Starting phenix.real_space_refine on Thu May 22 11:50:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eva_19996/05_2025/9eva_19996.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eva_19996/05_2025/9eva_19996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eva_19996/05_2025/9eva_19996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eva_19996/05_2025/9eva_19996.map" model { file = "/net/cci-nas-00/data/ceres_data/9eva_19996/05_2025/9eva_19996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eva_19996/05_2025/9eva_19996.cif" } resolution = 2.34 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: 5 Type Number sf(0) Gaussians Ca 10 9.91 5 S 55 5.16 5 C 14797 2.51 5 N 3739 2.21 5 O 4327 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 22928 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4633 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 559} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 4624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4624 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 560} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 4515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4515 Classifications: {'peptide': 573} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 545} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 4534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4534 Classifications: {'peptide': 579} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 551} Chain breaks: 3 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 4612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4612 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 558} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.89, per 1000 atoms: 0.56 Number of scatterers: 22928 At special positions: 0 Unit cell: (142.195, 143.888, 154.045, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 10 19.99 S 55 16.00 O 4327 8.00 N 3739 7.00 C 14797 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: 5.01 Conformation dependent library (CDL) restraints added in 2.8 seconds 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5378 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 29 sheets defined 29.5% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'A' and resid 88 through 100 removed outlier: 3.816A pdb=" N GLN A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.901A 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: 3.505A 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 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: 3.959A pdb=" N TYR A 518 " --> pdb=" O ASN A 514 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Proline residue: A 525 - end of helix removed outlier: 3.682A 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 removed outlier: 3.501A pdb=" N LEU A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) 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 removed outlier: 3.522A pdb=" N VAL A 591 " --> pdb=" O THR A 587 " (cutoff:3.500A) 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 106 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 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: 3.834A pdb=" N TYR B 518 " --> pdb=" O ASN B 514 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) Proline residue: B 525 - end of helix removed outlier: 3.702A 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 563 Processing helix chain 'B' and resid 564 through 567 Processing helix chain 'B' and resid 574 through 604 removed outlier: 3.525A pdb=" N VAL B 591 " --> pdb=" O THR B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 637 Proline residue: B 621 - end of helix removed outlier: 3.808A pdb=" N THR B 637 " --> pdb=" O LEU B 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 100 removed outlier: 3.816A 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 308 through 314 removed outlier: 3.748A pdb=" N LEU C 311 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ARG C 312 " --> pdb=" O PRO C 309 " (cutoff:3.500A) removed outlier: 4.044A 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: 3.839A pdb=" N TYR C 518 " --> pdb=" O ASN C 514 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL C 524 " --> pdb=" O LEU C 520 " (cutoff:3.500A) Proline residue: C 525 - end of helix removed outlier: 3.689A 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 563 removed outlier: 3.515A pdb=" N LEU C 554 " --> pdb=" O SER C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 567 Processing helix chain 'C' and resid 574 through 604 removed outlier: 3.579A pdb=" N VAL C 591 " --> pdb=" O THR C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 637 Proline residue: C 621 - end of helix removed outlier: 3.793A pdb=" N THR C 637 " --> pdb=" O LEU C 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 99 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 107 through 118 removed outlier: 3.709A pdb=" N THR D 111 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 3.505A 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 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: 3.909A pdb=" N TYR D 518 " --> pdb=" O ASN D 514 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N VAL D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Proline residue: D 525 - end of helix removed outlier: 3.693A 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 563 Processing helix chain 'D' and resid 564 through 567 Processing helix chain 'D' and resid 574 through 604 removed outlier: 3.510A pdb=" N VAL D 591 " --> pdb=" O THR D 587 " (cutoff:3.500A) 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: 3.816A 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 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: 3.929A 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: 3.621A 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 563 Processing helix chain 'E' and resid 564 through 567 Processing helix chain 'E' and resid 574 through 604 removed outlier: 3.520A pdb=" N VAL E 591 " --> pdb=" O THR E 587 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 636 Proline residue: E 621 - end of helix 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: 3.686A 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: 3.859A 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: 4.232A 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: 7.503A pdb=" N LEU A 247 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N PHE A 259 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.885A 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: 4.353A pdb=" N GLN A 411 " --> pdb=" O PHE A 424 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE A 424 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE A 413 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER A 422 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL A 415 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG A 420 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 341 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL A 352 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE A 339 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N THR A 354 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASP A 337 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N LYS A 356 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ALA A 335 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N SER A 358 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N GLY A 333 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N HIS A 360 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N THR A 331 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP A 328 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN A 464 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL A 330 " --> pdb=" O ASN A 464 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE A 466 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 6.350A 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: 5.066A pdb=" N SER A 503 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN A 502 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLU A 493 " --> pdb=" O ASN A 502 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ARG A 504 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE A 491 " --> pdb=" O ARG A 504 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR A 506 " --> pdb=" O GLN A 489 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLN A 489 " --> pdb=" O THR A 506 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR A 508 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR A 487 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 6.857A 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: 5.990A 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: 4.315A 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: 7.330A pdb=" N LEU B 247 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N PHE B 259 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.710A 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: 4.362A pdb=" N GLN B 411 " --> pdb=" O PHE B 424 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE B 424 " --> pdb=" O GLN B 411 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE B 413 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER B 422 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL B 415 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG B 420 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY B 341 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL B 352 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ILE B 339 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N THR B 354 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ASP B 337 " --> pdb=" O THR B 354 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N LYS B 356 " --> pdb=" O ALA B 335 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ALA B 335 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N SER B 358 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N GLY B 333 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N HIS B 360 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 9.401A pdb=" N THR B 331 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASP B 328 " --> pdb=" O ILE B 462 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASN B 464 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL B 330 " --> pdb=" O ASN B 464 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE B 466 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 6.325A 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: 4.981A pdb=" N SER B 503 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN B 502 " --> pdb=" O GLU B 493 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU B 493 " --> pdb=" O ASN B 502 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARG B 504 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE B 491 " --> pdb=" O ARG B 504 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR B 506 " --> pdb=" O GLN B 489 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN B 489 " --> pdb=" O THR B 506 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR B 508 " --> pdb=" O TYR B 487 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TYR B 487 " --> pdb=" O THR B 508 " (cutoff:3.500A) removed outlier: 6.852A 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 208 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 204 through 208 current: chain 'C' and resid 256 through 259 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 256 through 259 current: chain 'C' and resid 269 through 274 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 376 through 379 removed outlier: 4.328A pdb=" N GLN C 411 " --> pdb=" O PHE C 424 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N PHE C 424 " --> pdb=" O GLN C 411 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE C 413 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N SER C 422 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL C 415 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG C 420 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASN C 348 " --> pdb=" O GLY C 341 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLY C 341 " --> pdb=" O ASN C 348 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N SER C 350 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE C 339 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL C 352 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N HIS C 360 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N LEU C 329 " --> pdb=" O HIS C 360 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASP C 328 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN C 464 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL C 330 " --> pdb=" O ASN C 464 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE C 466 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL C 332 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 397 through 399 removed outlier: 5.001A pdb=" N SER C 503 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN C 502 " --> pdb=" O GLU C 493 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLU C 493 " --> pdb=" O ASN C 502 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG C 504 " --> pdb=" O ILE C 491 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE C 491 " --> pdb=" O ARG C 504 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR C 506 " --> pdb=" O GLN C 489 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN C 489 " --> pdb=" O THR C 506 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR C 508 " --> pdb=" O TYR C 487 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR C 487 " --> pdb=" O THR C 508 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU C 510 " --> pdb=" O THR C 485 " (cutoff:3.500A) Processing sheet with id=AB9, 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=AC1, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.685A pdb=" N GLY D 120 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 3.579A 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=AC2, first strand: chain 'D' and resid 204 through 212 removed outlier: 4.252A pdb=" N ALA D 298 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA D 234 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 218 through 222 removed outlier: 7.340A pdb=" N LEU D 247 " --> pdb=" O PHE D 259 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N PHE D 259 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU D 249 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 376 through 379 removed outlier: 4.330A pdb=" N GLN D 411 " --> pdb=" O PHE D 424 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N PHE D 424 " --> pdb=" O GLN D 411 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE D 413 " --> pdb=" O SER D 422 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER D 422 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL D 415 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARG D 420 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY D 341 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL D 352 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE D 339 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N THR D 354 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ASP D 337 " --> pdb=" O THR D 354 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N LYS D 356 " --> pdb=" O ALA D 335 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ALA D 335 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N SER D 358 " --> pdb=" O GLY D 333 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N GLY D 333 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N HIS D 360 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 9.406A pdb=" N THR D 331 " --> pdb=" O HIS D 360 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASP D 328 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN D 464 " --> pdb=" O ASP D 328 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL D 330 " --> pdb=" O ASN D 464 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE D 466 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL D 332 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 397 through 399 removed outlier: 5.062A pdb=" N SER D 503 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN D 502 " --> pdb=" O GLU D 493 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLU D 493 " --> pdb=" O ASN D 502 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ARG D 504 " --> pdb=" O ILE D 491 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE D 491 " --> pdb=" O ARG D 504 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR D 506 " --> pdb=" O GLN D 489 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLN D 489 " --> pdb=" O THR D 506 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR D 508 " --> pdb=" O TYR D 487 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR D 487 " --> pdb=" O THR D 508 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU D 510 " --> pdb=" O THR D 485 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 38 through 45 removed outlier: 5.996A pdb=" N SER E 167 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 120 through 122 removed outlier: 3.686A 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=AC8, first strand: chain 'E' and resid 204 through 212 removed outlier: 4.124A pdb=" N ALA E 298 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 218 through 222 removed outlier: 7.412A pdb=" N LEU E 247 " --> pdb=" O PHE E 259 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N PHE E 259 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU E 249 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 376 through 379 removed outlier: 4.293A pdb=" N GLN E 411 " --> pdb=" O PHE E 424 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N PHE E 424 " --> pdb=" O GLN E 411 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE E 413 " --> pdb=" O SER E 422 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N SER E 422 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL E 415 " --> pdb=" O ARG E 420 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG E 420 " --> pdb=" O VAL E 415 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY E 341 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL E 352 " --> pdb=" O ILE E 339 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE E 339 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N THR E 354 " --> pdb=" O ASP E 337 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ASP E 337 " --> pdb=" O THR E 354 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N LYS E 356 " --> pdb=" O ALA E 335 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ALA E 335 " --> pdb=" O LYS E 356 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N SER E 358 " --> pdb=" O GLY E 333 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N GLY E 333 " --> pdb=" O SER E 358 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N HIS E 360 " --> pdb=" O THR E 331 " (cutoff:3.500A) removed outlier: 9.295A pdb=" N THR E 331 " --> pdb=" O HIS E 360 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ASP E 328 " --> pdb=" O ILE E 462 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASN E 464 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL E 330 " --> pdb=" O ASN E 464 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE E 466 " --> pdb=" O VAL E 330 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL E 332 " --> pdb=" O ILE E 466 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 397 through 399 removed outlier: 5.043A pdb=" N SER E 503 " --> pdb=" O LEU E 454 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASN E 502 " --> pdb=" O GLU E 493 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU E 493 " --> pdb=" O ASN E 502 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ARG E 504 " --> pdb=" O ILE E 491 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE E 491 " --> pdb=" O ARG E 504 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR E 506 " --> pdb=" O GLN E 489 " (cutoff:3.500A) removed outlier: 4.395A 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: 4.389A pdb=" N TYR E 487 " --> pdb=" O THR E 508 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU E 510 " --> pdb=" O THR E 485 " (cutoff:3.500A) 1059 hydrogen bonds defined for protein. 2919 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.90 Time building geometry restraints manager: 6.00 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: 4918 1.33 - 1.45: 5432 1.45 - 1.57: 13008 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 23438 Sorted by residual: 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 1.63e+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 1.60e+01 bond pdb=" CA ALA E 99 " pdb=" C ALA E 99 " ideal model delta sigma weight residual 1.524 1.472 0.051 1.29e-02 6.01e+03 1.58e+01 bond pdb=" CA GLU A 103 " pdb=" C GLU A 103 " ideal model delta sigma weight residual 1.526 1.489 0.037 9.20e-03 1.18e+04 1.58e+01 bond pdb=" CA ALA A 99 " pdb=" C ALA A 99 " ideal model delta sigma weight residual 1.524 1.472 0.051 1.29e-02 6.01e+03 1.57e+01 ... (remaining 23433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 31409 1.97 - 3.94: 422 3.94 - 5.91: 47 5.91 - 7.89: 12 7.89 - 9.86: 6 Bond angle restraints: 31896 Sorted by residual: angle pdb=" N ILE C 199 " pdb=" CA ILE C 199 " pdb=" C ILE C 199 " ideal model delta sigma weight residual 109.34 119.20 -9.86 2.08e+00 2.31e-01 2.25e+01 angle pdb=" C LYS C 200 " pdb=" N PRO C 201 " pdb=" CA PRO C 201 " ideal model delta sigma weight residual 119.84 125.53 -5.69 1.25e+00 6.40e-01 2.08e+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 110.56 101.83 8.73 1.94e+00 2.66e-01 2.03e+01 angle pdb=" N TYR E 620 " pdb=" CA TYR E 620 " pdb=" C TYR E 620 " ideal model delta sigma weight residual 113.25 119.06 -5.81 1.30e+00 5.92e-01 2.00e+01 ... (remaining 31891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 13208 16.50 - 32.99: 430 32.99 - 49.49: 90 49.49 - 65.99: 25 65.99 - 82.48: 7 Dihedral angle restraints: 13760 sinusoidal: 5384 harmonic: 8376 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 -158.91 -21.09 0 5.00e+00 4.00e-02 1.78e+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 -159.67 -20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA PRO A 265 " pdb=" C PRO A 265 " pdb=" N GLY A 266 " pdb=" CA GLY A 266 " ideal model delta harmonic sigma weight residual -180.00 -159.69 -20.31 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 13757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3011 0.054 - 0.108: 513 0.108 - 0.162: 106 0.162 - 0.217: 1 0.217 - 0.271: 8 Chirality restraints: 3639 Sorted by residual: 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 1.83e+00 chirality pdb=" CA ASN E 104 " pdb=" N ASN E 104 " pdb=" C ASN E 104 " pdb=" CB ASN E 104 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA ASN A 104 " pdb=" N ASN A 104 " pdb=" C ASN A 104 " pdb=" CB ASN A 104 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 3636 not shown) Planarity restraints: 4125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 198 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.12e+00 pdb=" C GLU C 198 " -0.049 2.00e-02 2.50e+03 pdb=" O GLU C 198 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE C 199 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 619 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C ILE E 619 " -0.041 2.00e-02 2.50e+03 pdb=" O ILE E 619 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR E 620 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 200 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.52e+00 pdb=" N PRO C 201 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 201 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 201 " 0.028 5.00e-02 4.00e+02 ... (remaining 4122 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4611 2.78 - 3.31: 19923 3.31 - 3.84: 35568 3.84 - 4.37: 41196 4.37 - 4.90: 73905 Nonbonded interactions: 175203 Sorted by model distance: nonbonded pdb=" OG SER B 367 " pdb=" OD1 ASP B 369 " model vdw 2.252 3.040 nonbonded pdb=" OG SER C 367 " pdb=" OD1 ASP C 369 " model vdw 2.252 3.040 nonbonded pdb=" O TYR E 129 " pdb="CA CA E 702 " model vdw 2.273 2.510 nonbonded pdb=" OG SER B 533 " pdb=" OD1 ASN B 552 " model vdw 2.275 3.040 nonbonded pdb=" OG SER E 533 " pdb=" OD1 ASN E 552 " model vdw 2.308 3.040 ... (remaining 175198 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 through 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB )) or resid 108 or (resid 109 and (name N \ or name CA or name C or name O or name CB )) or resid 110 through 138 or (resid \ 139 and (name N or name CA or name C or name O or name CB )) or resid 140 throug \ h 198 or (resid 199 through 200 and (name N or name CA or name C or name O or na \ me CB )) or resid 201 or (resid 202 through 203 and (name N or name CA or name C \ or name O or name CB )) or resid 204 through 209 or resid 217 through 238 or re \ sid 245 through 287 or resid 301 through 310 or resid 322 through 368 or (resid \ 369 through 370 and (name N or name CA or name C or name O or name CB )) or resi \ d 371 through 637 or resid 701 through 702)) selection = (chain 'B' and (resid 37 through 95 or (resid 96 through 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB )) or resid 108 or (resid 109 and (name N \ or name CA or name C or name O or name CB )) or resid 110 through 198 or (resid \ 199 through 200 and (name N or name CA or name C or name O or name CB )) or resi \ d 201 through 209 or resid 217 through 238 or resid 245 or (resid 246 and (name \ N or name CA or name C or name O or name CB )) or resid 247 through 287 or resid \ 301 through 310 or resid 321 or resid 323 through 368 or (resid 369 through 370 \ and (name N or name CA or name C or name O or name CB )) or resid 371 through 6 \ 37 or resid 701 through 702)) selection = (chain 'C' and (resid 37 through 95 or (resid 96 through 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB )) or resid 108 or (resid 109 and (name N \ or name CA or name C or name O or name CB )) or resid 110 through 138 or (resid \ 139 and (name N or name CA or name C or name O or name CB )) or resid 140 throug \ h 201 or (resid 202 through 203 and (name N or name CA or name C or name O or na \ me CB )) or resid 204 through 245 or (resid 246 and (name N or name CA or name C \ or name O or name CB )) or resid 247 through 310 or resid 314 or resid 323 thro \ ugh 368 or (resid 369 through 370 and (name N or name CA or name C or name O or \ name CB )) or resid 371 through 637 or resid 701 through 702)) selection = (chain 'D' and (resid 37 through 198 or (resid 199 through 200 and (name N or na \ me CA or name C or name O or name CB )) or resid 201 through 209 or resid 217 th \ rough 238 or resid 245 or (resid 246 and (name N or name CA or name C or name O \ or name CB )) or resid 247 through 287 or resid 301 through 310 or resid 322 thr \ ough 369 or (resid 370 and (name N or name CA or name C or name O or name CB )) \ or resid 371 through 637 or resid 701 through 702)) selection = (chain 'E' and (resid 37 through 95 or (resid 96 through 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB )) or resid 108 or (resid 109 and (name N \ or name CA or name C or name O or name CB )) or resid 110 through 198 or (resid \ 199 through 200 and (name N or name CA or name C or name O or name CB )) or resi \ d 201 through 209 or resid 217 through 238 or resid 245 or (resid 246 and (name \ N or name CA or name C or name O or name CB )) or resid 247 through 287 or resid \ 301 through 310 or resid 322 through 368 or (resid 369 through 370 and (name N \ or name CA or name C or name O or name CB )) or resid 371 through 637 or resid 7 \ 01 through 702)) } 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: 2.730 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: 0.980 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 48.530 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 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 0.053 23438 Z= 0.222 Angle : 0.590 9.857 31896 Z= 0.341 Chirality : 0.045 0.271 3639 Planarity : 0.004 0.053 4125 Dihedral : 9.401 82.484 8382 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.54 % Favored : 97.36 % Rotamer: Outliers : 0.68 % Allowed : 3.27 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: 0.93 (0.16), residues: 2875 helix: 1.66 (0.21), residues: 702 sheet: 1.04 (0.16), residues: 977 loop : -0.34 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 630 HIS 0.003 0.001 HIS A 285 PHE 0.011 0.001 PHE B 561 TYR 0.014 0.001 TYR C 517 ARG 0.004 0.000 ARG D 578 Details of bonding type rmsd hydrogen bonds : bond 0.19100 ( 1059) hydrogen bonds : angle 6.35638 ( 2919) covalent geometry : bond 0.00340 (23438) covalent geometry : angle 0.59030 (31896) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 695 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7475 (mm-30) REVERT: A 425 GLU cc_start: 0.7823 (tt0) cc_final: 0.7462 (tt0) REVERT: A 480 GLU cc_start: 0.7964 (mp0) cc_final: 0.7456 (mp0) REVERT: A 481 GLU cc_start: 0.7762 (tt0) cc_final: 0.7474 (tt0) REVERT: B 58 MET cc_start: 0.6081 (mmp) cc_final: 0.5629 (mmm) REVERT: B 236 VAL cc_start: 0.8639 (p) cc_final: 0.8390 (m) REVERT: B 345 ARG cc_start: 0.7927 (mtp85) cc_final: 0.7666 (mtp85) REVERT: C 270 GLU cc_start: 0.6769 (pt0) cc_final: 0.6541 (pt0) REVERT: C 286 VAL cc_start: 0.4468 (OUTLIER) cc_final: 0.4157 (t) REVERT: C 437 ASP cc_start: 0.8123 (t0) cc_final: 0.7889 (t70) REVERT: D 58 MET cc_start: 0.0630 (mmp) cc_final: 0.0421 (mtt) REVERT: D 347 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7569 (mt-10) REVERT: D 364 LEU cc_start: 0.8401 (mp) cc_final: 0.8149 (mp) REVERT: E 207 GLU cc_start: 0.6817 (tt0) cc_final: 0.6607 (tt0) REVERT: E 425 GLU cc_start: 0.7614 (tt0) cc_final: 0.7287 (tt0) REVERT: E 480 GLU cc_start: 0.7755 (mp0) cc_final: 0.7336 (mp0) outliers start: 17 outliers final: 5 residues processed: 706 average time/residue: 1.4258 time to fit residues: 1145.0386 Evaluate side-chains 584 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 578 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 620 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 0.9980 chunk 218 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 168 optimal weight: 0.6980 chunk 261 optimal weight: 0.8980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 338 GLN A 344 GLN A 405 ASN A 409 GLN B 154 GLN B 360 HIS B 432 GLN B 476 GLN B 611 GLN C 409 GLN C 432 GLN C 611 GLN D 233 HIS D 338 GLN D 560 ASN D 611 GLN ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 432 GLN E 514 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.158883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.138105 restraints weight = 30457.254| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 1.83 r_work: 0.3727 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23438 Z= 0.198 Angle : 0.625 9.920 31896 Z= 0.337 Chirality : 0.047 0.162 3639 Planarity : 0.004 0.041 4125 Dihedral : 5.373 59.100 3146 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.95 % Allowed : 10.30 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: 0.93 (0.16), residues: 2875 helix: 1.65 (0.20), residues: 736 sheet: 1.12 (0.16), residues: 913 loop : -0.39 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 121 HIS 0.006 0.001 HIS B 204 PHE 0.027 0.002 PHE E 135 TYR 0.040 0.002 TYR C 53 ARG 0.009 0.001 ARG D 521 Details of bonding type rmsd hydrogen bonds : bond 0.07237 ( 1059) hydrogen bonds : angle 4.85708 ( 2919) covalent geometry : bond 0.00454 (23438) covalent geometry : angle 0.62507 (31896) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 601 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LEU cc_start: 0.8542 (tt) cc_final: 0.8323 (tp) REVERT: A 347 GLU cc_start: 0.8525 (mt-10) cc_final: 0.7638 (mt-10) REVERT: A 425 GLU cc_start: 0.8163 (tt0) cc_final: 0.7950 (tt0) REVERT: A 480 GLU cc_start: 0.8411 (mp0) cc_final: 0.7773 (mp0) REVERT: A 481 GLU cc_start: 0.8238 (tt0) cc_final: 0.8000 (tt0) REVERT: A 521 ARG cc_start: 0.8218 (mmm-85) cc_final: 0.7997 (mtp-110) REVERT: C 286 VAL cc_start: 0.4991 (OUTLIER) cc_final: 0.4618 (t) REVERT: C 347 GLU cc_start: 0.8563 (mt-10) cc_final: 0.7582 (mt-10) REVERT: C 425 GLU cc_start: 0.8036 (tt0) cc_final: 0.7753 (tt0) REVERT: C 468 ARG cc_start: 0.7831 (mtt180) cc_final: 0.7590 (mtt180) REVERT: C 480 GLU cc_start: 0.8265 (mp0) cc_final: 0.7841 (mp0) REVERT: C 620 TYR cc_start: 0.7556 (OUTLIER) cc_final: 0.7178 (t80) REVERT: D 58 MET cc_start: -0.0884 (mmp) cc_final: -0.1870 (mtt) REVERT: D 347 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7994 (mt-10) REVERT: D 370 GLN cc_start: 0.7600 (mp10) cc_final: 0.7304 (mp10) REVERT: E 109 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7512 (mp0) REVERT: E 347 GLU cc_start: 0.8580 (mt-10) cc_final: 0.7406 (tt0) REVERT: E 480 GLU cc_start: 0.8269 (mp0) cc_final: 0.8067 (mp0) REVERT: E 481 GLU cc_start: 0.8291 (tt0) cc_final: 0.8078 (tt0) outliers start: 74 outliers final: 35 residues processed: 632 average time/residue: 1.5144 time to fit residues: 1072.6851 Evaluate side-chains 625 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 588 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 550 SER Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 200 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 201 optimal weight: 4.9990 chunk 240 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 560 ASN B 154 GLN B 360 HIS B 432 GLN B 459 ASN B 476 GLN C 405 ASN C 432 GLN D 221 GLN D 432 GLN D 560 ASN E 70 ASN E 432 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.159987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.139387 restraints weight = 30385.735| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 1.85 r_work: 0.3747 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23438 Z= 0.138 Angle : 0.548 6.798 31896 Z= 0.294 Chirality : 0.044 0.168 3639 Planarity : 0.004 0.047 4125 Dihedral : 4.895 51.615 3138 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.35 % Allowed : 12.37 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: 1.11 (0.16), residues: 2875 helix: 1.94 (0.20), residues: 734 sheet: 1.20 (0.16), residues: 942 loop : -0.39 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 359 HIS 0.004 0.001 HIS B 360 PHE 0.023 0.002 PHE C 168 TYR 0.021 0.002 TYR C 53 ARG 0.011 0.000 ARG E 521 Details of bonding type rmsd hydrogen bonds : bond 0.05995 ( 1059) hydrogen bonds : angle 4.52058 ( 2919) covalent geometry : bond 0.00300 (23438) covalent geometry : angle 0.54804 (31896) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 585 time to evaluate : 2.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LEU cc_start: 0.8533 (tt) cc_final: 0.8324 (tp) REVERT: A 347 GLU cc_start: 0.8507 (mt-10) cc_final: 0.7617 (mt-10) REVERT: A 425 GLU cc_start: 0.8167 (tt0) cc_final: 0.7933 (tt0) REVERT: A 480 GLU cc_start: 0.8373 (mp0) cc_final: 0.7746 (mp0) REVERT: A 481 GLU cc_start: 0.8294 (tt0) cc_final: 0.8088 (tt0) REVERT: C 286 VAL cc_start: 0.4976 (OUTLIER) cc_final: 0.4597 (t) REVERT: C 347 GLU cc_start: 0.8566 (mt-10) cc_final: 0.7689 (mt-10) REVERT: C 425 GLU cc_start: 0.8016 (tt0) cc_final: 0.7780 (tt0) REVERT: C 480 GLU cc_start: 0.8250 (mp0) cc_final: 0.7871 (mp0) REVERT: C 620 TYR cc_start: 0.7544 (OUTLIER) cc_final: 0.7186 (t80) REVERT: D 58 MET cc_start: -0.0922 (mmp) cc_final: -0.2081 (mtm) REVERT: D 269 VAL cc_start: 0.7740 (t) cc_final: 0.7458 (m) REVERT: D 347 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8225 (mt-10) REVERT: D 370 GLN cc_start: 0.7613 (mp10) cc_final: 0.7308 (mp10) REVERT: E 347 GLU cc_start: 0.8558 (mt-10) cc_final: 0.7384 (tt0) REVERT: E 480 GLU cc_start: 0.8310 (mp0) cc_final: 0.8088 (mp0) REVERT: E 481 GLU cc_start: 0.8328 (tt0) cc_final: 0.8115 (tt0) REVERT: E 620 TYR cc_start: 0.7783 (OUTLIER) cc_final: 0.6827 (t80) outliers start: 84 outliers final: 45 residues processed: 617 average time/residue: 1.5073 time to fit residues: 1043.2160 Evaluate side-chains 628 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 580 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 270 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 373 CYS Chi-restraints excluded: chain E residue 500 SER Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 606 GLN Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 83 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 271 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 263 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN A 405 ASN A 409 GLN A 410 ASN A 502 ASN B 344 GLN B 360 HIS B 432 GLN B 464 ASN B 476 GLN C 144 HIS C 169 GLN C 233 HIS C 338 GLN C 432 GLN D 221 GLN D 432 GLN E 70 ASN E 344 GLN E 432 GLN E 560 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.153499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.133519 restraints weight = 30201.001| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.85 r_work: 0.3659 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.115 23438 Z= 0.392 Angle : 0.779 9.537 31896 Z= 0.424 Chirality : 0.055 0.262 3639 Planarity : 0.006 0.054 4125 Dihedral : 5.714 52.393 3138 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.03 % Favored : 96.94 % Rotamer: Outliers : 4.55 % Allowed : 12.37 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: 2875 helix: 1.30 (0.20), residues: 738 sheet: 0.89 (0.17), residues: 886 loop : -0.75 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 121 HIS 0.015 0.002 HIS B 204 PHE 0.036 0.003 PHE E 135 TYR 0.045 0.004 TYR C 53 ARG 0.014 0.001 ARG C 521 Details of bonding type rmsd hydrogen bonds : bond 0.09797 ( 1059) hydrogen bonds : angle 5.18684 ( 2919) covalent geometry : bond 0.00961 (23438) covalent geometry : angle 0.77878 (31896) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 606 time to evaluate : 2.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: A 235 LEU cc_start: 0.8554 (tt) cc_final: 0.8330 (tp) REVERT: A 248 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7867 (ptp-170) REVERT: A 347 GLU cc_start: 0.8543 (mt-10) cc_final: 0.7732 (mt-10) REVERT: A 425 GLU cc_start: 0.8206 (tt0) cc_final: 0.7975 (tt0) REVERT: A 480 GLU cc_start: 0.8428 (mp0) cc_final: 0.7830 (mp0) REVERT: A 481 GLU cc_start: 0.8348 (tt0) cc_final: 0.8129 (tt0) REVERT: B 345 ARG cc_start: 0.8511 (mtp85) cc_final: 0.8293 (mtp85) REVERT: C 58 MET cc_start: 0.6333 (OUTLIER) cc_final: 0.5857 (mtt) REVERT: C 110 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8096 (tm) REVERT: C 235 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8020 (pt) REVERT: C 286 VAL cc_start: 0.5391 (OUTLIER) cc_final: 0.4969 (t) REVERT: C 347 GLU cc_start: 0.8644 (mt-10) cc_final: 0.7800 (mt-10) REVERT: C 425 GLU cc_start: 0.8084 (tt0) cc_final: 0.7848 (tt0) REVERT: C 480 GLU cc_start: 0.8253 (mp0) cc_final: 0.7981 (mp0) REVERT: C 498 ARG cc_start: 0.6175 (OUTLIER) cc_final: 0.5908 (tpp-160) REVERT: C 566 ASP cc_start: 0.7430 (m-30) cc_final: 0.7169 (m-30) REVERT: C 598 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8396 (tttm) REVERT: C 620 TYR cc_start: 0.7798 (OUTLIER) cc_final: 0.7364 (t80) REVERT: D 58 MET cc_start: -0.0784 (mmp) cc_final: -0.1812 (mtt) REVERT: D 82 MET cc_start: 0.5975 (ptp) cc_final: 0.5589 (ptm) REVERT: D 269 VAL cc_start: 0.7910 (t) cc_final: 0.7666 (m) REVERT: D 374 THR cc_start: 0.6419 (OUTLIER) cc_final: 0.6191 (m) REVERT: D 468 ARG cc_start: 0.7524 (mtt180) cc_final: 0.7280 (mtt180) REVERT: D 520 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8658 (mp) REVERT: E 425 GLU cc_start: 0.7966 (tt0) cc_final: 0.7717 (tt0) REVERT: E 468 ARG cc_start: 0.8170 (mtt180) cc_final: 0.7968 (mtt180) REVERT: E 480 GLU cc_start: 0.8321 (mp0) cc_final: 0.8015 (mp0) REVERT: E 620 TYR cc_start: 0.7949 (OUTLIER) cc_final: 0.6984 (t80) outliers start: 114 outliers final: 63 residues processed: 655 average time/residue: 1.5254 time to fit residues: 1121.6929 Evaluate side-chains 663 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 588 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 270 GLU Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 373 CYS Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 564 SER Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 46 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 245 optimal weight: 0.8980 chunk 227 optimal weight: 0.8980 chunk 145 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 171 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 277 GLN A 344 GLN A 405 ASN A 409 GLN A 410 ASN A 432 GLN B 169 GLN B 360 HIS B 410 ASN B 432 GLN B 476 GLN C 169 GLN C 432 GLN D 206 GLN D 338 GLN D 611 GLN E 70 ASN E 432 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.157431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.137461 restraints weight = 30410.947| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.84 r_work: 0.3725 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23438 Z= 0.135 Angle : 0.556 7.149 31896 Z= 0.299 Chirality : 0.044 0.195 3639 Planarity : 0.004 0.046 4125 Dihedral : 5.033 52.018 3136 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.59 % Allowed : 15.20 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: 0.79 (0.16), residues: 2875 helix: 1.82 (0.20), residues: 733 sheet: 0.91 (0.16), residues: 935 loop : -0.58 (0.18), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 121 HIS 0.005 0.001 HIS C 144 PHE 0.018 0.002 PHE B 414 TYR 0.020 0.002 TYR E 517 ARG 0.012 0.000 ARG C 521 Details of bonding type rmsd hydrogen bonds : bond 0.05963 ( 1059) hydrogen bonds : angle 4.55580 ( 2919) covalent geometry : bond 0.00293 (23438) covalent geometry : angle 0.55610 (31896) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 578 time to evaluate : 2.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LEU cc_start: 0.8527 (tt) cc_final: 0.8294 (tp) REVERT: A 347 GLU cc_start: 0.8506 (mt-10) cc_final: 0.7582 (mt-10) REVERT: A 425 GLU cc_start: 0.8157 (tt0) cc_final: 0.7920 (tt0) REVERT: A 480 GLU cc_start: 0.8403 (mp0) cc_final: 0.7770 (mm-30) REVERT: A 481 GLU cc_start: 0.8328 (tt0) cc_final: 0.8083 (tt0) REVERT: C 58 MET cc_start: 0.6292 (OUTLIER) cc_final: 0.5829 (mtt) REVERT: C 235 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7985 (pt) REVERT: C 286 VAL cc_start: 0.5257 (OUTLIER) cc_final: 0.4869 (t) REVERT: C 347 GLU cc_start: 0.8598 (mt-10) cc_final: 0.7730 (mt-10) REVERT: C 425 GLU cc_start: 0.8006 (tt0) cc_final: 0.7752 (tt0) REVERT: C 480 GLU cc_start: 0.8228 (mp0) cc_final: 0.7965 (mp0) REVERT: C 498 ARG cc_start: 0.6057 (OUTLIER) cc_final: 0.5787 (tpp-160) REVERT: C 620 TYR cc_start: 0.7600 (OUTLIER) cc_final: 0.7213 (t80) REVERT: D 58 MET cc_start: -0.0882 (mmp) cc_final: -0.1986 (mtm) REVERT: D 269 VAL cc_start: 0.7794 (t) cc_final: 0.7519 (m) REVERT: D 370 GLN cc_start: 0.7903 (mp10) cc_final: 0.7529 (mp10) REVERT: E 277 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7858 (mp10) REVERT: E 425 GLU cc_start: 0.7975 (tt0) cc_final: 0.7698 (tt0) REVERT: E 468 ARG cc_start: 0.8340 (mtt180) cc_final: 0.8108 (mtt180) REVERT: E 480 GLU cc_start: 0.8319 (mp0) cc_final: 0.7989 (mp0) REVERT: E 620 TYR cc_start: 0.7800 (OUTLIER) cc_final: 0.6798 (t80) outliers start: 90 outliers final: 41 residues processed: 619 average time/residue: 1.4880 time to fit residues: 1034.6069 Evaluate side-chains 620 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 572 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 373 CYS Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 62 optimal weight: 0.8980 chunk 204 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 chunk 16 optimal weight: 0.0870 chunk 275 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 273 optimal weight: 5.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN A 405 ASN A 410 ASN B 360 HIS B 410 ASN B 432 GLN B 476 GLN C 60 GLN C 169 GLN C 409 GLN D 221 GLN D 432 GLN E 70 ASN E 432 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.156724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.137362 restraints weight = 30429.896| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.79 r_work: 0.3728 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23438 Z= 0.142 Angle : 0.562 7.749 31896 Z= 0.301 Chirality : 0.044 0.186 3639 Planarity : 0.004 0.046 4125 Dihedral : 4.914 51.103 3136 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.83 % Allowed : 16.64 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: 0.88 (0.16), residues: 2875 helix: 1.93 (0.20), residues: 731 sheet: 1.00 (0.16), residues: 917 loop : -0.56 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 121 HIS 0.005 0.001 HIS B 285 PHE 0.025 0.002 PHE C 168 TYR 0.024 0.002 TYR E 300 ARG 0.011 0.000 ARG A 521 Details of bonding type rmsd hydrogen bonds : bond 0.06025 ( 1059) hydrogen bonds : angle 4.46236 ( 2919) covalent geometry : bond 0.00314 (23438) covalent geometry : angle 0.56198 (31896) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 582 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7555 (mt-10) REVERT: A 425 GLU cc_start: 0.8182 (tt0) cc_final: 0.7946 (tt0) REVERT: A 480 GLU cc_start: 0.8338 (mp0) cc_final: 0.7708 (mm-30) REVERT: A 481 GLU cc_start: 0.8311 (tt0) cc_final: 0.8074 (tt0) REVERT: A 515 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8586 (mp) REVERT: B 578 ARG cc_start: 0.8481 (mtt-85) cc_final: 0.8235 (mtt-85) REVERT: C 58 MET cc_start: 0.6362 (OUTLIER) cc_final: 0.5895 (mtt) REVERT: C 235 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7981 (pt) REVERT: C 286 VAL cc_start: 0.5335 (OUTLIER) cc_final: 0.4987 (t) REVERT: C 347 GLU cc_start: 0.8576 (mt-10) cc_final: 0.7658 (mt-10) REVERT: C 425 GLU cc_start: 0.8030 (tt0) cc_final: 0.7798 (tt0) REVERT: C 480 GLU cc_start: 0.8212 (mp0) cc_final: 0.7952 (mp0) REVERT: C 498 ARG cc_start: 0.6049 (OUTLIER) cc_final: 0.5775 (tpp-160) REVERT: C 620 TYR cc_start: 0.7576 (OUTLIER) cc_final: 0.7191 (t80) REVERT: D 58 MET cc_start: -0.0758 (mmp) cc_final: -0.1888 (mtm) REVERT: D 82 MET cc_start: 0.5810 (ptp) cc_final: 0.5554 (ptm) REVERT: D 269 VAL cc_start: 0.7834 (t) cc_final: 0.7557 (m) REVERT: D 370 GLN cc_start: 0.7854 (mp10) cc_final: 0.7495 (mp10) REVERT: E 245 PRO cc_start: 0.8262 (Cg_endo) cc_final: 0.8036 (Cg_exo) REVERT: E 277 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7877 (mp10) REVERT: E 347 GLU cc_start: 0.8578 (mt-10) cc_final: 0.7445 (tt0) REVERT: E 468 ARG cc_start: 0.8265 (mtt180) cc_final: 0.8065 (mtt180) REVERT: E 480 GLU cc_start: 0.8307 (mp0) cc_final: 0.8071 (mp0) REVERT: E 481 GLU cc_start: 0.8296 (tt0) cc_final: 0.8088 (tt0) REVERT: E 620 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.6830 (t80) outliers start: 71 outliers final: 43 residues processed: 617 average time/residue: 1.4883 time to fit residues: 1034.9376 Evaluate side-chains 625 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 574 time to evaluate : 2.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 363 LYS Chi-restraints excluded: chain E residue 373 CYS Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 564 SER Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 238 optimal weight: 0.7980 chunk 281 optimal weight: 0.8980 chunk 90 optimal weight: 0.0030 chunk 105 optimal weight: 0.5980 chunk 272 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 241 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN A 405 ASN A 410 ASN A 502 ASN A 514 ASN B 360 HIS B 476 GLN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 GLN C 206 GLN C 409 GLN D 611 GLN E 70 ASN E 432 GLN E 459 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.158277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.138748 restraints weight = 30820.201| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.82 r_work: 0.3748 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23438 Z= 0.115 Angle : 0.531 8.472 31896 Z= 0.281 Chirality : 0.043 0.181 3639 Planarity : 0.004 0.041 4125 Dihedral : 4.714 50.122 3136 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.87 % Allowed : 17.24 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: 1.01 (0.16), residues: 2875 helix: 2.15 (0.20), residues: 729 sheet: 0.94 (0.16), residues: 971 loop : -0.48 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 121 HIS 0.005 0.001 HIS B 285 PHE 0.024 0.001 PHE C 168 TYR 0.020 0.001 TYR E 300 ARG 0.005 0.000 ARG C 521 Details of bonding type rmsd hydrogen bonds : bond 0.05107 ( 1059) hydrogen bonds : angle 4.27589 ( 2919) covalent geometry : bond 0.00247 (23438) covalent geometry : angle 0.53104 (31896) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 581 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 GLU cc_start: 0.8461 (mt-10) cc_final: 0.7548 (mt-10) REVERT: A 425 GLU cc_start: 0.8167 (tt0) cc_final: 0.7926 (tt0) REVERT: A 480 GLU cc_start: 0.8331 (mp0) cc_final: 0.7696 (mm-30) REVERT: A 481 GLU cc_start: 0.8328 (tt0) cc_final: 0.8079 (tt0) REVERT: C 58 MET cc_start: 0.6374 (mtt) cc_final: 0.5892 (mtt) REVERT: C 235 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7950 (pt) REVERT: C 286 VAL cc_start: 0.5294 (OUTLIER) cc_final: 0.4931 (t) REVERT: C 347 GLU cc_start: 0.8583 (mt-10) cc_final: 0.7785 (mt-10) REVERT: C 425 GLU cc_start: 0.7996 (tt0) cc_final: 0.7752 (tt0) REVERT: C 480 GLU cc_start: 0.8236 (mp0) cc_final: 0.7976 (mp0) REVERT: C 498 ARG cc_start: 0.5941 (OUTLIER) cc_final: 0.5672 (tpp-160) REVERT: D 58 MET cc_start: -0.0778 (mmp) cc_final: -0.1953 (mtm) REVERT: D 370 GLN cc_start: 0.7886 (mp10) cc_final: 0.7524 (mp10) REVERT: E 277 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7801 (mp10) REVERT: E 347 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8010 (mt-10) REVERT: E 468 ARG cc_start: 0.8354 (mtt180) cc_final: 0.8124 (mtt180) REVERT: E 480 GLU cc_start: 0.8301 (mp0) cc_final: 0.7940 (mp0) REVERT: E 620 TYR cc_start: 0.7812 (OUTLIER) cc_final: 0.6805 (t80) outliers start: 72 outliers final: 41 residues processed: 614 average time/residue: 1.4896 time to fit residues: 1026.3907 Evaluate side-chains 620 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 574 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 606 GLN Chi-restraints excluded: chain E residue 620 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 148 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 232 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 228 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 70 ASN A 169 GLN A 344 GLN A 405 ASN A 410 ASN A 432 GLN A 502 ASN A 514 ASN B 360 HIS B 476 GLN B 502 ASN C 169 GLN C 560 ASN D 221 GLN D 432 GLN E 70 ASN E 432 GLN E 560 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.154246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.135050 restraints weight = 30080.001| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.79 r_work: 0.3695 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 23438 Z= 0.220 Angle : 0.639 8.699 31896 Z= 0.344 Chirality : 0.047 0.206 3639 Planarity : 0.004 0.044 4125 Dihedral : 5.107 50.748 3136 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.99 % Allowed : 17.24 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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 (0.16), residues: 2875 helix: 1.74 (0.20), residues: 737 sheet: 0.94 (0.16), residues: 912 loop : -0.66 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 121 HIS 0.007 0.001 HIS B 204 PHE 0.025 0.002 PHE E 168 TYR 0.032 0.002 TYR C 53 ARG 0.006 0.000 ARG D 521 Details of bonding type rmsd hydrogen bonds : bond 0.07586 ( 1059) hydrogen bonds : angle 4.68279 ( 2919) covalent geometry : bond 0.00523 (23438) covalent geometry : angle 0.63939 (31896) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 578 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 GLU cc_start: 0.8514 (mt-10) cc_final: 0.7588 (tt0) REVERT: A 425 GLU cc_start: 0.8179 (tt0) cc_final: 0.7944 (tt0) REVERT: A 480 GLU cc_start: 0.8351 (mp0) cc_final: 0.7741 (mp0) REVERT: A 481 GLU cc_start: 0.8335 (tt0) cc_final: 0.8093 (tt0) REVERT: C 58 MET cc_start: 0.6698 (OUTLIER) cc_final: 0.6285 (mtt) REVERT: C 235 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8032 (pt) REVERT: C 286 VAL cc_start: 0.5383 (OUTLIER) cc_final: 0.5022 (t) REVERT: C 347 GLU cc_start: 0.8611 (mt-10) cc_final: 0.7851 (mt-10) REVERT: C 480 GLU cc_start: 0.8238 (mp0) cc_final: 0.7993 (mp0) REVERT: C 498 ARG cc_start: 0.6071 (OUTLIER) cc_final: 0.5788 (tpp-160) REVERT: C 620 TYR cc_start: 0.7622 (OUTLIER) cc_final: 0.7208 (t80) REVERT: D 58 MET cc_start: -0.0648 (mmp) cc_final: -0.1822 (mtm) REVERT: D 86 ILE cc_start: 0.0333 (OUTLIER) cc_final: 0.0049 (pp) REVERT: D 370 GLN cc_start: 0.7905 (mp10) cc_final: 0.7493 (mp10) REVERT: E 208 LEU cc_start: 0.7989 (mt) cc_final: 0.7773 (mp) REVERT: E 245 PRO cc_start: 0.8284 (Cg_endo) cc_final: 0.8039 (Cg_exo) REVERT: E 277 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7875 (mp10) REVERT: E 347 GLU cc_start: 0.8591 (mt-10) cc_final: 0.7495 (tt0) REVERT: E 468 ARG cc_start: 0.8262 (mtt180) cc_final: 0.8061 (mtt180) REVERT: E 480 GLU cc_start: 0.8313 (mp0) cc_final: 0.8102 (mp0) REVERT: E 620 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.6957 (t80) outliers start: 75 outliers final: 45 residues processed: 615 average time/residue: 1.5019 time to fit residues: 1034.8720 Evaluate side-chains 630 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 577 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 521 ARG Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 363 LYS Chi-restraints excluded: chain E residue 500 SER Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 564 SER Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 232 optimal weight: 4.9990 chunk 140 optimal weight: 0.2980 chunk 257 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 405 ASN A 410 ASN A 514 ASN B 360 HIS B 410 ASN B 476 GLN C 169 GLN C 560 ASN D 611 GLN E 70 ASN E 432 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.155688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.136412 restraints weight = 30500.471| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.82 r_work: 0.3718 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23438 Z= 0.155 Angle : 0.581 9.100 31896 Z= 0.310 Chirality : 0.044 0.204 3639 Planarity : 0.004 0.045 4125 Dihedral : 4.951 51.144 3136 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.51 % Allowed : 18.24 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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 (0.16), residues: 2875 helix: 1.90 (0.20), residues: 736 sheet: 0.92 (0.16), residues: 921 loop : -0.66 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 121 HIS 0.006 0.001 HIS B 285 PHE 0.018 0.002 PHE B 414 TYR 0.022 0.002 TYR C 53 ARG 0.005 0.000 ARG B 498 Details of bonding type rmsd hydrogen bonds : bond 0.06205 ( 1059) hydrogen bonds : angle 4.48453 ( 2919) covalent geometry : bond 0.00354 (23438) covalent geometry : angle 0.58136 (31896) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 576 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7560 (mt-10) REVERT: A 425 GLU cc_start: 0.8155 (tt0) cc_final: 0.7919 (tt0) REVERT: A 480 GLU cc_start: 0.8350 (mp0) cc_final: 0.7709 (mm-30) REVERT: A 481 GLU cc_start: 0.8343 (tt0) cc_final: 0.8093 (tt0) REVERT: C 58 MET cc_start: 0.6762 (mtt) cc_final: 0.6383 (mtt) REVERT: C 235 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7998 (pt) REVERT: C 286 VAL cc_start: 0.5376 (OUTLIER) cc_final: 0.5005 (t) REVERT: C 347 GLU cc_start: 0.8597 (mt-10) cc_final: 0.7804 (mt-10) REVERT: C 498 ARG cc_start: 0.6032 (OUTLIER) cc_final: 0.5756 (tpp-160) REVERT: C 620 TYR cc_start: 0.7600 (OUTLIER) cc_final: 0.7217 (t80) REVERT: D 58 MET cc_start: -0.0516 (mmp) cc_final: -0.1775 (mtm) REVERT: D 86 ILE cc_start: 0.0293 (OUTLIER) cc_final: 0.0021 (pp) REVERT: D 370 GLN cc_start: 0.7884 (mp10) cc_final: 0.7401 (mp10) REVERT: E 245 PRO cc_start: 0.8283 (Cg_endo) cc_final: 0.8065 (Cg_exo) REVERT: E 277 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7825 (mp10) REVERT: E 347 GLU cc_start: 0.8557 (mt-10) cc_final: 0.7415 (tt0) REVERT: E 620 TYR cc_start: 0.7841 (OUTLIER) cc_final: 0.6958 (t80) outliers start: 63 outliers final: 44 residues processed: 605 average time/residue: 1.5429 time to fit residues: 1049.7857 Evaluate side-chains 616 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 565 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 363 LYS Chi-restraints excluded: chain E residue 500 SER Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 26 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 232 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 169 GLN A 344 GLN A 405 ASN A 410 ASN A 432 GLN A 502 ASN A 514 ASN A 560 ASN B 360 HIS B 476 GLN C 169 GLN D 611 GLN E 70 ASN E 432 GLN E 560 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.154090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.134909 restraints weight = 30451.249| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.82 r_work: 0.3697 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23438 Z= 0.197 Angle : 0.623 9.417 31896 Z= 0.335 Chirality : 0.046 0.215 3639 Planarity : 0.004 0.044 4125 Dihedral : 5.099 51.090 3136 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.23 % Allowed : 18.68 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: 0.64 (0.16), residues: 2875 helix: 1.76 (0.20), residues: 738 sheet: 0.82 (0.16), residues: 938 loop : -0.72 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 615 HIS 0.006 0.001 HIS B 204 PHE 0.031 0.002 PHE C 168 TYR 0.031 0.002 TYR C 53 ARG 0.006 0.000 ARG D 521 Details of bonding type rmsd hydrogen bonds : bond 0.07135 ( 1059) hydrogen bonds : angle 4.64124 ( 2919) covalent geometry : bond 0.00464 (23438) covalent geometry : angle 0.62289 (31896) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 573 time to evaluate : 2.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 ARG cc_start: 0.8461 (mtp85) cc_final: 0.8253 (mtp85) REVERT: A 347 GLU cc_start: 0.8525 (mt-10) cc_final: 0.7653 (mt-10) REVERT: A 425 GLU cc_start: 0.8163 (tt0) cc_final: 0.7928 (tt0) REVERT: A 480 GLU cc_start: 0.8347 (mp0) cc_final: 0.7711 (mm-30) REVERT: A 481 GLU cc_start: 0.8343 (tt0) cc_final: 0.8099 (tt0) REVERT: C 58 MET cc_start: 0.6849 (mtt) cc_final: 0.6478 (mtt) REVERT: C 235 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8018 (pt) REVERT: C 286 VAL cc_start: 0.5409 (OUTLIER) cc_final: 0.5036 (t) REVERT: C 347 GLU cc_start: 0.8607 (mt-10) cc_final: 0.7931 (mt-10) REVERT: C 480 GLU cc_start: 0.8168 (mp0) cc_final: 0.7819 (mp0) REVERT: C 498 ARG cc_start: 0.6090 (OUTLIER) cc_final: 0.5812 (tpp-160) REVERT: C 620 TYR cc_start: 0.7664 (OUTLIER) cc_final: 0.7267 (t80) REVERT: D 58 MET cc_start: -0.0465 (mmp) cc_final: -0.1687 (mtm) REVERT: D 86 ILE cc_start: 0.0264 (OUTLIER) cc_final: -0.0014 (pp) REVERT: D 370 GLN cc_start: 0.7888 (mp10) cc_final: 0.7454 (mp10) REVERT: E 245 PRO cc_start: 0.8280 (Cg_endo) cc_final: 0.8053 (Cg_exo) REVERT: E 277 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7883 (mp10) REVERT: E 347 GLU cc_start: 0.8583 (mt-10) cc_final: 0.7480 (tt0) REVERT: E 620 TYR cc_start: 0.7911 (OUTLIER) cc_final: 0.6943 (t80) outliers start: 56 outliers final: 42 residues processed: 599 average time/residue: 1.5154 time to fit residues: 1015.0400 Evaluate side-chains 615 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 566 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 363 LYS Chi-restraints excluded: chain E residue 373 CYS Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 27 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 180 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 282 optimal weight: 0.0970 chunk 254 optimal weight: 4.9990 chunk 242 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 276 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 344 GLN A 405 ASN A 410 ASN A 514 ASN B 360 HIS B 410 ASN B 476 GLN C 169 GLN C 409 GLN D 611 GLN E 70 ASN E 432 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.156951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.137888 restraints weight = 30527.958| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.81 r_work: 0.3740 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23438 Z= 0.121 Angle : 0.551 8.998 31896 Z= 0.292 Chirality : 0.043 0.193 3639 Planarity : 0.004 0.043 4125 Dihedral : 4.804 50.791 3136 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.72 % Allowed : 19.43 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: 0.88 (0.16), residues: 2875 helix: 2.10 (0.20), residues: 727 sheet: 0.86 (0.16), residues: 946 loop : -0.58 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 615 HIS 0.005 0.001 HIS B 285 PHE 0.026 0.001 PHE C 168 TYR 0.021 0.002 TYR C 487 ARG 0.004 0.000 ARG D 521 Details of bonding type rmsd hydrogen bonds : bond 0.05294 ( 1059) hydrogen bonds : angle 4.33312 ( 2919) covalent geometry : bond 0.00258 (23438) covalent geometry : angle 0.55137 (31896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25293.34 seconds wall clock time: 434 minutes 21.79 seconds (26061.79 seconds total)