Starting phenix.real_space_refine on Thu May 29 13:04:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pqx_17827/05_2025/8pqx_17827.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pqx_17827/05_2025/8pqx_17827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pqx_17827/05_2025/8pqx_17827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pqx_17827/05_2025/8pqx_17827.map" model { file = "/net/cci-nas-00/data/ceres_data/8pqx_17827/05_2025/8pqx_17827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pqx_17827/05_2025/8pqx_17827.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 25 5.49 5 S 138 5.16 5 C 19836 2.51 5 N 5808 2.21 5 O 6231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32038 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5285 Classifications: {'peptide': 746} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 704} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 586 Unresolved non-hydrogen angles: 744 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 316 Chain: "B" Number of atoms: 5285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5285 Classifications: {'peptide': 746} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 704} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 586 Unresolved non-hydrogen angles: 744 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 316 Chain: "C" Number of atoms: 5285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5285 Classifications: {'peptide': 746} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 704} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 586 Unresolved non-hydrogen angles: 744 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 316 Chain: "D" Number of atoms: 5285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5285 Classifications: {'peptide': 746} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 704} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 586 Unresolved non-hydrogen angles: 744 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 316 Chain: "E" Number of atoms: 5285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5285 Classifications: {'peptide': 746} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 704} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 586 Unresolved non-hydrogen angles: 744 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 316 Chain: "F" Number of atoms: 5285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5285 Classifications: {'peptide': 746} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 704} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 586 Unresolved non-hydrogen angles: 744 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 316 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.39, per 1000 atoms: 0.57 Number of scatterers: 32038 At special positions: 0 Unit cell: (165.737, 123.708, 172.874, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 138 16.00 P 25 15.00 O 6231 8.00 N 5808 7.00 C 19836 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 691 " - pdb=" SG CYS A 695 " distance=2.05 Simple disulfide: pdb=" SG CYS B 691 " - pdb=" SG CYS B 695 " distance=2.05 Simple disulfide: pdb=" SG CYS C 691 " - pdb=" SG CYS C 695 " distance=2.05 Simple disulfide: pdb=" SG CYS D 691 " - pdb=" SG CYS D 695 " distance=2.05 Simple disulfide: pdb=" SG CYS E 691 " - pdb=" SG CYS E 695 " distance=2.05 Simple disulfide: pdb=" SG CYS F 691 " - pdb=" SG CYS F 695 " distance=2.05 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.67 Conformation dependent library (CDL) restraints added in 4.4 seconds 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8376 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 35 sheets defined 50.4% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'A' and resid 42 through 49 removed outlier: 3.669A pdb=" N GLU A 48 " --> pdb=" O PRO A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 removed outlier: 4.129A pdb=" N ASN A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 91' Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.698A pdb=" N PHE A 139 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 209 through 226 removed outlier: 5.111A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.573A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 278 through 296 Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.621A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 338 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.682A pdb=" N ILE A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 391 through 394 removed outlier: 3.686A pdb=" N VAL A 394 " --> pdb=" O ALA A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 391 through 394' Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 408 through 431 removed outlier: 3.789A pdb=" N ASP A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP A 431 " --> pdb=" O MET A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 444 removed outlier: 3.727A pdb=" N MET A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.577A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 506 Processing helix chain 'A' and resid 523 through 535 Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 557 through 569 removed outlier: 3.831A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 612 through 615 Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.532A pdb=" N ILE A 629 " --> pdb=" O PRO A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 649 through 662 Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 683 through 714 removed outlier: 3.892A pdb=" N ARG A 713 " --> pdb=" O ARG A 709 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 743 removed outlier: 3.679A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 761 Processing helix chain 'B' and resid 43 through 47 removed outlier: 3.757A pdb=" N MET B 46 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP B 47 " --> pdb=" O PRO B 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 43 through 47' Processing helix chain 'B' and resid 85 through 93 removed outlier: 4.117A pdb=" N ASN B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 136 removed outlier: 3.837A pdb=" N VAL B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 209 through 226 removed outlier: 5.111A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 233 removed outlier: 3.573A pdb=" N ILE B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 278 through 296 Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.620A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 338 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.682A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 391 through 394 removed outlier: 3.685A pdb=" N VAL B 394 " --> pdb=" O ALA B 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 391 through 394' Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 408 through 431 removed outlier: 3.790A pdb=" N ASP B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP B 431 " --> pdb=" O MET B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 444 removed outlier: 3.728A pdb=" N MET B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 removed outlier: 3.576A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 506 Processing helix chain 'B' and resid 523 through 535 Processing helix chain 'B' and resid 543 through 553 Processing helix chain 'B' and resid 557 through 569 removed outlier: 3.830A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 598 through 610 Processing helix chain 'B' and resid 612 through 615 Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.533A pdb=" N ILE B 629 " --> pdb=" O PRO B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 649 through 662 Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 714 removed outlier: 3.893A pdb=" N ARG B 713 " --> pdb=" O ARG B 709 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 743 removed outlier: 3.679A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 761 Processing helix chain 'C' and resid 43 through 47 removed outlier: 3.756A pdb=" N MET C 46 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP C 47 " --> pdb=" O PRO C 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 43 through 47' Processing helix chain 'C' and resid 85 through 93 removed outlier: 4.116A pdb=" N ASN C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 136 removed outlier: 3.838A pdb=" N VAL C 133 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 209 through 226 removed outlier: 5.111A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 233 removed outlier: 3.573A pdb=" N ILE C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 278 through 296 Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.621A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 338 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.681A pdb=" N ILE C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 391 through 394 removed outlier: 3.686A pdb=" N VAL C 394 " --> pdb=" O ALA C 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 391 through 394' Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 408 through 431 removed outlier: 3.790A pdb=" N ASP C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP C 431 " --> pdb=" O MET C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 444 removed outlier: 3.728A pdb=" N MET C 442 " --> pdb=" O ASP C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 removed outlier: 3.577A pdb=" N PHE C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 499 Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 506 Processing helix chain 'C' and resid 523 through 535 Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 557 through 569 removed outlier: 3.830A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 610 Processing helix chain 'C' and resid 612 through 615 Processing helix chain 'C' and resid 625 through 629 removed outlier: 3.532A pdb=" N ILE C 629 " --> pdb=" O PRO C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 Processing helix chain 'C' and resid 649 through 662 Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 714 removed outlier: 3.893A pdb=" N ARG C 713 " --> pdb=" O ARG C 709 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 743 removed outlier: 3.679A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 761 Processing helix chain 'D' and resid 85 through 92 removed outlier: 3.856A pdb=" N ASN D 91 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 136 removed outlier: 4.181A pdb=" N VAL D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 209 through 226 removed outlier: 5.111A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 233 removed outlier: 3.573A pdb=" N ILE D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 278 through 296 Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.621A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 338 Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.682A pdb=" N ILE D 353 " --> pdb=" O PRO D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 391 through 394 removed outlier: 3.685A pdb=" N VAL D 394 " --> pdb=" O ALA D 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 391 through 394' Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 408 through 431 removed outlier: 3.791A pdb=" N ASP D 428 " --> pdb=" O ARG D 424 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP D 431 " --> pdb=" O MET D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 444 removed outlier: 3.728A pdb=" N MET D 442 " --> pdb=" O ASP D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.576A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 499 Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 506 Processing helix chain 'D' and resid 523 through 535 Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'D' and resid 557 through 569 removed outlier: 3.830A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 610 Processing helix chain 'D' and resid 612 through 615 Processing helix chain 'D' and resid 625 through 629 removed outlier: 3.532A pdb=" N ILE D 629 " --> pdb=" O PRO D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 635 Processing helix chain 'D' and resid 649 through 662 Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 714 removed outlier: 3.892A pdb=" N ARG D 713 " --> pdb=" O ARG D 709 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 743 removed outlier: 3.680A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 761 Processing helix chain 'E' and resid 85 through 91 Processing helix chain 'E' and resid 120 through 124 removed outlier: 3.618A pdb=" N VAL E 123 " --> pdb=" O ASP E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 140 removed outlier: 3.765A pdb=" N VAL E 133 " --> pdb=" O ASN E 129 " (cutoff:3.500A) Proline residue: E 137 - end of helix Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 209 through 226 removed outlier: 5.112A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 233 removed outlier: 3.573A pdb=" N ILE E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 278 through 296 Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.620A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 338 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.682A pdb=" N ILE E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 391 through 394 removed outlier: 3.686A pdb=" N VAL E 394 " --> pdb=" O ALA E 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 391 through 394' Processing helix chain 'E' and resid 395 through 403 Processing helix chain 'E' and resid 408 through 431 removed outlier: 3.790A pdb=" N ASP E 428 " --> pdb=" O ARG E 424 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU E 429 " --> pdb=" O LYS E 425 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP E 431 " --> pdb=" O MET E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 444 removed outlier: 3.728A pdb=" N MET E 442 " --> pdb=" O ASP E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 458 removed outlier: 3.576A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 499 Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 506 Processing helix chain 'E' and resid 523 through 535 Processing helix chain 'E' and resid 543 through 553 Processing helix chain 'E' and resid 557 through 569 removed outlier: 3.831A pdb=" N GLU E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 598 through 610 Processing helix chain 'E' and resid 612 through 615 Processing helix chain 'E' and resid 625 through 629 removed outlier: 3.533A pdb=" N ILE E 629 " --> pdb=" O PRO E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 Processing helix chain 'E' and resid 649 through 662 Processing helix chain 'E' and resid 671 through 679 Processing helix chain 'E' and resid 683 through 714 removed outlier: 3.892A pdb=" N ARG E 713 " --> pdb=" O ARG E 709 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN E 714 " --> pdb=" O GLU E 710 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 743 removed outlier: 3.680A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 761 Processing helix chain 'F' and resid 85 through 92 Processing helix chain 'F' and resid 129 through 140 removed outlier: 4.330A pdb=" N VAL F 133 " --> pdb=" O ASN F 129 " (cutoff:3.500A) Proline residue: F 137 - end of helix Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 209 through 226 removed outlier: 5.111A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 233 removed outlier: 3.574A pdb=" N ILE F 233 " --> pdb=" O LEU F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 263 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 278 through 296 Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.621A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 338 Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.682A pdb=" N ILE F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 391 through 394 removed outlier: 3.685A pdb=" N VAL F 394 " --> pdb=" O ALA F 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 391 through 394' Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 408 through 431 removed outlier: 3.791A pdb=" N ASP F 428 " --> pdb=" O ARG F 424 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU F 429 " --> pdb=" O LYS F 425 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP F 431 " --> pdb=" O MET F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 444 removed outlier: 3.727A pdb=" N MET F 442 " --> pdb=" O ASP F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 458 removed outlier: 3.576A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 506 Processing helix chain 'F' and resid 523 through 535 Processing helix chain 'F' and resid 543 through 553 Processing helix chain 'F' and resid 557 through 569 removed outlier: 3.830A pdb=" N GLU F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 610 Processing helix chain 'F' and resid 612 through 615 Processing helix chain 'F' and resid 625 through 629 removed outlier: 3.533A pdb=" N ILE F 629 " --> pdb=" O PRO F 626 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 Processing helix chain 'F' and resid 649 through 662 Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 714 removed outlier: 3.892A pdb=" N ARG F 713 " --> pdb=" O ARG F 709 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN F 714 " --> pdb=" O GLU F 710 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 743 removed outlier: 3.680A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 761 Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 60 removed outlier: 3.628A pdb=" N LEU A 26 " --> pdb=" O ILE A 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.049A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 542 removed outlier: 4.369A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 69 Processing sheet with id=AA6, first strand: chain 'B' and resid 116 through 118 Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AA8, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.049A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 538 through 542 removed outlier: 4.369A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 26 through 27 Processing sheet with id=AB2, first strand: chain 'C' and resid 65 through 69 Processing sheet with id=AB3, first strand: chain 'C' and resid 116 through 118 Processing sheet with id=AB4, first strand: chain 'C' and resid 146 through 147 Processing sheet with id=AB5, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.049A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 538 through 542 removed outlier: 4.370A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 26 through 27 Processing sheet with id=AB8, first strand: chain 'D' and resid 65 through 70 Processing sheet with id=AB9, first strand: chain 'D' and resid 110 through 111 Processing sheet with id=AC1, first strand: chain 'D' and resid 153 through 156 Processing sheet with id=AC2, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.050A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 538 through 542 removed outlier: 4.370A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 26 through 27 Processing sheet with id=AC5, first strand: chain 'E' and resid 65 through 70 Processing sheet with id=AC6, first strand: chain 'E' and resid 110 through 111 Processing sheet with id=AC7, first strand: chain 'E' and resid 116 through 118 Processing sheet with id=AC8, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.049A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 538 through 542 removed outlier: 4.370A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 26 through 27 Processing sheet with id=AD2, first strand: chain 'F' and resid 41 through 42 removed outlier: 5.381A pdb=" N LEU F 41 " --> pdb=" O ASP F 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 65 through 69 Processing sheet with id=AD4, first strand: chain 'F' and resid 110 through 111 Processing sheet with id=AD5, first strand: chain 'F' and resid 116 through 117 Processing sheet with id=AD6, first strand: chain 'F' and resid 153 through 156 Processing sheet with id=AD7, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.049A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 538 through 542 removed outlier: 4.369A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) 1576 hydrogen bonds defined for protein. 4464 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: 13.36 Time building geometry restraints manager: 8.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 10650 1.34 - 1.47: 7091 1.47 - 1.60: 14480 1.60 - 1.73: 33 1.73 - 1.87: 234 Bond restraints: 32488 Sorted by residual: bond pdb=" CA ARG A 191 " pdb=" C ARG A 191 " ideal model delta sigma weight residual 1.531 1.488 0.043 1.12e-02 7.97e+03 1.47e+01 bond pdb=" N ARG A 191 " pdb=" CA ARG A 191 " ideal model delta sigma weight residual 1.462 1.433 0.030 1.23e-02 6.61e+03 5.78e+00 bond pdb=" CA GLU F 200 " pdb=" C GLU F 200 " ideal model delta sigma weight residual 1.522 1.492 0.030 1.26e-02 6.30e+03 5.75e+00 bond pdb=" C ARG A 191 " pdb=" O ARG A 191 " ideal model delta sigma weight residual 1.231 1.202 0.028 1.24e-02 6.50e+03 5.20e+00 bond pdb=" C GLU A 194 " pdb=" O GLU A 194 " ideal model delta sigma weight residual 1.236 1.213 0.023 1.26e-02 6.30e+03 3.42e+00 ... (remaining 32483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 43145 1.76 - 3.52: 815 3.52 - 5.28: 160 5.28 - 7.04: 46 7.04 - 8.80: 1 Bond angle restraints: 44167 Sorted by residual: angle pdb=" N GLU A 192 " pdb=" CA GLU A 192 " pdb=" C GLU A 192 " ideal model delta sigma weight residual 111.28 102.48 8.80 1.09e+00 8.42e-01 6.51e+01 angle pdb=" N ASN F 199 " pdb=" CA ASN F 199 " pdb=" C ASN F 199 " ideal model delta sigma weight residual 111.71 105.66 6.05 1.15e+00 7.56e-01 2.76e+01 angle pdb=" N GLU D 194 " pdb=" CA GLU D 194 " pdb=" C GLU D 194 " ideal model delta sigma weight residual 111.36 106.05 5.31 1.09e+00 8.42e-01 2.37e+01 angle pdb=" N GLU F 200 " pdb=" CA GLU F 200 " pdb=" C GLU F 200 " ideal model delta sigma weight residual 110.35 103.66 6.69 1.40e+00 5.10e-01 2.29e+01 angle pdb=" N LEU F 198 " pdb=" CA LEU F 198 " pdb=" C LEU F 198 " ideal model delta sigma weight residual 113.38 107.82 5.56 1.23e+00 6.61e-01 2.05e+01 ... (remaining 44162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.04: 19462 30.04 - 60.07: 435 60.07 - 90.11: 45 90.11 - 120.14: 3 120.14 - 150.18: 16 Dihedral angle restraints: 19961 sinusoidal: 7079 harmonic: 12882 Sorted by residual: dihedral pdb=" C5' ADP F 901 " pdb=" O5' ADP F 901 " pdb=" PA ADP F 901 " pdb=" O2A ADP F 901 " ideal model delta sinusoidal sigma weight residual -60.00 90.18 -150.18 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" C5' ADP F 902 " pdb=" O5' ADP F 902 " pdb=" PA ADP F 902 " pdb=" O2A ADP F 902 " ideal model delta sinusoidal sigma weight residual -60.00 85.97 -145.97 1 2.00e+01 2.50e-03 4.39e+01 dihedral pdb=" C5' ADP E 902 " pdb=" O5' ADP E 902 " pdb=" PA ADP E 902 " pdb=" O2A ADP E 902 " ideal model delta sinusoidal sigma weight residual -60.00 85.93 -145.92 1 2.00e+01 2.50e-03 4.39e+01 ... (remaining 19958 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4191 0.055 - 0.109: 836 0.109 - 0.164: 101 0.164 - 0.219: 1 0.219 - 0.274: 1 Chirality restraints: 5130 Sorted by residual: chirality pdb=" CA GLU A 194 " pdb=" N GLU A 194 " pdb=" C GLU A 194 " pdb=" CB GLU A 194 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA GLU A 192 " pdb=" N GLU A 192 " pdb=" C GLU A 192 " pdb=" CB GLU A 192 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CA ILE A 175 " pdb=" N ILE A 175 " pdb=" C ILE A 175 " pdb=" CB ILE A 175 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.30e-01 ... (remaining 5127 not shown) Planarity restraints: 5916 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 190 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.32e+00 pdb=" C LYS A 190 " -0.050 2.00e-02 2.50e+03 pdb=" O LYS A 190 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG A 191 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 194 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.07e+00 pdb=" C GLU F 194 " 0.043 2.00e-02 2.50e+03 pdb=" O GLU F 194 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU F 195 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 692 " -0.012 2.00e-02 2.50e+03 2.45e-02 6.00e+00 pdb=" C GLN D 692 " 0.042 2.00e-02 2.50e+03 pdb=" O GLN D 692 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG D 693 " -0.014 2.00e-02 2.50e+03 ... (remaining 5913 not shown) Histogram of nonbonded interaction distances: 0.57 - 1.43: 11 1.43 - 2.30: 88 2.30 - 3.17: 28877 3.17 - 4.03: 84753 4.03 - 4.90: 149463 Warning: very small nonbonded interaction distances. Nonbonded interactions: 263192 Sorted by model distance: nonbonded pdb=" CD GLU D 433 " pdb=" O LEU E 26 " model vdw 0.565 3.270 nonbonded pdb=" CD GLU D 433 " pdb=" C LEU E 26 " model vdw 0.807 3.500 nonbonded pdb=" OE2 GLU E 433 " pdb=" C LEU F 26 " model vdw 0.908 3.270 nonbonded pdb=" OE1 GLU D 433 " pdb=" O LEU E 26 " model vdw 1.055 3.040 nonbonded pdb=" CB GLU B 433 " pdb=" CB VAL C 99 " model vdw 1.131 3.870 ... (remaining 263187 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 21 through 766 or resid 902)) selection = (chain 'B' and (resid 21 through 766 or resid 902)) selection = (chain 'C' and (resid 21 through 766 or resid 902)) selection = (chain 'D' and (resid 21 through 766 or resid 902)) selection = (chain 'E' and (resid 21 through 766 or resid 902)) selection = (chain 'F' and (resid 21 through 766 or resid 902)) } 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: 2.370 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: 1.230 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 70.690 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5090 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 0.058 32500 Z= 0.159 Angle : 0.614 8.796 44179 Z= 0.322 Chirality : 0.043 0.274 5130 Planarity : 0.003 0.048 5916 Dihedral : 14.113 150.181 11567 Min Nonbonded Distance : 0.565 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.06 % Favored : 91.89 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % 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 (0.13), residues: 4464 helix: 1.14 (0.12), residues: 1921 sheet: -1.75 (0.20), residues: 587 loop : -1.72 (0.15), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 454 HIS 0.002 0.001 HIS D 384 PHE 0.013 0.001 PHE A 230 TYR 0.006 0.001 TYR E 203 ARG 0.003 0.000 ARG F 313 Details of bonding type rmsd hydrogen bonds : bond 0.16041 ( 1576) hydrogen bonds : angle 6.04174 ( 4464) SS BOND : bond 0.01836 ( 6) SS BOND : angle 3.31701 ( 12) covalent geometry : bond 0.00294 (32488) covalent geometry : angle 0.61167 (44167) Misc. bond : bond 0.00256 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 891 time to evaluate : 3.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.7963 (mmtt) cc_final: 0.7200 (tttt) REVERT: A 265 PHE cc_start: 0.7162 (t80) cc_final: 0.6840 (t80) REVERT: A 281 GLU cc_start: 0.6141 (tp30) cc_final: 0.5596 (mm-30) REVERT: A 288 LYS cc_start: 0.6763 (mtmm) cc_final: 0.6182 (pttm) REVERT: A 304 ASP cc_start: 0.6175 (p0) cc_final: 0.5741 (t0) REVERT: A 307 ASP cc_start: 0.7167 (p0) cc_final: 0.5577 (t70) REVERT: A 311 PRO cc_start: 0.6928 (Cg_exo) cc_final: 0.6717 (Cg_endo) REVERT: A 324 ILE cc_start: 0.6832 (mt) cc_final: 0.6488 (mm) REVERT: A 366 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6413 (mt-10) REVERT: A 401 ASN cc_start: 0.7281 (m-40) cc_final: 0.6712 (t0) REVERT: A 410 ASP cc_start: 0.7376 (t0) cc_final: 0.6593 (m-30) REVERT: A 442 MET cc_start: 0.3732 (ptp) cc_final: 0.3236 (tmm) REVERT: A 450 ASP cc_start: 0.7139 (m-30) cc_final: 0.6413 (p0) REVERT: A 456 LEU cc_start: 0.7554 (mt) cc_final: 0.7104 (mt) REVERT: A 484 ASP cc_start: 0.7136 (p0) cc_final: 0.6240 (m-30) REVERT: A 554 GLU cc_start: 0.5866 (mm-30) cc_final: 0.5546 (mm-30) REVERT: A 578 GLU cc_start: 0.6681 (tp30) cc_final: 0.6426 (mt-10) REVERT: A 603 GLN cc_start: 0.7298 (tp40) cc_final: 0.7010 (tp40) REVERT: A 635 ARG cc_start: 0.6292 (mmm-85) cc_final: 0.5889 (mmt90) REVERT: A 651 LYS cc_start: 0.7457 (mppt) cc_final: 0.7198 (mttm) REVERT: A 697 LEU cc_start: 0.6834 (mt) cc_final: 0.6548 (mt) REVERT: A 720 MET cc_start: -0.0168 (tpt) cc_final: -0.0528 (mmp) REVERT: A 730 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6434 (pm20) REVERT: A 740 MET cc_start: 0.6912 (mmp) cc_final: 0.6556 (mmp) REVERT: A 748 SER cc_start: 0.6655 (t) cc_final: 0.6246 (p) REVERT: A 757 MET cc_start: 0.7059 (ppp) cc_final: 0.5566 (mtt) REVERT: B 239 ARG cc_start: 0.5627 (mtt180) cc_final: 0.4831 (mtt-85) REVERT: B 252 THR cc_start: 0.8091 (t) cc_final: 0.7481 (m) REVERT: B 265 PHE cc_start: 0.7319 (t80) cc_final: 0.6871 (t80) REVERT: B 288 LYS cc_start: 0.7461 (mtmm) cc_final: 0.6917 (ttpp) REVERT: B 304 ASP cc_start: 0.6938 (p0) cc_final: 0.6529 (t0) REVERT: B 332 MET cc_start: 0.5777 (ptm) cc_final: 0.5489 (ptp) REVERT: B 340 HIS cc_start: 0.4032 (t70) cc_final: 0.3594 (m-70) REVERT: B 354 ASP cc_start: 0.7795 (t70) cc_final: 0.7492 (t0) REVERT: B 357 LEU cc_start: 0.7872 (mm) cc_final: 0.7661 (mt) REVERT: B 478 ASP cc_start: 0.7521 (t0) cc_final: 0.6848 (m-30) REVERT: B 504 LEU cc_start: 0.7941 (tp) cc_final: 0.7709 (mt) REVERT: B 624 ASN cc_start: 0.7236 (m110) cc_final: 0.7023 (m-40) REVERT: B 757 MET cc_start: 0.6801 (ppp) cc_final: 0.6532 (ppp) REVERT: C 210 ARG cc_start: 0.6878 (tpp-160) cc_final: 0.6313 (mmp80) REVERT: C 219 MET cc_start: 0.6909 (mtp) cc_final: 0.6687 (mtt) REVERT: C 241 ILE cc_start: 0.6517 (mt) cc_final: 0.6283 (mm) REVERT: C 252 THR cc_start: 0.8064 (t) cc_final: 0.7558 (m) REVERT: C 265 PHE cc_start: 0.6847 (t80) cc_final: 0.6580 (t80) REVERT: C 267 PHE cc_start: 0.7108 (t80) cc_final: 0.6851 (t80) REVERT: C 273 GLU cc_start: 0.6491 (tp30) cc_final: 0.5506 (pt0) REVERT: C 305 GLU cc_start: 0.6773 (mm-30) cc_final: 0.6414 (mt-10) REVERT: C 317 HIS cc_start: 0.3252 (t-90) cc_final: 0.2694 (m-70) REVERT: C 323 ARG cc_start: 0.6450 (ttp-170) cc_final: 0.5703 (ttm-80) REVERT: C 357 LEU cc_start: 0.6709 (mm) cc_final: 0.6331 (mt) REVERT: C 379 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6834 (tt0) REVERT: C 450 ASP cc_start: 0.7744 (m-30) cc_final: 0.7363 (t0) REVERT: C 483 GLU cc_start: 0.7122 (tp30) cc_final: 0.6663 (mm-30) REVERT: C 536 GLN cc_start: 0.6751 (mm110) cc_final: 0.6231 (mm-40) REVERT: C 558 ASN cc_start: 0.6817 (m110) cc_final: 0.6520 (t0) REVERT: C 586 ARG cc_start: 0.6755 (ttp80) cc_final: 0.6415 (ptm-80) REVERT: C 635 ARG cc_start: 0.5721 (mmm-85) cc_final: 0.5472 (mmp-170) REVERT: C 697 LEU cc_start: 0.6878 (mt) cc_final: 0.6588 (mp) REVERT: C 720 MET cc_start: -0.0034 (tpt) cc_final: -0.0353 (tpt) REVERT: C 740 MET cc_start: 0.7117 (mmp) cc_final: 0.6771 (mmm) REVERT: C 748 SER cc_start: 0.6401 (t) cc_final: 0.6064 (p) REVERT: C 751 ASP cc_start: 0.7114 (m-30) cc_final: 0.6811 (m-30) REVERT: D 265 PHE cc_start: 0.6855 (t80) cc_final: 0.6614 (t80) REVERT: D 267 PHE cc_start: 0.7196 (t80) cc_final: 0.6828 (t80) REVERT: D 273 GLU cc_start: 0.6027 (tp30) cc_final: 0.5745 (mt-10) REVERT: D 281 GLU cc_start: 0.5994 (tp30) cc_final: 0.5539 (tt0) REVERT: D 315 LYS cc_start: 0.6265 (tmtt) cc_final: 0.5996 (tmtt) REVERT: D 317 HIS cc_start: 0.5069 (t-90) cc_final: 0.4088 (m90) REVERT: D 340 HIS cc_start: 0.5449 (t70) cc_final: 0.4924 (t70) REVERT: D 475 THR cc_start: 0.7728 (t) cc_final: 0.7278 (p) REVERT: D 487 ARG cc_start: 0.7144 (ttp80) cc_final: 0.6865 (mtm110) REVERT: D 490 GLN cc_start: 0.7348 (mt0) cc_final: 0.7117 (tt0) REVERT: D 499 HIS cc_start: 0.7135 (m90) cc_final: 0.6926 (m-70) REVERT: D 502 LYS cc_start: 0.6747 (mmtp) cc_final: 0.6476 (mmmm) REVERT: D 543 LYS cc_start: 0.6940 (mttp) cc_final: 0.5861 (mmtt) REVERT: D 554 GLU cc_start: 0.6013 (mm-30) cc_final: 0.4939 (tp30) REVERT: D 556 GLU cc_start: 0.5913 (pt0) cc_final: 0.5599 (mp0) REVERT: D 578 GLU cc_start: 0.7000 (tp30) cc_final: 0.6026 (mp0) REVERT: D 607 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6484 (mm-30) REVERT: D 668 LYS cc_start: 0.6855 (mmtm) cc_final: 0.5956 (tttp) REVERT: D 674 PHE cc_start: 0.6029 (t80) cc_final: 0.5659 (t80) REVERT: D 740 MET cc_start: 0.7312 (mmp) cc_final: 0.7058 (mmm) REVERT: E 210 ARG cc_start: 0.6712 (tpp-160) cc_final: 0.6214 (ttp80) REVERT: E 217 LYS cc_start: 0.6673 (mtpt) cc_final: 0.6313 (mtmt) REVERT: E 252 THR cc_start: 0.7912 (t) cc_final: 0.7465 (m) REVERT: E 267 PHE cc_start: 0.7296 (t80) cc_final: 0.6973 (t80) REVERT: E 273 GLU cc_start: 0.6537 (tp30) cc_final: 0.5688 (mt-10) REVERT: E 281 GLU cc_start: 0.6828 (tp30) cc_final: 0.6621 (tt0) REVERT: E 288 LYS cc_start: 0.6928 (mtmm) cc_final: 0.6714 (mtpp) REVERT: E 304 ASP cc_start: 0.6436 (p0) cc_final: 0.5913 (t0) REVERT: E 475 THR cc_start: 0.7430 (t) cc_final: 0.6795 (p) REVERT: E 478 ASP cc_start: 0.7297 (t0) cc_final: 0.6693 (m-30) REVERT: E 483 GLU cc_start: 0.7404 (tp30) cc_final: 0.6634 (mp0) REVERT: E 484 ASP cc_start: 0.7375 (p0) cc_final: 0.6737 (t70) REVERT: E 505 LYS cc_start: 0.7261 (tptp) cc_final: 0.6929 (mtpp) REVERT: E 517 TYR cc_start: 0.7796 (p90) cc_final: 0.7575 (p90) REVERT: E 529 LYS cc_start: 0.6208 (mtpp) cc_final: 0.5922 (mttt) REVERT: E 543 LYS cc_start: 0.7293 (mttp) cc_final: 0.6639 (mmmt) REVERT: E 554 GLU cc_start: 0.6260 (mm-30) cc_final: 0.6009 (tt0) REVERT: E 560 ARG cc_start: 0.5935 (tpt170) cc_final: 0.5587 (tpt170) REVERT: E 564 ASP cc_start: 0.7448 (m-30) cc_final: 0.7077 (m-30) REVERT: E 586 ARG cc_start: 0.6865 (ttp80) cc_final: 0.6547 (ttp80) REVERT: E 598 ASP cc_start: 0.5780 (m-30) cc_final: 0.5353 (m-30) REVERT: E 674 PHE cc_start: 0.7317 (t80) cc_final: 0.6918 (t80) REVERT: E 696 LYS cc_start: 0.6828 (ttpt) cc_final: 0.6541 (ttpp) REVERT: E 757 MET cc_start: 0.6994 (ppp) cc_final: 0.5476 (mtp) REVERT: F 236 LYS cc_start: 0.6934 (mmtt) cc_final: 0.6162 (mtmt) REVERT: F 244 TYR cc_start: 0.7128 (p90) cc_final: 0.6573 (p90) REVERT: F 288 LYS cc_start: 0.7546 (mtmm) cc_final: 0.6967 (tptt) REVERT: F 291 GLU cc_start: 0.7455 (mt-10) cc_final: 0.6923 (mm-30) REVERT: F 304 ASP cc_start: 0.6502 (p0) cc_final: 0.6085 (t0) REVERT: F 392 ASP cc_start: 0.6785 (p0) cc_final: 0.6401 (t0) REVERT: F 410 ASP cc_start: 0.7428 (t0) cc_final: 0.7052 (m-30) REVERT: F 465 ARG cc_start: 0.5913 (ptm160) cc_final: 0.5634 (ptm160) REVERT: F 478 ASP cc_start: 0.7998 (t0) cc_final: 0.7772 (t0) REVERT: F 487 ARG cc_start: 0.7006 (ttp80) cc_final: 0.6768 (ptp90) REVERT: F 490 GLN cc_start: 0.7014 (mt0) cc_final: 0.6776 (tm-30) REVERT: F 561 GLU cc_start: 0.6687 (pm20) cc_final: 0.5959 (mp0) REVERT: F 578 GLU cc_start: 0.6742 (tp30) cc_final: 0.6081 (tt0) REVERT: F 624 ASN cc_start: 0.6674 (m110) cc_final: 0.6169 (m-40) REVERT: F 651 LYS cc_start: 0.7202 (mppt) cc_final: 0.6410 (ptmt) REVERT: F 658 LYS cc_start: 0.7382 (mmtp) cc_final: 0.7041 (mmmm) REVERT: F 669 ASP cc_start: 0.6401 (t70) cc_final: 0.6095 (m-30) REVERT: F 738 GLU cc_start: 0.7283 (mt-10) cc_final: 0.7070 (mt-10) REVERT: F 758 PHE cc_start: 0.6548 (t80) cc_final: 0.6337 (t80) outliers start: 0 outliers final: 0 residues processed: 891 average time/residue: 0.5166 time to fit residues: 684.3702 Evaluate side-chains 534 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 534 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 20.0000 chunk 336 optimal weight: 6.9990 chunk 186 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 227 optimal weight: 20.0000 chunk 179 optimal weight: 5.9990 chunk 348 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 211 optimal weight: 0.7980 chunk 259 optimal weight: 3.9990 chunk 403 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN A 602 ASN A 624 ASN A 641 GLN B 260 ASN B 460 ASN B 494 GLN B 602 ASN B 616 ASN B 624 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN C 624 ASN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 GLN D 602 ASN D 624 ASN E 327 GLN ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN E 602 ASN E 624 ASN F 327 GLN F 460 ASN F 494 GLN F 602 ASN F 624 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.202394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.168517 restraints weight = 42114.377| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 1.74 r_work: 0.3868 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 32500 Z= 0.200 Angle : 0.683 9.749 44179 Z= 0.342 Chirality : 0.047 0.210 5130 Planarity : 0.005 0.066 5916 Dihedral : 10.457 172.210 4901 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.45 % Favored : 93.53 % Rotamer: Outliers : 1.82 % Allowed : 10.03 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.13), residues: 4464 helix: 0.74 (0.12), residues: 1913 sheet: -1.69 (0.19), residues: 632 loop : -1.28 (0.15), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 454 HIS 0.006 0.001 HIS C 340 PHE 0.017 0.002 PHE A 230 TYR 0.014 0.002 TYR B 244 ARG 0.006 0.001 ARG E 365 Details of bonding type rmsd hydrogen bonds : bond 0.04879 ( 1576) hydrogen bonds : angle 5.28826 ( 4464) SS BOND : bond 0.01843 ( 6) SS BOND : angle 4.06989 ( 12) covalent geometry : bond 0.00454 (32488) covalent geometry : angle 0.68022 (44167) Misc. bond : bond 0.00394 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 540 time to evaluate : 3.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8014 (mmtt) cc_final: 0.7718 (tttt) REVERT: A 307 ASP cc_start: 0.7264 (p0) cc_final: 0.7032 (t70) REVERT: A 322 ARG cc_start: 0.6548 (mtt90) cc_final: 0.6282 (mtm-85) REVERT: A 364 ASP cc_start: 0.4744 (m-30) cc_final: 0.4526 (t0) REVERT: A 484 ASP cc_start: 0.7269 (p0) cc_final: 0.6831 (m-30) REVERT: A 757 MET cc_start: 0.7160 (ppp) cc_final: 0.6191 (mtm) REVERT: B 239 ARG cc_start: 0.6529 (mtt180) cc_final: 0.6029 (mtt-85) REVERT: B 252 THR cc_start: 0.8934 (t) cc_final: 0.8544 (m) REVERT: B 357 LEU cc_start: 0.8997 (mm) cc_final: 0.8715 (mt) REVERT: B 504 LEU cc_start: 0.8086 (tp) cc_final: 0.7854 (mt) REVERT: C 252 THR cc_start: 0.9102 (t) cc_final: 0.8717 (m) REVERT: C 317 HIS cc_start: 0.3298 (t-90) cc_final: 0.2789 (m-70) REVERT: C 323 ARG cc_start: 0.8082 (ttp-170) cc_final: 0.7547 (ttm-80) REVERT: C 373 ASP cc_start: 0.6831 (p0) cc_final: 0.6619 (p0) REVERT: C 624 ASN cc_start: 0.7643 (m-40) cc_final: 0.7432 (m110) REVERT: C 664 SER cc_start: 0.7547 (p) cc_final: 0.6986 (p) REVERT: C 720 MET cc_start: -0.0826 (tpt) cc_final: -0.1542 (tpt) REVERT: C 740 MET cc_start: 0.7688 (mmp) cc_final: 0.7060 (mmm) REVERT: C 742 PHE cc_start: 0.6388 (OUTLIER) cc_final: 0.5873 (t80) REVERT: D 317 HIS cc_start: 0.4959 (t-90) cc_final: 0.4545 (m90) REVERT: D 554 GLU cc_start: 0.6782 (mm-30) cc_final: 0.5906 (tp30) REVERT: D 565 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7292 (ttpp) REVERT: D 668 LYS cc_start: 0.6894 (mmtm) cc_final: 0.6418 (tttp) REVERT: D 740 MET cc_start: 0.8064 (mmp) cc_final: 0.7809 (mmm) REVERT: E 252 THR cc_start: 0.8942 (t) cc_final: 0.8453 (m) REVERT: E 505 LYS cc_start: 0.7359 (tptp) cc_final: 0.7088 (ttpt) REVERT: E 598 ASP cc_start: 0.7923 (m-30) cc_final: 0.7367 (m-30) REVERT: E 696 LYS cc_start: 0.7510 (ttpt) cc_final: 0.7279 (ttpp) REVERT: E 755 TYR cc_start: 0.6510 (m-80) cc_final: 0.6048 (m-80) REVERT: E 757 MET cc_start: 0.6521 (ppp) cc_final: 0.5719 (mtp) REVERT: F 230 PHE cc_start: 0.7062 (t80) cc_final: 0.6747 (t80) REVERT: F 236 LYS cc_start: 0.7194 (mmtt) cc_final: 0.6718 (mttp) REVERT: F 242 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8066 (tt) REVERT: F 244 TYR cc_start: 0.8240 (p90) cc_final: 0.7847 (p90) REVERT: F 389 LYS cc_start: 0.6342 (tttt) cc_final: 0.5332 (mptt) REVERT: F 561 GLU cc_start: 0.7185 (pm20) cc_final: 0.6862 (mp0) REVERT: F 741 ARG cc_start: 0.6408 (mmp-170) cc_final: 0.6067 (mmp80) REVERT: F 755 TYR cc_start: 0.7093 (m-80) cc_final: 0.6565 (m-80) outliers start: 51 outliers final: 25 residues processed: 560 average time/residue: 0.5045 time to fit residues: 438.2796 Evaluate side-chains 464 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 436 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 752 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 232 optimal weight: 20.0000 chunk 321 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 230 optimal weight: 0.8980 chunk 254 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 220 optimal weight: 10.0000 chunk 260 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN B 348 ASN B 460 ASN C 348 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 692 GLN ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 460 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.201282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3978 r_free = 0.3978 target = 0.162734 restraints weight = 42570.630| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.40 r_work: 0.3784 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 32500 Z= 0.157 Angle : 0.626 7.052 44179 Z= 0.312 Chirality : 0.045 0.219 5130 Planarity : 0.005 0.057 5916 Dihedral : 10.285 179.574 4901 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.18 % Allowed : 12.13 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % 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: -0.70 (0.13), residues: 4464 helix: 0.63 (0.12), residues: 1920 sheet: -1.56 (0.19), residues: 572 loop : -1.15 (0.15), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 551 HIS 0.008 0.001 HIS E 340 PHE 0.016 0.002 PHE C 360 TYR 0.014 0.002 TYR F 203 ARG 0.009 0.001 ARG D 487 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 1576) hydrogen bonds : angle 5.13703 ( 4464) SS BOND : bond 0.02067 ( 6) SS BOND : angle 4.04030 ( 12) covalent geometry : bond 0.00356 (32488) covalent geometry : angle 0.62244 (44167) Misc. bond : bond 0.00375 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 477 time to evaluate : 3.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8091 (mmtt) cc_final: 0.7703 (tttt) REVERT: A 307 ASP cc_start: 0.7370 (p0) cc_final: 0.6998 (t70) REVERT: A 322 ARG cc_start: 0.6480 (mtt90) cc_final: 0.6148 (mtm-85) REVERT: A 364 ASP cc_start: 0.4989 (m-30) cc_final: 0.4646 (t0) REVERT: A 484 ASP cc_start: 0.7140 (p0) cc_final: 0.6710 (m-30) REVERT: A 757 MET cc_start: 0.6979 (ppp) cc_final: 0.6103 (mtm) REVERT: B 239 ARG cc_start: 0.6511 (mtt180) cc_final: 0.5965 (mtt-85) REVERT: B 252 THR cc_start: 0.8890 (t) cc_final: 0.8519 (m) REVERT: B 288 LYS cc_start: 0.7445 (ttpt) cc_final: 0.7228 (ttpp) REVERT: B 357 LEU cc_start: 0.9042 (mm) cc_final: 0.8771 (mt) REVERT: B 460 ASN cc_start: 0.5220 (OUTLIER) cc_final: 0.4925 (m110) REVERT: B 504 LEU cc_start: 0.8137 (tp) cc_final: 0.7886 (mt) REVERT: C 230 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.6838 (m-80) REVERT: C 252 THR cc_start: 0.9048 (t) cc_final: 0.8673 (m) REVERT: C 281 GLU cc_start: 0.7383 (tp30) cc_final: 0.6234 (tt0) REVERT: C 317 HIS cc_start: 0.3304 (t-90) cc_final: 0.2819 (m-70) REVERT: C 323 ARG cc_start: 0.7890 (ttp-170) cc_final: 0.7328 (ttm-80) REVERT: C 365 ARG cc_start: 0.6876 (OUTLIER) cc_final: 0.6394 (mtm110) REVERT: C 373 ASP cc_start: 0.6700 (p0) cc_final: 0.6460 (p0) REVERT: C 720 MET cc_start: -0.1168 (tpt) cc_final: -0.1812 (tpt) REVERT: C 740 MET cc_start: 0.7670 (mmp) cc_final: 0.7008 (mmm) REVERT: C 742 PHE cc_start: 0.6326 (OUTLIER) cc_final: 0.5819 (t80) REVERT: D 554 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6115 (tt0) REVERT: D 565 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7409 (ttpp) REVERT: D 668 LYS cc_start: 0.6944 (mmtm) cc_final: 0.6432 (tttp) REVERT: D 720 MET cc_start: 0.2771 (mmm) cc_final: 0.2339 (mmp) REVERT: D 740 MET cc_start: 0.8064 (mmp) cc_final: 0.7832 (mmm) REVERT: E 347 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8521 (m) REVERT: E 560 ARG cc_start: 0.7283 (tpt170) cc_final: 0.6618 (tpt-90) REVERT: E 561 GLU cc_start: 0.7209 (pt0) cc_final: 0.6936 (pt0) REVERT: E 696 LYS cc_start: 0.7519 (ttpt) cc_final: 0.7025 (ttpp) REVERT: E 755 TYR cc_start: 0.6443 (m-80) cc_final: 0.6144 (m-80) REVERT: E 757 MET cc_start: 0.6519 (ppp) cc_final: 0.5759 (mtp) REVERT: F 236 LYS cc_start: 0.7555 (mmtt) cc_final: 0.7229 (mttp) REVERT: F 242 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8014 (tt) REVERT: F 244 TYR cc_start: 0.8021 (p90) cc_final: 0.7706 (p90) REVERT: F 267 PHE cc_start: 0.7971 (t80) cc_final: 0.7680 (t80) REVERT: F 332 MET cc_start: 0.6865 (mtm) cc_final: 0.6604 (mtp) REVERT: F 389 LYS cc_start: 0.6392 (tttt) cc_final: 0.5250 (mptt) REVERT: F 561 GLU cc_start: 0.7167 (pm20) cc_final: 0.6883 (mp0) REVERT: F 741 ARG cc_start: 0.6265 (mmp-170) cc_final: 0.5907 (mmp80) outliers start: 61 outliers final: 34 residues processed: 503 average time/residue: 0.4539 time to fit residues: 356.7082 Evaluate side-chains 457 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 416 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 752 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 319 optimal weight: 1.9990 chunk 146 optimal weight: 0.0770 chunk 63 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 408 optimal weight: 7.9990 chunk 206 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 264 optimal weight: 8.9990 chunk 430 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 230 optimal weight: 10.0000 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 398 GLN B 460 ASN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN C 348 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 HIS D 404 HIS ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN F 460 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.199867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.167315 restraints weight = 42208.653| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 1.55 r_work: 0.3844 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3723 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 32500 Z= 0.156 Angle : 0.617 10.049 44179 Z= 0.305 Chirality : 0.045 0.255 5130 Planarity : 0.005 0.056 5916 Dihedral : 10.123 168.314 4901 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.28 % Allowed : 14.24 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % 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 (0.13), residues: 4464 helix: 0.61 (0.12), residues: 1918 sheet: -1.58 (0.20), residues: 572 loop : -1.03 (0.15), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 454 HIS 0.009 0.001 HIS D 404 PHE 0.020 0.002 PHE C 360 TYR 0.013 0.002 TYR C 755 ARG 0.009 0.001 ARG D 487 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 1576) hydrogen bonds : angle 5.02692 ( 4464) SS BOND : bond 0.02100 ( 6) SS BOND : angle 4.07684 ( 12) covalent geometry : bond 0.00358 (32488) covalent geometry : angle 0.61335 (44167) Misc. bond : bond 0.00378 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 443 time to evaluate : 3.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7782 (tttt) REVERT: A 307 ASP cc_start: 0.7576 (p0) cc_final: 0.7284 (t70) REVERT: A 327 GLN cc_start: 0.7838 (tp40) cc_final: 0.7534 (tp-100) REVERT: A 364 ASP cc_start: 0.5022 (m-30) cc_final: 0.4813 (t0) REVERT: A 484 ASP cc_start: 0.7174 (p0) cc_final: 0.6800 (m-30) REVERT: A 757 MET cc_start: 0.7014 (ppp) cc_final: 0.6280 (mtm) REVERT: B 239 ARG cc_start: 0.6642 (mtt180) cc_final: 0.6122 (mtt-85) REVERT: B 252 THR cc_start: 0.8964 (t) cc_final: 0.8595 (m) REVERT: B 357 LEU cc_start: 0.8967 (mm) cc_final: 0.8670 (mt) REVERT: B 460 ASN cc_start: 0.5640 (OUTLIER) cc_final: 0.5376 (m110) REVERT: B 504 LEU cc_start: 0.8118 (tp) cc_final: 0.7858 (mt) REVERT: C 230 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.6877 (m-80) REVERT: C 252 THR cc_start: 0.9066 (t) cc_final: 0.8738 (m) REVERT: C 281 GLU cc_start: 0.7388 (tp30) cc_final: 0.6328 (tt0) REVERT: C 323 ARG cc_start: 0.8035 (ttp-170) cc_final: 0.7487 (ttm-80) REVERT: C 365 ARG cc_start: 0.6931 (OUTLIER) cc_final: 0.6567 (mtm110) REVERT: C 373 ASP cc_start: 0.6853 (p0) cc_final: 0.6596 (p0) REVERT: C 550 MET cc_start: 0.8162 (mtm) cc_final: 0.7910 (mtm) REVERT: C 720 MET cc_start: -0.1298 (tpt) cc_final: -0.2008 (tpt) REVERT: C 740 MET cc_start: 0.7782 (mmp) cc_final: 0.7006 (mmm) REVERT: C 742 PHE cc_start: 0.6233 (OUTLIER) cc_final: 0.5740 (t80) REVERT: D 404 HIS cc_start: 0.6283 (OUTLIER) cc_final: 0.5702 (t-90) REVERT: D 554 GLU cc_start: 0.6871 (mm-30) cc_final: 0.6442 (tt0) REVERT: D 565 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7385 (ttpp) REVERT: D 668 LYS cc_start: 0.7044 (mmtm) cc_final: 0.6636 (tttm) REVERT: D 720 MET cc_start: 0.3060 (mmm) cc_final: 0.2590 (mmm) REVERT: D 740 MET cc_start: 0.8139 (mmp) cc_final: 0.7913 (mmm) REVERT: E 347 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8492 (m) REVERT: E 554 GLU cc_start: 0.6571 (mm-30) cc_final: 0.6240 (tt0) REVERT: E 560 ARG cc_start: 0.7420 (tpt170) cc_final: 0.7036 (tpt-90) REVERT: E 677 LYS cc_start: 0.7536 (ttmm) cc_final: 0.7216 (tttm) REVERT: E 696 LYS cc_start: 0.7551 (ttpt) cc_final: 0.7145 (ttpp) REVERT: E 755 TYR cc_start: 0.6479 (m-80) cc_final: 0.6193 (m-80) REVERT: E 757 MET cc_start: 0.6348 (ppp) cc_final: 0.5797 (mtp) REVERT: F 236 LYS cc_start: 0.7611 (mmtt) cc_final: 0.7320 (mttp) REVERT: F 242 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8136 (tt) REVERT: F 244 TYR cc_start: 0.8064 (p90) cc_final: 0.7847 (p90) REVERT: F 327 GLN cc_start: 0.7367 (tp40) cc_final: 0.7081 (tp-100) REVERT: F 389 LYS cc_start: 0.6550 (tttt) cc_final: 0.5390 (mptt) REVERT: F 560 ARG cc_start: 0.7146 (tpt170) cc_final: 0.6828 (ttp80) REVERT: F 561 GLU cc_start: 0.7383 (pm20) cc_final: 0.6981 (mp0) REVERT: F 741 ARG cc_start: 0.6285 (mmp-170) cc_final: 0.5853 (mmp80) REVERT: F 755 TYR cc_start: 0.7139 (m-80) cc_final: 0.6784 (m-80) outliers start: 64 outliers final: 36 residues processed: 475 average time/residue: 0.4883 time to fit residues: 363.3863 Evaluate side-chains 433 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 389 time to evaluate : 3.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 690 ILE Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 651 LYS Chi-restraints excluded: chain F residue 752 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 440 optimal weight: 0.0270 chunk 369 optimal weight: 0.7980 chunk 148 optimal weight: 10.0000 chunk 348 optimal weight: 0.0980 chunk 120 optimal weight: 3.9990 chunk 234 optimal weight: 30.0000 chunk 77 optimal weight: 50.0000 chunk 44 optimal weight: 0.8980 chunk 416 optimal weight: 0.2980 chunk 140 optimal weight: 5.9990 chunk 246 optimal weight: 3.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 603 GLN B 460 ASN B 558 ASN C 348 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 460 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.201068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.166203 restraints weight = 42217.064| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 1.83 r_work: 0.3848 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 32500 Z= 0.129 Angle : 0.594 9.014 44179 Z= 0.291 Chirality : 0.044 0.208 5130 Planarity : 0.004 0.052 5916 Dihedral : 9.876 160.788 4901 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.25 % Allowed : 15.20 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % 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: -0.52 (0.13), residues: 4464 helix: 0.71 (0.12), residues: 1918 sheet: -1.49 (0.20), residues: 557 loop : -0.99 (0.15), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 551 HIS 0.017 0.001 HIS D 404 PHE 0.018 0.001 PHE C 267 TYR 0.020 0.001 TYR C 755 ARG 0.010 0.000 ARG D 487 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 1576) hydrogen bonds : angle 4.89665 ( 4464) SS BOND : bond 0.02096 ( 6) SS BOND : angle 3.97325 ( 12) covalent geometry : bond 0.00291 (32488) covalent geometry : angle 0.59022 (44167) Misc. bond : bond 0.00352 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 430 time to evaluate : 3.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8024 (mmtt) cc_final: 0.7738 (tttt) REVERT: A 307 ASP cc_start: 0.7593 (p0) cc_final: 0.7269 (t70) REVERT: A 442 MET cc_start: 0.3583 (OUTLIER) cc_final: 0.2879 (tmm) REVERT: A 484 ASP cc_start: 0.7056 (p0) cc_final: 0.6733 (m-30) REVERT: A 757 MET cc_start: 0.7048 (ppp) cc_final: 0.6266 (mtm) REVERT: B 239 ARG cc_start: 0.6644 (mtt180) cc_final: 0.6136 (mtt-85) REVERT: B 252 THR cc_start: 0.8958 (t) cc_final: 0.8566 (m) REVERT: B 357 LEU cc_start: 0.8957 (mm) cc_final: 0.8662 (mt) REVERT: B 460 ASN cc_start: 0.5202 (OUTLIER) cc_final: 0.4985 (m110) REVERT: B 504 LEU cc_start: 0.8068 (tp) cc_final: 0.7803 (mt) REVERT: B 755 TYR cc_start: 0.7381 (m-80) cc_final: 0.7044 (m-80) REVERT: C 230 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.6864 (m-80) REVERT: C 252 THR cc_start: 0.9057 (t) cc_final: 0.8740 (m) REVERT: C 281 GLU cc_start: 0.7298 (tp30) cc_final: 0.6335 (tt0) REVERT: C 323 ARG cc_start: 0.8044 (ttp-170) cc_final: 0.7470 (ttm-80) REVERT: C 365 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6492 (mtm110) REVERT: C 373 ASP cc_start: 0.6901 (p0) cc_final: 0.6637 (p0) REVERT: C 720 MET cc_start: -0.1355 (tpt) cc_final: -0.2007 (tpt) REVERT: C 740 MET cc_start: 0.7762 (mmp) cc_final: 0.6991 (mmm) REVERT: C 742 PHE cc_start: 0.6190 (OUTLIER) cc_final: 0.5718 (t80) REVERT: D 236 LYS cc_start: 0.6768 (mmtm) cc_final: 0.6239 (tppt) REVERT: D 554 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6340 (tt0) REVERT: D 565 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7412 (ttpp) REVERT: D 668 LYS cc_start: 0.7016 (mmtm) cc_final: 0.6541 (tttp) REVERT: D 720 MET cc_start: 0.3416 (mmm) cc_final: 0.2988 (mmm) REVERT: D 740 MET cc_start: 0.8083 (mmp) cc_final: 0.7809 (mmm) REVERT: E 554 GLU cc_start: 0.6437 (mm-30) cc_final: 0.6117 (tt0) REVERT: E 560 ARG cc_start: 0.7412 (tpt170) cc_final: 0.7061 (tpt-90) REVERT: E 677 LYS cc_start: 0.7460 (ttmm) cc_final: 0.7178 (tttm) REVERT: E 696 LYS cc_start: 0.7516 (ttpt) cc_final: 0.7145 (ttpp) REVERT: E 755 TYR cc_start: 0.6432 (m-80) cc_final: 0.6118 (m-80) REVERT: E 757 MET cc_start: 0.6323 (ppp) cc_final: 0.5767 (mtp) REVERT: F 236 LYS cc_start: 0.7455 (mmtt) cc_final: 0.7092 (mtmt) REVERT: F 389 LYS cc_start: 0.6508 (tttt) cc_final: 0.5372 (mptt) REVERT: F 560 ARG cc_start: 0.7157 (tpt170) cc_final: 0.6867 (ttp80) REVERT: F 561 GLU cc_start: 0.7378 (pm20) cc_final: 0.6979 (mp0) REVERT: F 755 TYR cc_start: 0.7056 (m-80) cc_final: 0.6663 (m-80) outliers start: 63 outliers final: 38 residues processed: 464 average time/residue: 0.4706 time to fit residues: 341.8405 Evaluate side-chains 441 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 397 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 410 ASP Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 651 LYS Chi-restraints excluded: chain F residue 752 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 11 optimal weight: 40.0000 chunk 411 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 352 optimal weight: 3.9990 chunk 390 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 chunk 132 optimal weight: 0.6980 chunk 178 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 154 optimal weight: 6.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN B 260 ASN B 460 ASN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 ASN C 348 ASN C 398 GLN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 HIS F 460 ASN F 589 ASN F 692 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.197515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.165287 restraints weight = 42495.314| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 1.59 r_work: 0.3801 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 32500 Z= 0.176 Angle : 0.627 8.484 44179 Z= 0.309 Chirality : 0.045 0.205 5130 Planarity : 0.005 0.056 5916 Dihedral : 9.902 165.974 4901 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.43 % Allowed : 16.56 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % 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: -0.57 (0.13), residues: 4464 helix: 0.60 (0.12), residues: 1924 sheet: -1.50 (0.20), residues: 557 loop : -0.93 (0.15), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 551 HIS 0.006 0.001 HIS E 340 PHE 0.027 0.002 PHE C 267 TYR 0.018 0.002 TYR C 755 ARG 0.009 0.001 ARG D 487 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 1576) hydrogen bonds : angle 4.96243 ( 4464) SS BOND : bond 0.02249 ( 6) SS BOND : angle 4.42354 ( 12) covalent geometry : bond 0.00410 (32488) covalent geometry : angle 0.62235 (44167) Misc. bond : bond 0.00391 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 422 time to evaluate : 3.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7784 (tttt) REVERT: A 307 ASP cc_start: 0.7593 (p0) cc_final: 0.7343 (t70) REVERT: A 442 MET cc_start: 0.3300 (OUTLIER) cc_final: 0.2661 (tmm) REVERT: A 484 ASP cc_start: 0.7124 (p0) cc_final: 0.6809 (m-30) REVERT: A 757 MET cc_start: 0.6749 (ppp) cc_final: 0.6300 (mtm) REVERT: B 239 ARG cc_start: 0.6681 (mtt180) cc_final: 0.6078 (mtt-85) REVERT: B 252 THR cc_start: 0.8987 (t) cc_final: 0.8626 (m) REVERT: B 275 MET cc_start: 0.7220 (mtm) cc_final: 0.6991 (mtm) REVERT: B 357 LEU cc_start: 0.8979 (mm) cc_final: 0.8693 (mt) REVERT: B 460 ASN cc_start: 0.5893 (OUTLIER) cc_final: 0.5647 (m110) REVERT: B 504 LEU cc_start: 0.8108 (tp) cc_final: 0.7836 (mt) REVERT: B 755 TYR cc_start: 0.7425 (m-80) cc_final: 0.7187 (m-80) REVERT: C 230 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.7266 (t80) REVERT: C 252 THR cc_start: 0.9075 (t) cc_final: 0.8772 (m) REVERT: C 281 GLU cc_start: 0.7376 (tp30) cc_final: 0.6366 (tt0) REVERT: C 323 ARG cc_start: 0.8025 (ttp-170) cc_final: 0.7473 (ttm-80) REVERT: C 365 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6668 (mtm110) REVERT: C 373 ASP cc_start: 0.7125 (p0) cc_final: 0.6907 (p0) REVERT: C 492 LEU cc_start: 0.8636 (mt) cc_final: 0.8435 (mp) REVERT: C 720 MET cc_start: -0.1356 (tpt) cc_final: -0.1962 (tpt) REVERT: C 740 MET cc_start: 0.7809 (mmp) cc_final: 0.7031 (mmm) REVERT: C 742 PHE cc_start: 0.6285 (OUTLIER) cc_final: 0.5908 (t80) REVERT: D 420 LEU cc_start: 0.8331 (mm) cc_final: 0.8127 (mm) REVERT: D 554 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6657 (tt0) REVERT: D 561 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6567 (pt0) REVERT: D 565 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7491 (ttpp) REVERT: D 668 LYS cc_start: 0.7282 (mmtm) cc_final: 0.6831 (tttm) REVERT: D 720 MET cc_start: 0.3556 (mmm) cc_final: 0.3127 (mmm) REVERT: E 677 LYS cc_start: 0.7422 (ttmm) cc_final: 0.7086 (tttm) REVERT: E 740 MET cc_start: 0.6764 (mmm) cc_final: 0.6395 (mmm) REVERT: E 755 TYR cc_start: 0.6735 (m-80) cc_final: 0.6441 (m-80) REVERT: E 757 MET cc_start: 0.6482 (ppp) cc_final: 0.5905 (mtp) REVERT: F 236 LYS cc_start: 0.7474 (mmtt) cc_final: 0.7129 (mtmt) REVERT: F 389 LYS cc_start: 0.6569 (tttt) cc_final: 0.5432 (mptt) REVERT: F 561 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: F 730 GLU cc_start: 0.7317 (pm20) cc_final: 0.7115 (pm20) REVERT: F 755 TYR cc_start: 0.7221 (m-80) cc_final: 0.6923 (m-80) outliers start: 68 outliers final: 45 residues processed: 456 average time/residue: 0.4577 time to fit residues: 326.7857 Evaluate side-chains 440 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 387 time to evaluate : 3.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 608 MET Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 651 LYS Chi-restraints excluded: chain F residue 752 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 173 optimal weight: 2.9990 chunk 268 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 312 optimal weight: 30.0000 chunk 124 optimal weight: 0.8980 chunk 431 optimal weight: 0.8980 chunk 169 optimal weight: 0.4980 chunk 4 optimal weight: 9.9990 chunk 443 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 405 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 558 ASN ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 GLN ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 460 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.195416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.164719 restraints weight = 42272.244| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 1.58 r_work: 0.3771 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 32500 Z= 0.190 Angle : 0.646 8.909 44179 Z= 0.319 Chirality : 0.045 0.211 5130 Planarity : 0.005 0.063 5916 Dihedral : 9.930 167.361 4901 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.36 % Allowed : 17.38 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % 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: -0.69 (0.13), residues: 4464 helix: 0.60 (0.12), residues: 1888 sheet: -1.55 (0.19), residues: 607 loop : -1.05 (0.15), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 454 HIS 0.006 0.001 HIS E 340 PHE 0.023 0.002 PHE F 363 TYR 0.017 0.002 TYR C 755 ARG 0.015 0.001 ARG E 465 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 1576) hydrogen bonds : angle 5.02104 ( 4464) SS BOND : bond 0.02217 ( 6) SS BOND : angle 4.75473 ( 12) covalent geometry : bond 0.00443 (32488) covalent geometry : angle 0.64087 (44167) Misc. bond : bond 0.00427 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 418 time to evaluate : 3.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8034 (mmtt) cc_final: 0.7547 (mmtm) REVERT: A 307 ASP cc_start: 0.7618 (p0) cc_final: 0.7163 (t70) REVERT: A 442 MET cc_start: 0.3459 (mpp) cc_final: 0.2876 (tmm) REVERT: A 757 MET cc_start: 0.6769 (ppp) cc_final: 0.6269 (mtt) REVERT: B 239 ARG cc_start: 0.6815 (mtt180) cc_final: 0.6234 (mtt-85) REVERT: B 252 THR cc_start: 0.9042 (t) cc_final: 0.8623 (m) REVERT: B 357 LEU cc_start: 0.9126 (mm) cc_final: 0.8827 (mt) REVERT: B 460 ASN cc_start: 0.5834 (OUTLIER) cc_final: 0.5605 (m-40) REVERT: B 504 LEU cc_start: 0.8047 (tp) cc_final: 0.7782 (mt) REVERT: B 628 ILE cc_start: 0.8694 (pt) cc_final: 0.8464 (pt) REVERT: C 230 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7345 (t80) REVERT: C 252 THR cc_start: 0.9047 (t) cc_final: 0.8758 (m) REVERT: C 323 ARG cc_start: 0.7872 (ttp-170) cc_final: 0.7311 (ttm-80) REVERT: C 365 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6769 (mtm110) REVERT: C 427 MET cc_start: 0.6286 (OUTLIER) cc_final: 0.5697 (tmm) REVERT: C 464 LEU cc_start: 0.3733 (tp) cc_final: 0.3378 (tp) REVERT: C 720 MET cc_start: -0.1340 (tpt) cc_final: -0.1911 (tpt) REVERT: C 740 MET cc_start: 0.7958 (mmp) cc_final: 0.7158 (mmm) REVERT: D 420 LEU cc_start: 0.8360 (mm) cc_final: 0.8154 (mm) REVERT: D 554 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6667 (tt0) REVERT: D 560 ARG cc_start: 0.7528 (tpt170) cc_final: 0.6822 (tpp80) REVERT: D 561 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6708 (pt0) REVERT: D 565 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7615 (ttpp) REVERT: D 668 LYS cc_start: 0.7437 (mmtm) cc_final: 0.6900 (tttm) REVERT: D 720 MET cc_start: 0.3576 (mmm) cc_final: 0.3206 (mmp) REVERT: D 740 MET cc_start: 0.7901 (mmm) cc_final: 0.7671 (mmm) REVERT: E 433 GLU cc_start: 0.0659 (OUTLIER) cc_final: 0.0015 (mm-30) REVERT: E 554 GLU cc_start: 0.6695 (mm-30) cc_final: 0.6250 (mm-30) REVERT: E 560 ARG cc_start: 0.7648 (tpt170) cc_final: 0.7304 (tpt-90) REVERT: E 677 LYS cc_start: 0.7419 (ttmm) cc_final: 0.7092 (tttm) REVERT: E 755 TYR cc_start: 0.6845 (m-80) cc_final: 0.6592 (m-80) REVERT: E 757 MET cc_start: 0.6505 (ppp) cc_final: 0.5961 (mtp) REVERT: F 236 LYS cc_start: 0.7682 (mmtt) cc_final: 0.7315 (mttp) REVERT: F 389 LYS cc_start: 0.6704 (tttt) cc_final: 0.5495 (mptt) REVERT: F 561 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: F 755 TYR cc_start: 0.7328 (m-80) cc_final: 0.7019 (m-80) outliers start: 66 outliers final: 43 residues processed: 454 average time/residue: 0.4637 time to fit residues: 330.5989 Evaluate side-chains 441 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 390 time to evaluate : 3.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 651 LYS Chi-restraints excluded: chain F residue 752 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 242 optimal weight: 2.9990 chunk 426 optimal weight: 0.9980 chunk 384 optimal weight: 40.0000 chunk 45 optimal weight: 1.9990 chunk 366 optimal weight: 3.9990 chunk 340 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 406 optimal weight: 3.9990 chunk 20 optimal weight: 0.0980 chunk 215 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.195041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.164319 restraints weight = 42274.425| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 1.67 r_work: 0.3747 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 32500 Z= 0.186 Angle : 0.651 9.919 44179 Z= 0.322 Chirality : 0.045 0.211 5130 Planarity : 0.005 0.057 5916 Dihedral : 9.896 168.215 4901 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.36 % Allowed : 17.74 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % 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: -0.71 (0.13), residues: 4464 helix: 0.59 (0.12), residues: 1855 sheet: -1.47 (0.20), residues: 582 loop : -1.10 (0.14), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 454 HIS 0.009 0.001 HIS E 340 PHE 0.021 0.002 PHE F 363 TYR 0.018 0.002 TYR C 755 ARG 0.015 0.001 ARG F 560 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 1576) hydrogen bonds : angle 5.01849 ( 4464) SS BOND : bond 0.02380 ( 6) SS BOND : angle 4.80307 ( 12) covalent geometry : bond 0.00434 (32488) covalent geometry : angle 0.64639 (44167) Misc. bond : bond 0.00425 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 406 time to evaluate : 3.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7514 (mmtm) REVERT: A 307 ASP cc_start: 0.7703 (p0) cc_final: 0.7223 (t70) REVERT: A 442 MET cc_start: 0.3547 (mpp) cc_final: 0.3012 (tmm) REVERT: A 678 MET cc_start: 0.5549 (OUTLIER) cc_final: 0.4871 (tpp) REVERT: A 720 MET cc_start: 0.0770 (mmp) cc_final: 0.0563 (mmt) REVERT: A 757 MET cc_start: 0.6828 (ppp) cc_final: 0.6411 (mtt) REVERT: B 239 ARG cc_start: 0.6870 (mtt180) cc_final: 0.6317 (mtt-85) REVERT: B 252 THR cc_start: 0.9056 (t) cc_final: 0.8617 (m) REVERT: B 357 LEU cc_start: 0.9133 (mm) cc_final: 0.8837 (mt) REVERT: B 504 LEU cc_start: 0.8056 (tp) cc_final: 0.7795 (mt) REVERT: B 561 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7090 (pm20) REVERT: B 628 ILE cc_start: 0.8736 (pt) cc_final: 0.8534 (pt) REVERT: B 755 TYR cc_start: 0.7317 (m-80) cc_final: 0.7044 (m-80) REVERT: C 230 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7496 (t80) REVERT: C 252 THR cc_start: 0.9017 (t) cc_final: 0.8760 (m) REVERT: C 323 ARG cc_start: 0.7913 (ttp-170) cc_final: 0.7377 (ttm-80) REVERT: C 340 HIS cc_start: 0.5360 (OUTLIER) cc_final: 0.5069 (t70) REVERT: C 365 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6833 (mtm110) REVERT: C 427 MET cc_start: 0.6306 (OUTLIER) cc_final: 0.5685 (tmm) REVERT: C 720 MET cc_start: -0.1238 (tpt) cc_final: -0.1742 (tpt) REVERT: C 740 MET cc_start: 0.7979 (mmp) cc_final: 0.7195 (mmm) REVERT: D 420 LEU cc_start: 0.8423 (mm) cc_final: 0.8186 (mm) REVERT: D 554 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6247 (mt-10) REVERT: D 560 ARG cc_start: 0.7596 (tpt170) cc_final: 0.7123 (tpp80) REVERT: D 561 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6718 (pt0) REVERT: D 565 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7651 (ttpp) REVERT: D 668 LYS cc_start: 0.7516 (mmtm) cc_final: 0.6964 (tttm) REVERT: D 720 MET cc_start: 0.3504 (mmm) cc_final: 0.3171 (mmp) REVERT: E 433 GLU cc_start: 0.0603 (OUTLIER) cc_final: 0.0316 (mm-30) REVERT: E 554 GLU cc_start: 0.6698 (mm-30) cc_final: 0.6211 (tt0) REVERT: E 607 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7581 (mm-30) REVERT: E 677 LYS cc_start: 0.7445 (ttmm) cc_final: 0.7122 (tttm) REVERT: E 757 MET cc_start: 0.6540 (ppp) cc_final: 0.6019 (mtp) REVERT: F 236 LYS cc_start: 0.7823 (mmtt) cc_final: 0.7472 (mttp) REVERT: F 389 LYS cc_start: 0.6826 (tttt) cc_final: 0.5456 (mmmt) REVERT: F 395 ASP cc_start: 0.5580 (p0) cc_final: 0.5352 (p0) REVERT: F 560 ARG cc_start: 0.7323 (tpt-90) cc_final: 0.6965 (ttp80) REVERT: F 561 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: F 755 TYR cc_start: 0.7334 (m-80) cc_final: 0.7030 (m-80) outliers start: 66 outliers final: 46 residues processed: 447 average time/residue: 0.4591 time to fit residues: 322.1607 Evaluate side-chains 431 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 375 time to evaluate : 3.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 651 LYS Chi-restraints excluded: chain F residue 752 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 296 optimal weight: 20.0000 chunk 271 optimal weight: 1.9990 chunk 192 optimal weight: 0.6980 chunk 141 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 359 optimal weight: 4.9990 chunk 345 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 GLN ** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 HIS ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.191376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.162038 restraints weight = 42224.850| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 1.57 r_work: 0.3722 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 32500 Z= 0.236 Angle : 0.708 9.413 44179 Z= 0.352 Chirality : 0.047 0.211 5130 Planarity : 0.006 0.097 5916 Dihedral : 10.151 171.225 4901 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.50 % Allowed : 18.24 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.13), residues: 4464 helix: 0.29 (0.12), residues: 1896 sheet: -1.52 (0.20), residues: 582 loop : -1.23 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 454 HIS 0.011 0.001 HIS E 340 PHE 0.026 0.002 PHE F 363 TYR 0.024 0.003 TYR E 755 ARG 0.012 0.001 ARG D 487 Details of bonding type rmsd hydrogen bonds : bond 0.04411 ( 1576) hydrogen bonds : angle 5.22891 ( 4464) SS BOND : bond 0.02209 ( 6) SS BOND : angle 5.14744 ( 12) covalent geometry : bond 0.00554 (32488) covalent geometry : angle 0.70307 (44167) Misc. bond : bond 0.00518 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 389 time to evaluate : 3.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8084 (mmtt) cc_final: 0.7625 (mmtm) REVERT: A 442 MET cc_start: 0.3501 (mpp) cc_final: 0.3149 (tmm) REVERT: A 678 MET cc_start: 0.5694 (OUTLIER) cc_final: 0.5131 (tpt) REVERT: A 757 MET cc_start: 0.6861 (ppp) cc_final: 0.6660 (mtt) REVERT: B 239 ARG cc_start: 0.6789 (mtt180) cc_final: 0.6213 (mtt-85) REVERT: B 252 THR cc_start: 0.9107 (t) cc_final: 0.8668 (m) REVERT: B 357 LEU cc_start: 0.9208 (mm) cc_final: 0.8912 (mt) REVERT: B 504 LEU cc_start: 0.8037 (tp) cc_final: 0.7716 (mt) REVERT: B 560 ARG cc_start: 0.7446 (tpt170) cc_final: 0.7205 (ttt90) REVERT: B 598 ASP cc_start: 0.8500 (t0) cc_final: 0.8101 (t70) REVERT: B 628 ILE cc_start: 0.8722 (pt) cc_final: 0.8513 (pt) REVERT: C 230 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7637 (t80) REVERT: C 340 HIS cc_start: 0.5636 (OUTLIER) cc_final: 0.5231 (t70) REVERT: C 365 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6901 (mtm110) REVERT: C 720 MET cc_start: -0.1171 (tpt) cc_final: -0.1696 (tpt) REVERT: C 740 MET cc_start: 0.7998 (mmp) cc_final: 0.7217 (mmm) REVERT: D 554 GLU cc_start: 0.7360 (mm-30) cc_final: 0.6396 (mm-30) REVERT: D 560 ARG cc_start: 0.7614 (tpt170) cc_final: 0.7360 (tpt170) REVERT: D 561 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6666 (pt0) REVERT: D 565 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7655 (ttpp) REVERT: D 668 LYS cc_start: 0.7655 (mmtm) cc_final: 0.7039 (tttm) REVERT: D 720 MET cc_start: 0.3781 (mmm) cc_final: 0.3400 (mmp) REVERT: E 433 GLU cc_start: 0.0588 (OUTLIER) cc_final: 0.0383 (mm-30) REVERT: E 554 GLU cc_start: 0.6864 (mm-30) cc_final: 0.6446 (tt0) REVERT: E 607 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7521 (mm-30) REVERT: E 677 LYS cc_start: 0.7439 (ttmm) cc_final: 0.7106 (tttm) REVERT: E 757 MET cc_start: 0.6508 (ppp) cc_final: 0.6001 (mtp) REVERT: F 236 LYS cc_start: 0.7938 (mmtt) cc_final: 0.7569 (mttp) REVERT: F 256 ARG cc_start: 0.7319 (ttm-80) cc_final: 0.7056 (mtp-110) REVERT: F 327 GLN cc_start: 0.7562 (tp40) cc_final: 0.7228 (tp-100) REVERT: F 389 LYS cc_start: 0.7050 (tttt) cc_final: 0.5722 (mmmt) REVERT: F 561 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7157 (mp0) outliers start: 70 outliers final: 52 residues processed: 432 average time/residue: 0.4609 time to fit residues: 311.8144 Evaluate side-chains 424 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 364 time to evaluate : 3.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 598 ASP Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 651 LYS Chi-restraints excluded: chain F residue 752 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 158 optimal weight: 20.0000 chunk 330 optimal weight: 0.6980 chunk 394 optimal weight: 0.8980 chunk 170 optimal weight: 0.8980 chunk 403 optimal weight: 0.6980 chunk 3 optimal weight: 50.0000 chunk 151 optimal weight: 50.0000 chunk 338 optimal weight: 9.9990 chunk 91 optimal weight: 30.0000 chunk 373 optimal weight: 30.0000 chunk 365 optimal weight: 4.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.191842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.161858 restraints weight = 42345.124| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 1.50 r_work: 0.3746 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 32500 Z= 0.207 Angle : 0.687 9.082 44179 Z= 0.340 Chirality : 0.046 0.238 5130 Planarity : 0.005 0.093 5916 Dihedral : 10.047 169.046 4901 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.14 % Allowed : 18.81 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % 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: -0.97 (0.13), residues: 4464 helix: 0.32 (0.12), residues: 1896 sheet: -1.53 (0.20), residues: 566 loop : -1.24 (0.14), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 454 HIS 0.011 0.001 HIS E 340 PHE 0.021 0.002 PHE F 363 TYR 0.028 0.002 TYR F 244 ARG 0.019 0.001 ARG F 560 Details of bonding type rmsd hydrogen bonds : bond 0.04263 ( 1576) hydrogen bonds : angle 5.15519 ( 4464) SS BOND : bond 0.02057 ( 6) SS BOND : angle 4.94163 ( 12) covalent geometry : bond 0.00486 (32488) covalent geometry : angle 0.68192 (44167) Misc. bond : bond 0.00480 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 380 time to evaluate : 3.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8051 (mmtt) cc_final: 0.7585 (mmtm) REVERT: A 442 MET cc_start: 0.3541 (mpp) cc_final: 0.3197 (tmm) REVERT: A 678 MET cc_start: 0.5584 (OUTLIER) cc_final: 0.5109 (tpt) REVERT: B 239 ARG cc_start: 0.6704 (mtt180) cc_final: 0.6181 (mtt-85) REVERT: B 252 THR cc_start: 0.9087 (t) cc_final: 0.8642 (m) REVERT: B 357 LEU cc_start: 0.9188 (mm) cc_final: 0.8890 (mt) REVERT: B 504 LEU cc_start: 0.8007 (tp) cc_final: 0.7709 (mt) REVERT: B 560 ARG cc_start: 0.7419 (tpt170) cc_final: 0.7164 (ttt90) REVERT: B 628 ILE cc_start: 0.8703 (pt) cc_final: 0.8502 (pt) REVERT: C 230 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7602 (t80) REVERT: C 252 THR cc_start: 0.9041 (t) cc_final: 0.8693 (m) REVERT: C 323 ARG cc_start: 0.7885 (ttp-170) cc_final: 0.7435 (ttm-80) REVERT: C 340 HIS cc_start: 0.5678 (OUTLIER) cc_final: 0.5243 (t70) REVERT: C 365 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6870 (mtm110) REVERT: C 720 MET cc_start: -0.1039 (tpt) cc_final: -0.1575 (tpt) REVERT: C 740 MET cc_start: 0.7932 (mmp) cc_final: 0.7200 (mmm) REVERT: D 397 GLU cc_start: 0.7879 (tp30) cc_final: 0.7278 (pm20) REVERT: D 554 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6408 (mm-30) REVERT: D 560 ARG cc_start: 0.7578 (tpt170) cc_final: 0.7341 (tpt170) REVERT: D 561 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6726 (pt0) REVERT: D 565 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7710 (ttpp) REVERT: D 668 LYS cc_start: 0.7704 (mmtm) cc_final: 0.7063 (tttm) REVERT: D 720 MET cc_start: 0.3733 (mmm) cc_final: 0.3357 (mmp) REVERT: D 740 MET cc_start: 0.7923 (mmm) cc_final: 0.7639 (mmm) REVERT: E 332 MET cc_start: 0.8012 (mtp) cc_final: 0.7772 (mtp) REVERT: E 554 GLU cc_start: 0.6760 (mm-30) cc_final: 0.6338 (tt0) REVERT: E 677 LYS cc_start: 0.7426 (ttmm) cc_final: 0.7027 (tttm) REVERT: E 757 MET cc_start: 0.6480 (ppp) cc_final: 0.6175 (mtp) REVERT: F 236 LYS cc_start: 0.7962 (mmtt) cc_final: 0.7561 (mttp) REVERT: F 327 GLN cc_start: 0.7497 (tp40) cc_final: 0.7193 (tp-100) REVERT: F 389 LYS cc_start: 0.7046 (tttt) cc_final: 0.5733 (mmmt) REVERT: F 395 ASP cc_start: 0.5507 (p0) cc_final: 0.5229 (p0) REVERT: F 560 ARG cc_start: 0.7090 (tpt-90) cc_final: 0.6614 (ttp80) outliers start: 60 outliers final: 43 residues processed: 416 average time/residue: 0.4557 time to fit residues: 297.6381 Evaluate side-chains 407 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 358 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain F residue 460 ASN Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 651 LYS Chi-restraints excluded: chain F residue 752 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 245 optimal weight: 0.8980 chunk 363 optimal weight: 0.5980 chunk 358 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 439 optimal weight: 2.9990 chunk 229 optimal weight: 8.9990 chunk 151 optimal weight: 50.0000 chunk 72 optimal weight: 7.9990 chunk 422 optimal weight: 0.9980 chunk 128 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.194189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.160362 restraints weight = 42114.078| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 1.71 r_work: 0.3772 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 32500 Z= 0.155 Angle : 0.648 9.372 44179 Z= 0.320 Chirality : 0.045 0.245 5130 Planarity : 0.005 0.086 5916 Dihedral : 9.761 166.450 4901 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.75 % Allowed : 19.74 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % 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: -0.83 (0.13), residues: 4464 helix: 0.47 (0.12), residues: 1896 sheet: -1.65 (0.20), residues: 607 loop : -1.12 (0.15), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 454 HIS 0.009 0.001 HIS E 340 PHE 0.024 0.002 PHE A 506 TYR 0.027 0.002 TYR F 244 ARG 0.013 0.001 ARG D 487 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 1576) hydrogen bonds : angle 5.01799 ( 4464) SS BOND : bond 0.02136 ( 6) SS BOND : angle 4.39468 ( 12) covalent geometry : bond 0.00359 (32488) covalent geometry : angle 0.64438 (44167) Misc. bond : bond 0.00410 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17781.05 seconds wall clock time: 307 minutes 16.06 seconds (18436.06 seconds total)