Starting phenix.real_space_refine on Thu May 22 21:37:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ev1_19991/05_2025/9ev1_19991.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ev1_19991/05_2025/9ev1_19991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ev1_19991/05_2025/9ev1_19991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ev1_19991/05_2025/9ev1_19991.map" model { file = "/net/cci-nas-00/data/ceres_data/9ev1_19991/05_2025/9ev1_19991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ev1_19991/05_2025/9ev1_19991.cif" } resolution = 2.63 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= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 15123 2.51 5 N 3846 2.21 5 O 4468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23492 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4703 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 572} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 4705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4705 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 572} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 4705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4705 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 572} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 4689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4689 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 572} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 4690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4690 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 572} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 14.78, per 1000 atoms: 0.63 Number of scatterers: 23492 At special positions: 0 Unit cell: (146.427, 141.349, 154.891, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 4468 8.00 N 3846 7.00 C 15123 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: 6.09 Conformation dependent library (CDL) restraints added in 4.1 seconds 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5530 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 30 sheets defined 29.4% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 88 through 100 removed outlier: 3.815A pdb=" N GLN A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 118 removed outlier: 3.709A pdb=" N THR A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.942A pdb=" N SER A 314 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 365 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 382 through 391 Processing helix chain 'A' and resid 514 through 536 removed outlier: 3.864A pdb=" N TYR A 518 " --> pdb=" O ASN A 514 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Proline residue: A 525 - end of helix removed outlier: 3.837A pdb=" N ILE A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 541 through 564 Processing helix chain 'A' and resid 565 through 567 No H-bonds generated for 'chain 'A' and resid 565 through 567' Processing helix chain 'A' and resid 574 through 604 Processing helix chain 'A' and resid 605 through 636 Proline residue: A 621 - end of helix Processing helix chain 'B' and resid 88 through 100 removed outlier: 3.816A pdb=" N GLN B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 118 removed outlier: 3.709A pdb=" N THR B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'B' and resid 196 through 199 Processing helix chain 'B' and resid 310 through 314 removed outlier: 3.983A pdb=" N SER B 314 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 365 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 382 through 391 Processing helix chain 'B' and resid 514 through 536 removed outlier: 3.837A pdb=" N TYR B 518 " --> pdb=" O ASN B 514 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N VAL B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) Proline residue: B 525 - end of helix removed outlier: 3.770A pdb=" N ILE B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 539 No H-bonds generated for 'chain 'B' and resid 537 through 539' Processing helix chain 'B' and resid 541 through 564 removed outlier: 3.507A pdb=" N LEU B 554 " --> pdb=" O SER B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 567 No H-bonds generated for 'chain 'B' and resid 565 through 567' Processing helix chain 'B' and resid 574 through 604 Processing helix chain 'B' and resid 605 through 636 Proline residue: B 621 - end of helix Processing helix chain 'C' and resid 88 through 100 removed outlier: 3.815A pdb=" N GLN C 94 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 118 removed outlier: 3.709A pdb=" N THR C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG C 116 " --> pdb=" O ALA C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 182 Processing helix chain 'C' and resid 196 through 199 Processing helix chain 'C' and resid 310 through 314 removed outlier: 4.103A pdb=" N SER C 314 " --> pdb=" O LEU C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 365 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 382 through 391 Processing helix chain 'C' and resid 514 through 536 removed outlier: 3.834A pdb=" N TYR C 518 " --> pdb=" O ASN C 514 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N VAL C 524 " --> pdb=" O LEU C 520 " (cutoff:3.500A) Proline residue: C 525 - end of helix removed outlier: 3.828A pdb=" N ILE C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 539 No H-bonds generated for 'chain 'C' and resid 537 through 539' Processing helix chain 'C' and resid 541 through 564 removed outlier: 3.510A pdb=" N LEU C 554 " --> pdb=" O SER C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 567 No H-bonds generated for 'chain 'C' and resid 565 through 567' Processing helix chain 'C' and resid 574 through 604 Processing helix chain 'C' and resid 605 through 637 Proline residue: C 621 - end of helix removed outlier: 3.925A pdb=" N THR C 637 " --> pdb=" O LEU C 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 100 removed outlier: 3.815A pdb=" N GLN D 94 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 118 removed outlier: 3.709A pdb=" N THR D 111 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 310 through 314 removed outlier: 4.098A pdb=" N SER D 314 " --> pdb=" O LEU D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 365 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'D' and resid 382 through 391 Processing helix chain 'D' and resid 514 through 536 removed outlier: 3.866A pdb=" N TYR D 518 " --> pdb=" O ASN D 514 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Proline residue: D 525 - end of helix removed outlier: 3.845A pdb=" N ILE D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 539 No H-bonds generated for 'chain 'D' and resid 537 through 539' Processing helix chain 'D' and resid 541 through 564 removed outlier: 3.502A pdb=" N LEU D 554 " --> pdb=" O SER D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 567 No H-bonds generated for 'chain 'D' and resid 565 through 567' Processing helix chain 'D' and resid 574 through 604 Processing helix chain 'D' and resid 605 through 636 Proline residue: D 621 - end of helix Processing helix chain 'E' and resid 88 through 100 removed outlier: 3.817A pdb=" N GLN E 94 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL E 95 " --> pdb=" O SER E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 118 removed outlier: 3.709A pdb=" N THR E 111 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'E' and resid 196 through 199 Processing helix chain 'E' and resid 310 through 314 removed outlier: 4.062A pdb=" N SER E 314 " --> pdb=" O LEU E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 365 Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'E' and resid 382 through 391 Processing helix chain 'E' and resid 514 through 536 removed outlier: 3.837A pdb=" N TYR E 518 " --> pdb=" O ASN E 514 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Proline residue: E 525 - end of helix removed outlier: 3.800A pdb=" N ILE E 536 " --> pdb=" O VAL E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 539 No H-bonds generated for 'chain 'E' and resid 537 through 539' Processing helix chain 'E' and resid 541 through 564 removed outlier: 3.517A pdb=" N LEU E 554 " --> pdb=" O SER E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 567 No H-bonds generated for 'chain 'E' and resid 565 through 567' Processing helix chain 'E' and resid 574 through 604 Processing helix chain 'E' and resid 605 through 637 Proline residue: E 621 - end of helix removed outlier: 3.922A pdb=" N THR E 637 " --> pdb=" O LEU E 633 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 45 removed outlier: 5.995A pdb=" N SER A 167 " --> pdb=" O THR A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.685A pdb=" N GLY A 120 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 79 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY A 141 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP A 57 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 204 through 212 removed outlier: 4.227A pdb=" N ALA A 298 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 218 through 222 removed outlier: 7.324A pdb=" N LEU A 247 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE A 259 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU A 249 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 376 through 379 removed outlier: 4.319A pdb=" N GLN A 411 " --> pdb=" O PHE A 424 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE A 424 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE A 413 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N SER A 422 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL A 415 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG A 420 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A 341 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL A 352 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ILE A 339 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N THR A 354 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ASP A 337 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N LYS A 356 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ALA A 335 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N SER A 358 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N GLY A 333 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N HIS A 360 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N THR A 331 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASP A 328 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASN A 464 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL A 330 " --> pdb=" O ASN A 464 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE A 466 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL A 332 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 399 removed outlier: 5.084A pdb=" N SER A 503 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN A 502 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLU A 493 " --> pdb=" O ASN A 502 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG A 504 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE A 491 " --> pdb=" O ARG A 504 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR A 506 " --> pdb=" O GLN A 489 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN A 489 " --> pdb=" O THR A 506 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR A 508 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR A 487 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU A 510 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 38 through 45 removed outlier: 5.995A pdb=" N SER B 167 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.686A pdb=" N GLY B 120 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 79 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLY B 141 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP B 57 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 204 through 212 removed outlier: 4.192A pdb=" N ALA B 298 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 218 through 222 removed outlier: 7.427A pdb=" N LEU B 247 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE B 259 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU B 249 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 376 through 379 removed outlier: 4.313A pdb=" N GLN B 411 " --> pdb=" O PHE B 424 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE B 424 " --> pdb=" O GLN B 411 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE B 413 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N SER B 422 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL B 415 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ARG B 420 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY B 341 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL B 352 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE B 339 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N THR B 354 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ASP B 337 " --> pdb=" O THR B 354 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N LYS B 356 " --> pdb=" O ALA B 335 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ALA B 335 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N SER B 358 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N GLY B 333 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N HIS B 360 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N THR B 331 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASP B 328 " --> pdb=" O ILE B 462 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN B 464 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL B 330 " --> pdb=" O ASN B 464 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE B 466 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL B 332 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 397 through 399 removed outlier: 5.067A pdb=" N SER B 503 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN B 502 " --> pdb=" O GLU B 493 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLU B 493 " --> pdb=" O ASN B 502 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ARG B 504 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE B 491 " --> pdb=" O ARG B 504 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR B 506 " --> pdb=" O GLN B 489 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN B 489 " --> pdb=" O THR B 506 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR B 508 " --> pdb=" O TYR B 487 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR B 487 " --> pdb=" O THR B 508 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU B 510 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 38 through 45 removed outlier: 5.995A pdb=" N SER C 167 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.686A pdb=" N GLY C 120 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 79 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY C 141 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP C 57 " --> pdb=" O GLY C 141 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 204 through 212 removed outlier: 4.269A pdb=" N ALA C 298 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 218 through 222 removed outlier: 7.245A pdb=" N LEU C 247 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N PHE C 259 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU C 249 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 376 through 379 removed outlier: 4.198A pdb=" N GLN C 411 " --> pdb=" O PHE C 424 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N PHE C 424 " --> pdb=" O GLN C 411 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE C 413 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N SER C 422 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL C 415 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG C 420 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY C 341 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL C 352 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ILE C 339 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N THR C 354 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASP C 337 " --> pdb=" O THR C 354 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N LYS C 356 " --> pdb=" O ALA C 335 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ALA C 335 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER C 358 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N GLY C 333 " --> pdb=" O SER C 358 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N HIS C 360 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N THR C 331 " --> pdb=" O HIS C 360 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASP C 328 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASN C 464 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL C 330 " --> pdb=" O ASN C 464 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE C 466 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL C 332 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 397 through 399 removed outlier: 5.038A pdb=" N SER C 503 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN C 502 " --> pdb=" O GLU C 493 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLU C 493 " --> pdb=" O ASN C 502 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG C 504 " --> pdb=" O ILE C 491 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE C 491 " --> pdb=" O ARG C 504 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR C 506 " --> pdb=" O GLN C 489 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLN C 489 " --> pdb=" O THR C 506 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR C 508 " --> pdb=" O TYR C 487 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR C 487 " --> pdb=" O THR C 508 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU C 510 " --> pdb=" O THR C 485 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 38 through 45 removed outlier: 5.996A pdb=" N SER D 167 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.686A pdb=" N GLY D 120 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 79 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY D 141 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP D 57 " --> pdb=" O GLY D 141 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 204 through 212 removed outlier: 4.110A pdb=" N ALA D 298 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 218 through 222 removed outlier: 3.521A pdb=" N ASP D 287 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU D 247 " --> pdb=" O PHE D 259 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N PHE D 259 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU D 249 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 376 through 379 removed outlier: 4.279A pdb=" N GLN D 411 " --> pdb=" O PHE D 424 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N PHE D 424 " --> pdb=" O GLN D 411 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE D 413 " --> pdb=" O SER D 422 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER D 422 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL D 415 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG D 420 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY D 341 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL D 352 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ILE D 339 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N THR D 354 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ASP D 337 " --> pdb=" O THR D 354 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N LYS D 356 " --> pdb=" O ALA D 335 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ALA D 335 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N SER D 358 " --> pdb=" O GLY D 333 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLY D 333 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N HIS D 360 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N THR D 331 " --> pdb=" O HIS D 360 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASP D 328 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN D 464 " --> pdb=" O ASP D 328 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL D 330 " --> pdb=" O ASN D 464 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE D 466 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL D 332 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 397 through 399 removed outlier: 5.125A pdb=" N SER D 503 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN D 502 " --> pdb=" O GLU D 493 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLU D 493 " --> pdb=" O ASN D 502 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG D 504 " --> pdb=" O ILE D 491 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE D 491 " --> pdb=" O ARG D 504 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR D 506 " --> pdb=" O GLN D 489 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLN D 489 " --> pdb=" O THR D 506 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR D 508 " --> pdb=" O TYR D 487 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR D 487 " --> pdb=" O THR D 508 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU D 510 " --> pdb=" O THR D 485 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 38 through 45 removed outlier: 5.995A pdb=" N SER E 167 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 120 through 122 removed outlier: 3.685A pdb=" N GLY E 120 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL E 79 " --> pdb=" O ASP E 122 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY E 141 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP E 57 " --> pdb=" O GLY E 141 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 204 through 212 removed outlier: 4.330A pdb=" N ALA E 298 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 218 through 222 removed outlier: 7.448A pdb=" N LEU E 247 " --> pdb=" O PHE E 259 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N PHE E 259 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU E 249 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 376 through 379 removed outlier: 4.229A pdb=" N GLN E 411 " --> pdb=" O PHE E 424 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N PHE E 424 " --> pdb=" O GLN E 411 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE E 413 " --> pdb=" O SER E 422 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N SER E 422 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL E 415 " --> pdb=" O ARG E 420 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG E 420 " --> pdb=" O VAL E 415 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY E 341 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL E 352 " --> pdb=" O ILE E 339 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE E 339 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N THR E 354 " --> pdb=" O ASP E 337 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ASP E 337 " --> pdb=" O THR E 354 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N LYS E 356 " --> pdb=" O ALA E 335 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ALA E 335 " --> pdb=" O LYS E 356 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N SER E 358 " --> pdb=" O GLY E 333 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N GLY E 333 " --> pdb=" O SER E 358 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N HIS E 360 " --> pdb=" O THR E 331 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N THR E 331 " --> pdb=" O HIS E 360 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ASP E 328 " --> pdb=" O ILE E 462 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN E 464 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL E 330 " --> pdb=" O ASN E 464 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE E 466 " --> pdb=" O VAL E 330 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL E 332 " --> pdb=" O ILE E 466 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 397 through 399 removed outlier: 4.964A pdb=" N SER E 503 " --> pdb=" O LEU E 454 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN E 502 " --> pdb=" O GLU E 493 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLU E 493 " --> pdb=" O ASN E 502 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG E 504 " --> pdb=" O ILE E 491 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE E 491 " --> pdb=" O ARG E 504 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR E 506 " --> pdb=" O GLN E 489 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLN E 489 " --> pdb=" O THR E 506 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR E 508 " --> pdb=" O TYR E 487 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR E 487 " --> pdb=" O THR E 508 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU E 510 " --> pdb=" O THR E 485 " (cutoff:3.500A) 1100 hydrogen bonds defined for protein. 3024 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: 8.46 Time building geometry restraints manager: 7.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4907 1.33 - 1.45: 5720 1.45 - 1.57: 13325 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 24032 Sorted by residual: bond pdb=" CA GLU D 103 " pdb=" C GLU D 103 " ideal model delta sigma weight residual 1.526 1.489 0.037 9.20e-03 1.18e+04 1.63e+01 bond pdb=" CA GLU E 103 " pdb=" C GLU E 103 " ideal model delta sigma weight residual 1.526 1.489 0.037 9.20e-03 1.18e+04 1.62e+01 bond pdb=" CA ALA B 99 " pdb=" C ALA B 99 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.29e-02 6.01e+03 1.62e+01 bond pdb=" CA GLU B 103 " pdb=" C GLU B 103 " ideal model delta sigma weight residual 1.526 1.489 0.037 9.20e-03 1.18e+04 1.61e+01 bond pdb=" CA ALA D 99 " pdb=" C ALA D 99 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.29e-02 6.01e+03 1.60e+01 ... (remaining 24027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 32167 1.75 - 3.50: 465 3.50 - 5.25: 62 5.25 - 7.01: 16 7.01 - 8.76: 16 Bond angle restraints: 32726 Sorted by residual: angle pdb=" N TYR B 620 " pdb=" CA TYR B 620 " pdb=" C TYR B 620 " ideal model delta sigma weight residual 113.25 119.42 -6.17 1.30e+00 5.92e-01 2.25e+01 angle pdb=" N GLU D 103 " pdb=" CA GLU D 103 " pdb=" C GLU D 103 " ideal model delta sigma weight residual 110.56 101.80 8.76 1.94e+00 2.66e-01 2.04e+01 angle pdb=" N GLU E 103 " pdb=" CA GLU E 103 " pdb=" C GLU E 103 " ideal model delta sigma weight residual 110.56 101.82 8.74 1.94e+00 2.66e-01 2.03e+01 angle pdb=" N GLU A 103 " pdb=" CA GLU A 103 " pdb=" C GLU A 103 " ideal model delta sigma weight residual 110.56 101.85 8.71 1.94e+00 2.66e-01 2.02e+01 angle pdb=" N GLU C 103 " pdb=" CA GLU C 103 " pdb=" C GLU C 103 " ideal model delta sigma weight residual 110.56 101.87 8.69 1.94e+00 2.66e-01 2.01e+01 ... (remaining 32721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.37: 13473 14.37 - 28.74: 462 28.74 - 43.11: 148 43.11 - 57.47: 28 57.47 - 71.84: 12 Dihedral angle restraints: 14123 sinusoidal: 5488 harmonic: 8635 Sorted by residual: dihedral pdb=" CA ILE D 522 " pdb=" C ILE D 522 " pdb=" N PHE D 523 " pdb=" CA PHE D 523 " ideal model delta harmonic sigma weight residual -180.00 -160.74 -19.26 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ILE E 522 " pdb=" C ILE E 522 " pdb=" N PHE E 523 " pdb=" CA PHE E 523 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ILE B 522 " pdb=" C ILE B 522 " pdb=" N PHE B 523 " pdb=" CA PHE B 523 " ideal model delta harmonic sigma weight residual -180.00 -161.36 -18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 14120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3144 0.056 - 0.112: 477 0.112 - 0.168: 88 0.168 - 0.224: 0 0.224 - 0.280: 10 Chirality restraints: 3719 Sorted by residual: chirality pdb=" CA TYR B 620 " pdb=" N TYR B 620 " pdb=" C TYR B 620 " pdb=" CB TYR B 620 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA TYR E 620 " pdb=" N TYR E 620 " pdb=" C TYR E 620 " pdb=" CB TYR E 620 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA TYR A 620 " pdb=" N TYR A 620 " pdb=" C TYR A 620 " pdb=" CB TYR A 620 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 3716 not shown) Planarity restraints: 4260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 200 " -0.039 5.00e-02 4.00e+02 5.96e-02 5.69e+00 pdb=" N PRO E 201 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO E 201 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 201 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 619 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.12e+00 pdb=" C ILE B 619 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE B 619 " -0.013 2.00e-02 2.50e+03 pdb=" N TYR B 620 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 619 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C ILE E 619 " 0.034 2.00e-02 2.50e+03 pdb=" O ILE E 619 " -0.013 2.00e-02 2.50e+03 pdb=" N TYR E 620 " -0.011 2.00e-02 2.50e+03 ... (remaining 4257 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 438 2.69 - 3.24: 21416 3.24 - 3.80: 34187 3.80 - 4.35: 45401 4.35 - 4.90: 78267 Nonbonded interactions: 179709 Sorted by model distance: nonbonded pdb=" NZ LYS B 255 " pdb=" OD2 ASP C 124 " model vdw 2.140 3.120 nonbonded pdb=" OG SER A 533 " pdb=" OD1 ASN A 552 " model vdw 2.159 3.040 nonbonded pdb=" OG SER D 533 " pdb=" OD1 ASN D 552 " model vdw 2.183 3.040 nonbonded pdb=" OG SER E 367 " pdb=" OD1 ASP E 369 " model vdw 2.198 3.040 nonbonded pdb=" OG SER E 533 " pdb=" OD1 ASN E 552 " model vdw 2.205 3.040 ... (remaining 179704 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 37 through 95 or (resid 96 and (name N or name CA or name \ C or name O or name CB )) or resid 97 through 213 or (resid 214 and (name N or n \ ame CA or name C or name O or name CB )) or resid 215 through 288 or (resid 289 \ through 290 and (name N or name CA or name C or name O or name CB )) or resid 29 \ 1 or (resid 292 through 294 and (name N or name CA or name C or name O or name C \ B )) or resid 295 through 296 or (resid 297 through 298 and (name N or name CA o \ r name C or name O or name CB )) or resid 299 through 312 or (resid 313 and (nam \ e N or name CA or name C or name O or name CB )) or resid 314 through 315 or (re \ sid 316 through 317 and (name N or name CA or name C or name O or name CB )) or \ resid 318 or (resid 319 and (name N or name CA or name C or name O or name CB )) \ or resid 320 through 637)) selection = (chain 'B' and (resid 37 through 95 or (resid 96 and (name N or name CA or name \ C or name O or name CB )) or resid 97 through 106 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB )) or resid 108 through 198 or (resid 199 \ through 200 and (name N or name CA or name C or name O or name CB )) or resid 20 \ 1 through 213 or (resid 214 and (name N or name CA or name C or name O or name C \ B )) or resid 215 through 291 or (resid 292 through 294 and (name N or name CA o \ r name C or name O or name CB )) or resid 295 through 296 or (resid 297 through \ 298 and (name N or name CA or name C or name O or name CB )) or resid 299 throug \ h 312 or (resid 313 and (name N or name CA or name C or name O or name CB )) or \ resid 314 through 315 or (resid 316 through 317 and (name N or name CA or name C \ or name O or name CB )) or resid 318 through 637)) selection = (chain 'C' and (resid 37 through 95 or (resid 96 and (name N or name CA or name \ C or name O or name CB )) or resid 97 through 106 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB )) or resid 108 through 198 or (resid 199 \ through 200 and (name N or name CA or name C or name O or name CB )) or resid 20 \ 1 through 213 or (resid 214 and (name N or name CA or name C or name O or name C \ B )) or resid 215 through 291 or (resid 292 through 294 and (name N or name CA o \ r name C or name O or name CB )) or resid 295 through 296 or (resid 297 through \ 298 and (name N or name CA or name C or name O or name CB )) or resid 299 throug \ h 312 or (resid 313 and (name N or name CA or name C or name O or name CB )) or \ resid 314 through 315 or (resid 316 through 317 and (name N or name CA or name C \ or name O or name CB )) or resid 318 through 637)) selection = (chain 'D' and (resid 37 through 95 or (resid 96 and (name N or name CA or name \ C or name O or name CB )) or resid 97 through 106 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB )) or resid 108 through 291 or (resid 292 \ through 294 and (name N or name CA or name C or name O or name CB )) or resid 29 \ 5 through 312 or (resid 313 and (name N or name CA or name C or name O or name C \ B )) or resid 314 through 315 or (resid 316 through 317 and (name N or name CA o \ r name C or name O or name CB )) or resid 318 or (resid 319 and (name N or name \ CA or name C or name O or name CB )) or resid 320 through 637)) selection = (chain 'E' and (resid 37 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB )) or resid 108 through 198 or (resid 199 through 200 a \ nd (name N or name CA or name C or name O or name CB )) or resid 201 through 213 \ or (resid 214 and (name N or name CA or name C or name O or name CB )) or resid \ 215 through 288 or (resid 289 through 290 and (name N or name CA or name C or n \ ame O or name CB )) or (resid 291 through 294 and (name N or name CA or name C o \ r name O or name CB )) or resid 295 through 296 or (resid 297 through 298 and (n \ ame N or name CA or name C or name O or name CB )) or resid 299 through 637)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 55.010 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.100 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:10.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 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 0.052 24032 Z= 0.222 Angle : 0.557 8.757 32726 Z= 0.318 Chirality : 0.045 0.280 3719 Planarity : 0.004 0.060 4260 Dihedral : 8.791 71.843 8593 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.01 % Favored : 96.76 % Rotamer: Outliers : 0.43 % Allowed : 2.94 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.81 (0.15), residues: 2995 helix: 1.73 (0.21), residues: 705 sheet: 0.83 (0.16), residues: 1015 loop : -0.33 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 534 HIS 0.003 0.001 HIS C 285 PHE 0.011 0.001 PHE A 561 TYR 0.008 0.001 TYR B 517 ARG 0.002 0.000 ARG B 599 Details of bonding type rmsd hydrogen bonds : bond 0.19596 ( 1100) hydrogen bonds : angle 6.46429 ( 3024) covalent geometry : bond 0.00323 (24032) covalent geometry : angle 0.55742 (32726) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 574 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.2886 (mmp) cc_final: 0.2044 (pmm) REVERT: A 274 THR cc_start: 0.7751 (t) cc_final: 0.7503 (m) REVERT: A 303 LEU cc_start: 0.7967 (tp) cc_final: 0.7628 (mp) REVERT: A 345 ARG cc_start: 0.7391 (mtp85) cc_final: 0.7136 (mtp85) REVERT: B 221 GLN cc_start: 0.7312 (mm-40) cc_final: 0.7042 (mm-40) REVERT: B 400 TYR cc_start: 0.7927 (t80) cc_final: 0.7398 (t80) REVERT: B 487 TYR cc_start: 0.8170 (p90) cc_final: 0.7965 (p90) REVERT: C 58 MET cc_start: 0.2198 (mmp) cc_final: 0.1938 (mmp) REVERT: D 232 PHE cc_start: 0.7251 (t80) cc_final: 0.7047 (t80) REVERT: D 255 LYS cc_start: 0.5869 (OUTLIER) cc_final: 0.5526 (tmtp) REVERT: D 487 TYR cc_start: 0.8099 (p90) cc_final: 0.7362 (p90) REVERT: D 635 PHE cc_start: 0.8140 (m-80) cc_final: 0.7900 (m-80) outliers start: 11 outliers final: 3 residues processed: 585 average time/residue: 1.3521 time to fit residues: 901.2788 Evaluate side-chains 481 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 477 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain E residue 279 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 153 optimal weight: 0.4980 chunk 121 optimal weight: 6.9990 chunk 235 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 272 optimal weight: 0.0040 overall best weight: 1.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS B 160 GLN B 344 GLN B 597 GLN B 611 GLN C 154 GLN C 204 HIS C 206 GLN C 233 HIS C 338 GLN C 344 GLN C 409 GLN D 338 GLN E 338 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.173344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.139569 restraints weight = 33426.591| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.36 r_work: 0.3608 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 24032 Z= 0.247 Angle : 0.645 8.319 32726 Z= 0.349 Chirality : 0.048 0.184 3719 Planarity : 0.005 0.043 4260 Dihedral : 4.932 53.529 3250 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.31 % Allowed : 9.87 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.72 (0.15), residues: 2995 helix: 1.48 (0.20), residues: 755 sheet: 0.96 (0.16), residues: 970 loop : -0.48 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 359 HIS 0.009 0.002 HIS E 144 PHE 0.029 0.002 PHE C 414 TYR 0.030 0.003 TYR B 53 ARG 0.006 0.001 ARG B 406 Details of bonding type rmsd hydrogen bonds : bond 0.07829 ( 1100) hydrogen bonds : angle 5.07834 ( 3024) covalent geometry : bond 0.00592 (24032) covalent geometry : angle 0.64481 (32726) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 504 time to evaluate : 2.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLN cc_start: 0.7758 (pp30) cc_final: 0.7415 (pp30) REVERT: A 231 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8115 (m) REVERT: A 274 THR cc_start: 0.8311 (t) cc_final: 0.8047 (p) REVERT: A 303 LEU cc_start: 0.8207 (tp) cc_final: 0.7922 (mp) REVERT: A 345 ARG cc_start: 0.8240 (mtp85) cc_final: 0.7965 (mtp85) REVERT: B 160 GLN cc_start: 0.7534 (tp-100) cc_final: 0.7190 (tp-100) REVERT: B 598 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8359 (tmtm) REVERT: C 44 TYR cc_start: 0.7729 (t80) cc_final: 0.7403 (t80) REVERT: C 58 MET cc_start: 0.3312 (mmp) cc_final: 0.2764 (mmp) REVERT: C 121 TRP cc_start: 0.6298 (p-90) cc_final: 0.5860 (p-90) REVERT: C 270 GLU cc_start: 0.7686 (pt0) cc_final: 0.7453 (pt0) REVERT: C 425 GLU cc_start: 0.8230 (tt0) cc_final: 0.7937 (tt0) REVERT: C 615 TRP cc_start: 0.8154 (m-10) cc_final: 0.7920 (m-10) REVERT: D 109 GLU cc_start: 0.7633 (mp0) cc_final: 0.7374 (mp0) REVERT: D 186 PRO cc_start: 0.7922 (Cg_exo) cc_final: 0.7530 (Cg_endo) REVERT: D 255 LYS cc_start: 0.6747 (OUTLIER) cc_final: 0.6367 (tmtp) REVERT: D 406 ARG cc_start: 0.8751 (ttm170) cc_final: 0.8391 (ttm170) REVERT: D 480 GLU cc_start: 0.7522 (mp0) cc_final: 0.7207 (mp0) REVERT: D 487 TYR cc_start: 0.8665 (p90) cc_final: 0.7876 (p90) REVERT: E 340 VAL cc_start: 0.8695 (p) cc_final: 0.8457 (t) REVERT: E 580 MET cc_start: 0.8764 (mmm) cc_final: 0.8560 (mmm) REVERT: E 597 GLN cc_start: 0.8762 (mt0) cc_final: 0.8529 (mt0) outliers start: 59 outliers final: 37 residues processed: 521 average time/residue: 1.4759 time to fit residues: 867.3232 Evaluate side-chains 527 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 487 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 598 LYS Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 512 LYS Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 521 ARG Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 603 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 180 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 chunk 57 optimal weight: 0.6980 chunk 252 optimal weight: 8.9990 chunk 279 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS A 432 GLN C 204 HIS C 206 GLN C 338 GLN D 409 GLN D 432 GLN E 338 GLN E 411 GLN E 560 ASN E 606 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.172711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.139465 restraints weight = 33258.769| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.34 r_work: 0.3625 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 24032 Z= 0.168 Angle : 0.557 8.404 32726 Z= 0.297 Chirality : 0.044 0.158 3719 Planarity : 0.004 0.054 4260 Dihedral : 4.642 32.983 3246 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.06 % Allowed : 11.99 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.78 (0.15), residues: 2995 helix: 1.74 (0.20), residues: 750 sheet: 0.93 (0.16), residues: 975 loop : -0.52 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 359 HIS 0.010 0.001 HIS C 233 PHE 0.030 0.002 PHE C 414 TYR 0.017 0.002 TYR B 53 ARG 0.005 0.000 ARG C 445 Details of bonding type rmsd hydrogen bonds : bond 0.06435 ( 1100) hydrogen bonds : angle 4.74210 ( 3024) covalent geometry : bond 0.00389 (24032) covalent geometry : angle 0.55726 (32726) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 478 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLN cc_start: 0.7881 (pp30) cc_final: 0.7468 (pp30) REVERT: A 274 THR cc_start: 0.8268 (t) cc_final: 0.8022 (p) REVERT: A 345 ARG cc_start: 0.8196 (mtp85) cc_final: 0.7923 (mtp85) REVERT: B 82 MET cc_start: 0.6906 (ptp) cc_final: 0.6586 (ttm) REVERT: B 117 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7185 (mp) REVERT: B 160 GLN cc_start: 0.7610 (tp-100) cc_final: 0.7296 (tp-100) REVERT: B 224 ARG cc_start: 0.8078 (ptm160) cc_final: 0.7867 (ptm160) REVERT: B 400 TYR cc_start: 0.8408 (t80) cc_final: 0.8066 (t80) REVERT: B 403 GLN cc_start: 0.7812 (tp40) cc_final: 0.7444 (tt0) REVERT: B 598 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8294 (tmtm) REVERT: C 58 MET cc_start: 0.3253 (mmp) cc_final: 0.2735 (mmp) REVERT: C 121 TRP cc_start: 0.6289 (p-90) cc_final: 0.5872 (p-90) REVERT: C 270 GLU cc_start: 0.7576 (pt0) cc_final: 0.7344 (pt0) REVERT: C 425 GLU cc_start: 0.8264 (tt0) cc_final: 0.7987 (tt0) REVERT: C 615 TRP cc_start: 0.8131 (m-10) cc_final: 0.7857 (m-10) REVERT: D 109 GLU cc_start: 0.7740 (mp0) cc_final: 0.7151 (mm-30) REVERT: D 255 LYS cc_start: 0.6727 (OUTLIER) cc_final: 0.6337 (tmtp) REVERT: D 480 GLU cc_start: 0.7566 (mp0) cc_final: 0.7216 (mp0) REVERT: D 487 TYR cc_start: 0.8661 (p90) cc_final: 0.7870 (p90) REVERT: E 220 THR cc_start: 0.8531 (p) cc_final: 0.8322 (m) REVERT: E 279 ILE cc_start: 0.8034 (mt) cc_final: 0.7780 (mp) REVERT: E 340 VAL cc_start: 0.8599 (p) cc_final: 0.8361 (t) REVERT: E 481 GLU cc_start: 0.8111 (tt0) cc_final: 0.7859 (tt0) outliers start: 78 outliers final: 43 residues processed: 513 average time/residue: 1.4541 time to fit residues: 842.9211 Evaluate side-chains 514 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 468 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 598 LYS Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 512 LYS Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain E residue 620 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 76 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 268 optimal weight: 0.0980 chunk 82 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 216 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 225 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS A 403 GLN A 432 GLN C 154 GLN C 204 HIS C 206 GLN C 338 GLN C 409 GLN C 471 GLN D 409 GLN E 338 GLN E 560 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.174939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.141745 restraints weight = 33898.943| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.39 r_work: 0.3645 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 24032 Z= 0.118 Angle : 0.508 8.619 32726 Z= 0.269 Chirality : 0.042 0.153 3719 Planarity : 0.004 0.046 4260 Dihedral : 4.405 32.182 3244 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.06 % Allowed : 12.46 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.91 (0.16), residues: 2995 helix: 1.99 (0.20), residues: 745 sheet: 0.71 (0.15), residues: 1085 loop : -0.36 (0.19), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 359 HIS 0.006 0.001 HIS C 204 PHE 0.028 0.001 PHE C 414 TYR 0.016 0.001 TYR C 487 ARG 0.004 0.000 ARG C 521 Details of bonding type rmsd hydrogen bonds : bond 0.05245 ( 1100) hydrogen bonds : angle 4.44556 ( 3024) covalent geometry : bond 0.00255 (24032) covalent geometry : angle 0.50777 (32726) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 478 time to evaluate : 2.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLN cc_start: 0.7910 (pp30) cc_final: 0.7520 (pp30) REVERT: A 274 THR cc_start: 0.8227 (t) cc_final: 0.7986 (p) REVERT: B 82 MET cc_start: 0.6938 (ptp) cc_final: 0.6673 (ttm) REVERT: B 160 GLN cc_start: 0.7629 (tp-100) cc_final: 0.7312 (tp-100) REVERT: B 224 ARG cc_start: 0.8160 (ptm160) cc_final: 0.7945 (ptm160) REVERT: B 400 TYR cc_start: 0.8359 (t80) cc_final: 0.8071 (t80) REVERT: B 498 ARG cc_start: 0.5995 (OUTLIER) cc_final: 0.5750 (tpp-160) REVERT: C 58 MET cc_start: 0.3287 (mmp) cc_final: 0.2804 (mmp) REVERT: C 121 TRP cc_start: 0.6336 (p-90) cc_final: 0.5935 (p-90) REVERT: C 270 GLU cc_start: 0.7607 (pt0) cc_final: 0.7368 (pt0) REVERT: C 425 GLU cc_start: 0.8257 (tt0) cc_final: 0.7969 (tt0) REVERT: C 498 ARG cc_start: 0.5752 (OUTLIER) cc_final: 0.5440 (tpp-160) REVERT: C 615 TRP cc_start: 0.8141 (m-10) cc_final: 0.7886 (m-10) REVERT: D 109 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7288 (mm-30) REVERT: D 255 LYS cc_start: 0.6718 (OUTLIER) cc_final: 0.6337 (tmtp) REVERT: D 480 GLU cc_start: 0.7626 (mp0) cc_final: 0.7267 (mp0) REVERT: D 487 TYR cc_start: 0.8671 (p90) cc_final: 0.7897 (p90) REVERT: E 279 ILE cc_start: 0.8027 (mt) cc_final: 0.7773 (mp) REVERT: E 300 TYR cc_start: 0.7033 (m-80) cc_final: 0.6762 (m-80) REVERT: E 340 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8258 (t) REVERT: E 481 GLU cc_start: 0.8099 (tt0) cc_final: 0.7826 (tt0) outliers start: 78 outliers final: 52 residues processed: 514 average time/residue: 1.5008 time to fit residues: 868.5840 Evaluate side-chains 524 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 467 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 514 ASN Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 521 ARG Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 515 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 37 optimal weight: 2.9990 chunk 297 optimal weight: 1.9990 chunk 279 optimal weight: 4.9990 chunk 160 optimal weight: 0.0970 chunk 146 optimal weight: 9.9990 chunk 278 optimal weight: 2.9990 chunk 147 optimal weight: 0.0980 chunk 82 optimal weight: 0.6980 chunk 200 optimal weight: 20.0000 chunk 192 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 360 HIS B 169 GLN C 154 GLN C 204 HIS D 560 ASN E 40 HIS E 221 GLN E 344 GLN E 446 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.173727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.140718 restraints weight = 33780.087| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.34 r_work: 0.3641 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24032 Z= 0.128 Angle : 0.520 7.703 32726 Z= 0.273 Chirality : 0.043 0.154 3719 Planarity : 0.004 0.048 4260 Dihedral : 4.369 31.801 3244 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.06 % Allowed : 13.17 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.98 (0.16), residues: 2995 helix: 2.31 (0.20), residues: 715 sheet: 0.63 (0.16), residues: 1050 loop : -0.28 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 359 HIS 0.012 0.001 HIS C 204 PHE 0.029 0.001 PHE C 414 TYR 0.014 0.001 TYR C 487 ARG 0.004 0.000 ARG C 521 Details of bonding type rmsd hydrogen bonds : bond 0.05398 ( 1100) hydrogen bonds : angle 4.42003 ( 3024) covalent geometry : bond 0.00287 (24032) covalent geometry : angle 0.51956 (32726) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 474 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLN cc_start: 0.7926 (pp30) cc_final: 0.7530 (pp30) REVERT: A 274 THR cc_start: 0.8230 (t) cc_final: 0.8000 (p) REVERT: A 345 ARG cc_start: 0.8147 (mtp85) cc_final: 0.7879 (mtp85) REVERT: B 82 MET cc_start: 0.6843 (ptp) cc_final: 0.6634 (ttm) REVERT: B 160 GLN cc_start: 0.7650 (tp-100) cc_final: 0.7303 (tp-100) REVERT: B 224 ARG cc_start: 0.8131 (ptm160) cc_final: 0.7906 (ptm160) REVERT: B 400 TYR cc_start: 0.8351 (t80) cc_final: 0.8073 (t80) REVERT: B 498 ARG cc_start: 0.6005 (OUTLIER) cc_final: 0.5735 (tpp-160) REVERT: C 58 MET cc_start: 0.3515 (mmp) cc_final: 0.3114 (mmp) REVERT: C 121 TRP cc_start: 0.6382 (p-90) cc_final: 0.6051 (p-90) REVERT: C 270 GLU cc_start: 0.7598 (pt0) cc_final: 0.7357 (pt0) REVERT: C 425 GLU cc_start: 0.8243 (tt0) cc_final: 0.8010 (tt0) REVERT: C 498 ARG cc_start: 0.5735 (OUTLIER) cc_final: 0.5499 (tpp-160) REVERT: C 615 TRP cc_start: 0.8106 (m-10) cc_final: 0.7852 (m-10) REVERT: D 105 ASP cc_start: 0.6327 (t0) cc_final: 0.5985 (t0) REVERT: D 109 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7249 (mm-30) REVERT: D 255 LYS cc_start: 0.6715 (OUTLIER) cc_final: 0.6337 (tmtp) REVERT: D 480 GLU cc_start: 0.7627 (mp0) cc_final: 0.7271 (mp0) REVERT: D 487 TYR cc_start: 0.8668 (p90) cc_final: 0.7881 (p90) REVERT: E 279 ILE cc_start: 0.8040 (mt) cc_final: 0.7783 (mp) REVERT: E 300 TYR cc_start: 0.7065 (m-80) cc_final: 0.6819 (m-80) REVERT: E 340 VAL cc_start: 0.8462 (OUTLIER) cc_final: 0.8234 (t) REVERT: E 481 GLU cc_start: 0.8114 (tt0) cc_final: 0.7903 (tt0) outliers start: 78 outliers final: 57 residues processed: 513 average time/residue: 1.4917 time to fit residues: 862.4482 Evaluate side-chains 531 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 469 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 514 ASN Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 521 ARG Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 620 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 9.9990 chunk 203 optimal weight: 7.9990 chunk 260 optimal weight: 6.9990 chunk 108 optimal weight: 0.0970 chunk 121 optimal weight: 1.9990 chunk 243 optimal weight: 8.9990 chunk 249 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS B 169 GLN C 204 HIS C 409 GLN E 144 HIS E 560 ASN E 597 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.169683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.136654 restraints weight = 33192.375| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.34 r_work: 0.3576 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 24032 Z= 0.276 Angle : 0.651 9.804 32726 Z= 0.346 Chirality : 0.048 0.154 3719 Planarity : 0.005 0.054 4260 Dihedral : 4.844 32.935 3244 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.37 % Allowed : 13.28 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.44 (0.15), residues: 2995 helix: 1.53 (0.20), residues: 750 sheet: 0.56 (0.16), residues: 1010 loop : -0.65 (0.17), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 121 HIS 0.013 0.002 HIS E 144 PHE 0.039 0.002 PHE C 414 TYR 0.030 0.002 TYR B 53 ARG 0.007 0.001 ARG E 521 Details of bonding type rmsd hydrogen bonds : bond 0.08044 ( 1100) hydrogen bonds : angle 4.95042 ( 3024) covalent geometry : bond 0.00673 (24032) covalent geometry : angle 0.65082 (32726) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 484 time to evaluate : 2.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLN cc_start: 0.7998 (pp30) cc_final: 0.7619 (pp30) REVERT: A 345 ARG cc_start: 0.8243 (mtp85) cc_final: 0.7976 (mtp85) REVERT: A 439 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8461 (mp) REVERT: A 479 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7240 (mm-30) REVERT: B 82 MET cc_start: 0.7001 (ptp) cc_final: 0.6644 (ttm) REVERT: B 132 SER cc_start: 0.7671 (p) cc_final: 0.7256 (t) REVERT: B 160 GLN cc_start: 0.7740 (tp-100) cc_final: 0.7412 (tp-100) REVERT: B 498 ARG cc_start: 0.6077 (OUTLIER) cc_final: 0.5826 (tpp-160) REVERT: C 58 MET cc_start: 0.3341 (mmp) cc_final: 0.3029 (mmp) REVERT: C 249 LEU cc_start: 0.8507 (tt) cc_final: 0.8273 (tp) REVERT: C 270 GLU cc_start: 0.7619 (pt0) cc_final: 0.7402 (pt0) REVERT: C 347 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8112 (mt-10) REVERT: C 615 TRP cc_start: 0.8179 (m-10) cc_final: 0.7925 (m-10) REVERT: D 105 ASP cc_start: 0.6347 (t0) cc_final: 0.6114 (t0) REVERT: D 109 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7285 (mm-30) REVERT: D 255 LYS cc_start: 0.6829 (OUTLIER) cc_final: 0.6456 (tmtp) REVERT: D 480 GLU cc_start: 0.7670 (mp0) cc_final: 0.7335 (mp0) REVERT: D 487 TYR cc_start: 0.8667 (p90) cc_final: 0.7902 (p90) outliers start: 86 outliers final: 61 residues processed: 525 average time/residue: 1.5298 time to fit residues: 907.3374 Evaluate side-chains 537 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 472 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 521 ARG Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 620 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 84 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 167 optimal weight: 0.5980 chunk 172 optimal weight: 0.8980 chunk 194 optimal weight: 0.0970 chunk 248 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 70 ASN A 360 HIS C 154 GLN C 204 HIS C 206 GLN C 338 GLN C 606 GLN E 338 GLN E 560 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.173315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.140578 restraints weight = 33594.406| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.36 r_work: 0.3635 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24032 Z= 0.121 Angle : 0.525 10.188 32726 Z= 0.276 Chirality : 0.043 0.155 3719 Planarity : 0.004 0.054 4260 Dihedral : 4.438 31.696 3244 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.47 % Allowed : 15.36 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.85 (0.16), residues: 2995 helix: 2.26 (0.20), residues: 715 sheet: 0.53 (0.15), residues: 1095 loop : -0.39 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 359 HIS 0.020 0.001 HIS C 204 PHE 0.032 0.001 PHE C 414 TYR 0.017 0.001 TYR C 632 ARG 0.006 0.000 ARG E 521 Details of bonding type rmsd hydrogen bonds : bond 0.05208 ( 1100) hydrogen bonds : angle 4.46830 ( 3024) covalent geometry : bond 0.00257 (24032) covalent geometry : angle 0.52511 (32726) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 473 time to evaluate : 2.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLN cc_start: 0.7997 (pp30) cc_final: 0.7620 (pp30) REVERT: A 345 ARG cc_start: 0.8130 (mtp85) cc_final: 0.7860 (mtp85) REVERT: A 479 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7185 (mm-30) REVERT: B 82 MET cc_start: 0.6898 (ptp) cc_final: 0.6663 (ttm) REVERT: B 132 SER cc_start: 0.7612 (p) cc_final: 0.7154 (t) REVERT: B 160 GLN cc_start: 0.7704 (tp-100) cc_final: 0.7337 (tp-100) REVERT: B 400 TYR cc_start: 0.8368 (t80) cc_final: 0.8027 (t80) REVERT: B 498 ARG cc_start: 0.6028 (OUTLIER) cc_final: 0.5781 (tpp-160) REVERT: C 58 MET cc_start: 0.3255 (mmp) cc_final: 0.2966 (mmp) REVERT: C 615 TRP cc_start: 0.8102 (m-10) cc_final: 0.7830 (m-10) REVERT: D 255 LYS cc_start: 0.6779 (OUTLIER) cc_final: 0.6495 (tmtp) REVERT: D 480 GLU cc_start: 0.7621 (mp0) cc_final: 0.7265 (mp0) REVERT: D 487 TYR cc_start: 0.8695 (p90) cc_final: 0.7927 (p90) REVERT: E 279 ILE cc_start: 0.8023 (mt) cc_final: 0.7773 (mp) REVERT: E 300 TYR cc_start: 0.7044 (m-80) cc_final: 0.6815 (m-80) REVERT: E 481 GLU cc_start: 0.8095 (tt0) cc_final: 0.7779 (tt0) outliers start: 63 outliers final: 49 residues processed: 506 average time/residue: 1.5037 time to fit residues: 856.1720 Evaluate side-chains 518 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 467 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 521 ARG Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 396 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 292 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 252 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 154 GLN A 360 HIS C 154 GLN D 432 GLN E 560 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.170709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.137831 restraints weight = 33343.141| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.36 r_work: 0.3601 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24032 Z= 0.183 Angle : 0.582 10.685 32726 Z= 0.307 Chirality : 0.045 0.157 3719 Planarity : 0.004 0.048 4260 Dihedral : 4.567 32.488 3244 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.90 % Allowed : 15.32 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.74 (0.16), residues: 2995 helix: 2.06 (0.20), residues: 720 sheet: 0.61 (0.16), residues: 995 loop : -0.48 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 121 HIS 0.006 0.001 HIS E 144 PHE 0.025 0.002 PHE B 232 TYR 0.020 0.002 TYR B 53 ARG 0.006 0.000 ARG E 521 Details of bonding type rmsd hydrogen bonds : bond 0.06650 ( 1100) hydrogen bonds : angle 4.66079 ( 3024) covalent geometry : bond 0.00432 (24032) covalent geometry : angle 0.58245 (32726) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 476 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLN cc_start: 0.8028 (pp30) cc_final: 0.7641 (pp30) REVERT: A 345 ARG cc_start: 0.8185 (mtp85) cc_final: 0.7917 (mtp85) REVERT: A 432 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7288 (mm-40) REVERT: A 479 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7234 (mm-30) REVERT: B 82 MET cc_start: 0.6886 (ptp) cc_final: 0.6624 (ttm) REVERT: B 132 SER cc_start: 0.7639 (p) cc_final: 0.7365 (t) REVERT: B 160 GLN cc_start: 0.7714 (tp-100) cc_final: 0.7372 (tp-100) REVERT: B 400 TYR cc_start: 0.8407 (t80) cc_final: 0.8051 (t80) REVERT: B 498 ARG cc_start: 0.6044 (OUTLIER) cc_final: 0.5805 (tpp-160) REVERT: C 270 GLU cc_start: 0.7639 (pt0) cc_final: 0.7402 (pt0) REVERT: C 347 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8084 (mt-10) REVERT: C 425 GLU cc_start: 0.8257 (tt0) cc_final: 0.8043 (tt0) REVERT: C 615 TRP cc_start: 0.8125 (m-10) cc_final: 0.7873 (m-10) REVERT: D 105 ASP cc_start: 0.6096 (t0) cc_final: 0.5856 (t0) REVERT: D 109 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: D 255 LYS cc_start: 0.6818 (OUTLIER) cc_final: 0.6429 (tmtp) REVERT: D 345 ARG cc_start: 0.7994 (mtp85) cc_final: 0.7680 (mtp85) REVERT: D 480 GLU cc_start: 0.7634 (mp0) cc_final: 0.7281 (mp0) REVERT: D 487 TYR cc_start: 0.8681 (p90) cc_final: 0.7912 (p90) REVERT: E 279 ILE cc_start: 0.8042 (mt) cc_final: 0.7789 (mp) REVERT: E 300 TYR cc_start: 0.7070 (m-80) cc_final: 0.6866 (m-80) REVERT: E 481 GLU cc_start: 0.8117 (tt0) cc_final: 0.7811 (tt0) outliers start: 74 outliers final: 54 residues processed: 511 average time/residue: 1.5099 time to fit residues: 867.5676 Evaluate side-chains 528 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 470 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 521 ARG Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 620 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 65 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 205 optimal weight: 0.0970 chunk 27 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 293 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 144 optimal weight: 0.4980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 360 HIS C 154 GLN C 206 GLN C 233 HIS C 272 ASN D 432 GLN E 344 GLN E 560 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.172977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.140305 restraints weight = 33521.480| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.36 r_work: 0.3636 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24032 Z= 0.122 Angle : 0.533 11.495 32726 Z= 0.277 Chirality : 0.043 0.153 3719 Planarity : 0.004 0.050 4260 Dihedral : 4.361 31.741 3244 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.27 % Allowed : 16.26 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.89 (0.16), residues: 2995 helix: 2.35 (0.20), residues: 715 sheet: 0.49 (0.15), residues: 1095 loop : -0.33 (0.19), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 359 HIS 0.005 0.001 HIS E 144 PHE 0.030 0.001 PHE C 414 TYR 0.018 0.001 TYR C 487 ARG 0.006 0.000 ARG E 521 Details of bonding type rmsd hydrogen bonds : bond 0.05139 ( 1100) hydrogen bonds : angle 4.40915 ( 3024) covalent geometry : bond 0.00269 (24032) covalent geometry : angle 0.53290 (32726) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 467 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLN cc_start: 0.8014 (pp30) cc_final: 0.7602 (pp30) REVERT: A 345 ARG cc_start: 0.8118 (mtp85) cc_final: 0.7847 (mtp85) REVERT: A 479 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7206 (mm-30) REVERT: B 82 MET cc_start: 0.6871 (ptp) cc_final: 0.6646 (ttm) REVERT: B 160 GLN cc_start: 0.7727 (tp-100) cc_final: 0.7363 (tp-100) REVERT: B 400 TYR cc_start: 0.8353 (t80) cc_final: 0.7964 (t80) REVERT: B 498 ARG cc_start: 0.6016 (OUTLIER) cc_final: 0.5743 (tpp-160) REVERT: C 615 TRP cc_start: 0.8076 (m-10) cc_final: 0.7796 (m-10) REVERT: D 105 ASP cc_start: 0.6141 (t0) cc_final: 0.5926 (t0) REVERT: D 109 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: D 255 LYS cc_start: 0.6782 (OUTLIER) cc_final: 0.6404 (tmtp) REVERT: D 345 ARG cc_start: 0.7914 (mtp85) cc_final: 0.7591 (mtp85) REVERT: D 480 GLU cc_start: 0.7633 (mp0) cc_final: 0.7276 (mp0) REVERT: D 487 TYR cc_start: 0.8682 (p90) cc_final: 0.7905 (p90) REVERT: E 279 ILE cc_start: 0.8022 (mt) cc_final: 0.7781 (mp) REVERT: E 300 TYR cc_start: 0.7060 (m-80) cc_final: 0.6838 (m-80) REVERT: E 303 LEU cc_start: 0.8139 (tp) cc_final: 0.7711 (mp) REVERT: E 481 GLU cc_start: 0.8090 (tt0) cc_final: 0.7566 (tt0) REVERT: E 521 ARG cc_start: 0.8210 (mmm-85) cc_final: 0.7935 (mmm-85) outliers start: 58 outliers final: 49 residues processed: 498 average time/residue: 1.5182 time to fit residues: 850.4822 Evaluate side-chains 515 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 463 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 391 ASN Chi-restraints excluded: chain D residue 521 ARG Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 620 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 52 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 242 optimal weight: 4.9990 chunk 89 optimal weight: 0.0060 chunk 256 optimal weight: 0.8980 chunk 260 optimal weight: 0.1980 chunk 222 optimal weight: 0.2980 chunk 167 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 360 HIS C 154 GLN C 391 ASN D 432 GLN E 344 GLN E 560 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.174636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.142209 restraints weight = 33702.988| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.33 r_work: 0.3662 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 24032 Z= 0.105 Angle : 0.512 11.846 32726 Z= 0.266 Chirality : 0.042 0.170 3719 Planarity : 0.004 0.047 4260 Dihedral : 4.185 31.280 3244 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.00 % Allowed : 16.85 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.02 (0.16), residues: 2995 helix: 2.50 (0.20), residues: 715 sheet: 0.54 (0.15), residues: 1095 loop : -0.26 (0.19), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 359 HIS 0.005 0.001 HIS E 144 PHE 0.028 0.001 PHE C 414 TYR 0.016 0.001 TYR C 487 ARG 0.006 0.000 ARG E 521 Details of bonding type rmsd hydrogen bonds : bond 0.04388 ( 1100) hydrogen bonds : angle 4.24156 ( 3024) covalent geometry : bond 0.00225 (24032) covalent geometry : angle 0.51250 (32726) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 470 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLN cc_start: 0.8057 (pp30) cc_final: 0.7669 (pp30) REVERT: A 345 ARG cc_start: 0.8131 (mtp85) cc_final: 0.7858 (mtp85) REVERT: A 479 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7207 (mm-30) REVERT: B 132 SER cc_start: 0.7602 (p) cc_final: 0.7341 (t) REVERT: B 160 GLN cc_start: 0.7698 (tp-100) cc_final: 0.7306 (tp-100) REVERT: B 400 TYR cc_start: 0.8357 (t80) cc_final: 0.8034 (t80) REVERT: B 498 ARG cc_start: 0.5861 (OUTLIER) cc_final: 0.5611 (tpp-160) REVERT: C 224 ARG cc_start: 0.8378 (ptm160) cc_final: 0.8130 (mtp180) REVERT: C 345 ARG cc_start: 0.8070 (mtp180) cc_final: 0.7760 (ttt-90) REVERT: C 425 GLU cc_start: 0.8211 (tt0) cc_final: 0.7964 (tt0) REVERT: C 615 TRP cc_start: 0.7969 (m-10) cc_final: 0.7695 (m-10) REVERT: D 255 LYS cc_start: 0.6758 (OUTLIER) cc_final: 0.6393 (tmtp) REVERT: D 345 ARG cc_start: 0.7891 (mtp85) cc_final: 0.7585 (mtp85) REVERT: D 480 GLU cc_start: 0.7650 (mp0) cc_final: 0.7319 (mp0) REVERT: D 487 TYR cc_start: 0.8668 (p90) cc_final: 0.7908 (p90) REVERT: E 279 ILE cc_start: 0.8015 (mt) cc_final: 0.7757 (mp) REVERT: E 481 GLU cc_start: 0.8060 (tt0) cc_final: 0.7528 (tt0) outliers start: 51 outliers final: 40 residues processed: 498 average time/residue: 1.4954 time to fit residues: 839.4201 Evaluate side-chains 496 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 454 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 521 ARG Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 415 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 13 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 41 optimal weight: 0.0980 chunk 58 optimal weight: 0.0470 chunk 18 optimal weight: 3.9990 chunk 44 optimal weight: 0.0370 chunk 133 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS C 154 GLN C 272 ASN D 432 GLN E 344 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.174935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.142505 restraints weight = 33543.511| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.32 r_work: 0.3669 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24032 Z= 0.103 Angle : 0.510 8.126 32726 Z= 0.265 Chirality : 0.042 0.149 3719 Planarity : 0.004 0.048 4260 Dihedral : 4.138 31.264 3244 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.96 % Allowed : 17.08 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.09 (0.16), residues: 2995 helix: 2.53 (0.20), residues: 715 sheet: 0.58 (0.15), residues: 1105 loop : -0.20 (0.19), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 121 HIS 0.004 0.001 HIS B 285 PHE 0.026 0.001 PHE A 168 TYR 0.017 0.001 TYR C 487 ARG 0.013 0.000 ARG D 116 Details of bonding type rmsd hydrogen bonds : bond 0.04277 ( 1100) hydrogen bonds : angle 4.19730 ( 3024) covalent geometry : bond 0.00220 (24032) covalent geometry : angle 0.50970 (32726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24619.17 seconds wall clock time: 422 minutes 51.27 seconds (25371.27 seconds total)