved from start: 1.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.450 14975 Angle : 0.743 27.495 20232 Chirality : 0.044 0.174 2395 Planarity : 0.004 0.076 2578 Dihedral : 8.002 116.481 2111 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer Outliers : 0.00 % 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: -2.24 (0.19), residues: 1875 helix: -1.34 (0.17), residues: 827 sheet: -1.57 (0.38), residues: 164 loop : -1.49 (0.21), residues: 884 =============================================================================== Job complete usr+sys time: 2401.37 seconds wall clock time: 45 minutes 26.06 seconds (2726.06 seconds total)