Starting phenix.real_space_refine on Fri Jun 27 19:06:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pqx_17827/06_2025/8pqx_17827.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pqx_17827/06_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_17827/06_2025/8pqx_17827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pqx_17827/06_2025/8pqx_17827.map" model { file = "/net/cci-nas-00/data/ceres_data/8pqx_17827/06_2025/8pqx_17827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pqx_17827/06_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-5710/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: 19.67, per 1000 atoms: 0.61 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: 8.40 Conformation dependent library (CDL) restraints added in 4.5 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: 4.05 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: 12.52 Time building geometry restraints manager: 9.79 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: 2.150 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: 1.390 Check model and map are aligned: 0.250 Set scattering table: 0.310 Process input model: 74.250 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.160 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.390 ------------------------------------------------------------------------------- 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 : 3.343 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: 0.5365 time to fit residues: 711.3992 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 : 3.668 ------------------------------------------------------------------------------- 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 = 123)---------------| | r_work = 0.4078 r_free = 0.4078 target = 0.167738 restraints weight = 42114.377| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 1.86 r_work: 0.3866 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 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 : 3.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8042 (mmtt) cc_final: 0.7717 (tttt) REVERT: A 307 ASP cc_start: 0.7303 (p0) cc_final: 0.7042 (t70) REVERT: A 322 ARG cc_start: 0.6582 (mtt90) cc_final: 0.6313 (mtm-85) REVERT: A 364 ASP cc_start: 0.4766 (m-30) cc_final: 0.4533 (t0) REVERT: A 484 ASP cc_start: 0.7267 (p0) cc_final: 0.6831 (m-30) REVERT: A 757 MET cc_start: 0.7193 (ppp) cc_final: 0.6178 (mtm) REVERT: B 239 ARG cc_start: 0.6567 (mtt180) cc_final: 0.6049 (mtt-85) REVERT: B 252 THR cc_start: 0.8943 (t) cc_final: 0.8553 (m) REVERT: B 288 LYS cc_start: 0.7672 (mtmm) cc_final: 0.7449 (ttpt) REVERT: B 357 LEU cc_start: 0.9006 (mm) cc_final: 0.8715 (mt) REVERT: B 504 LEU cc_start: 0.8101 (tp) cc_final: 0.7860 (mt) REVERT: C 252 THR cc_start: 0.9103 (t) cc_final: 0.8717 (m) REVERT: C 317 HIS cc_start: 0.3292 (t-90) cc_final: 0.2778 (m-70) REVERT: C 323 ARG cc_start: 0.8064 (ttp-170) cc_final: 0.7523 (ttm-80) REVERT: C 624 ASN cc_start: 0.7653 (m-40) cc_final: 0.7436 (m110) REVERT: C 664 SER cc_start: 0.7587 (p) cc_final: 0.7019 (p) REVERT: C 720 MET cc_start: -0.0814 (tpt) cc_final: -0.1551 (tpt) REVERT: C 740 MET cc_start: 0.7726 (mmp) cc_final: 0.7089 (mmm) REVERT: C 742 PHE cc_start: 0.6444 (OUTLIER) cc_final: 0.5929 (t80) REVERT: D 317 HIS cc_start: 0.4982 (t-90) cc_final: 0.4519 (m90) REVERT: D 554 GLU cc_start: 0.6795 (mm-30) cc_final: 0.5920 (tp30) REVERT: D 565 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7290 (ttpp) REVERT: D 668 LYS cc_start: 0.6937 (mmtm) cc_final: 0.6417 (tttp) REVERT: D 740 MET cc_start: 0.8085 (mmp) cc_final: 0.7826 (mmm) REVERT: E 252 THR cc_start: 0.8944 (t) cc_final: 0.8455 (m) REVERT: E 505 LYS cc_start: 0.7384 (tptp) cc_final: 0.7097 (ttpt) REVERT: E 598 ASP cc_start: 0.7928 (m-30) cc_final: 0.7369 (m-30) REVERT: E 696 LYS cc_start: 0.7533 (ttpt) cc_final: 0.7294 (ttpp) REVERT: E 755 TYR cc_start: 0.6536 (m-80) cc_final: 0.6044 (m-80) REVERT: E 757 MET cc_start: 0.6587 (ppp) cc_final: 0.5734 (mtp) REVERT: F 230 PHE cc_start: 0.7069 (t80) cc_final: 0.6740 (t80) REVERT: F 236 LYS cc_start: 0.7206 (mmtt) cc_final: 0.6704 (mttp) REVERT: F 242 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8066 (tt) REVERT: F 244 TYR cc_start: 0.8245 (p90) cc_final: 0.7851 (p90) REVERT: F 389 LYS cc_start: 0.6353 (tttt) cc_final: 0.5334 (mptt) REVERT: F 561 GLU cc_start: 0.7197 (pm20) cc_final: 0.6875 (mp0) REVERT: F 669 ASP cc_start: 0.6705 (t70) cc_final: 0.6495 (m-30) REVERT: F 741 ARG cc_start: 0.6410 (mmp-170) cc_final: 0.6070 (mmp80) REVERT: F 755 TYR cc_start: 0.7115 (m-80) cc_final: 0.6559 (m-80) outliers start: 51 outliers final: 25 residues processed: 560 average time/residue: 0.5274 time to fit residues: 460.3918 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 : 3.594 ------------------------------------------------------------------------------- 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: 0.9990 chunk 230 optimal weight: 0.9980 chunk 254 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 220 optimal weight: 0.9980 chunk 260 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 139 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.201341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3981 r_free = 0.3981 target = 0.162730 restraints weight = 42561.183| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.60 r_work: 0.3796 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3190 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= 0.159 Angle : 0.626 7.495 44179 Z= 0.312 Chirality : 0.045 0.225 5130 Planarity : 0.005 0.057 5916 Dihedral : 10.291 179.868 4901 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.18 % Allowed : 12.17 % Favored : 85.65 % 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 0.017 0.002 PHE C 360 TYR 0.014 0.002 TYR F 203 ARG 0.010 0.001 ARG C 365 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 1576) hydrogen bonds : angle 5.14314 ( 4464) SS BOND : bond 0.02026 ( 6) SS BOND : angle 4.11945 ( 12) covalent geometry : bond 0.00363 (32488) covalent geometry : angle 0.62259 (44167) Misc. bond : bond 0.00383 ( 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 537 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 476 time to evaluate : 3.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7700 (tttt) REVERT: A 307 ASP cc_start: 0.7360 (p0) cc_final: 0.7023 (t70) REVERT: A 322 ARG cc_start: 0.6461 (mtt90) cc_final: 0.6134 (mtm-85) REVERT: A 364 ASP cc_start: 0.4957 (m-30) cc_final: 0.4631 (t0) REVERT: A 484 ASP cc_start: 0.7116 (p0) cc_final: 0.6705 (m-30) REVERT: A 757 MET cc_start: 0.6990 (ppp) cc_final: 0.6104 (mtm) REVERT: B 239 ARG cc_start: 0.6470 (mtt180) cc_final: 0.5936 (mtt-85) REVERT: B 252 THR cc_start: 0.8884 (t) cc_final: 0.8517 (m) REVERT: B 288 LYS cc_start: 0.7807 (mtmm) cc_final: 0.7502 (ttpt) REVERT: B 357 LEU cc_start: 0.9035 (mm) cc_final: 0.8773 (mt) REVERT: B 460 ASN cc_start: 0.5235 (OUTLIER) cc_final: 0.4948 (m110) REVERT: B 504 LEU cc_start: 0.8132 (tp) cc_final: 0.7880 (mt) REVERT: C 230 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.6814 (m-80) REVERT: C 252 THR cc_start: 0.9042 (t) cc_final: 0.8665 (m) REVERT: C 281 GLU cc_start: 0.7380 (tp30) cc_final: 0.6213 (tt0) REVERT: C 317 HIS cc_start: 0.3328 (t-90) cc_final: 0.2837 (m-70) REVERT: C 323 ARG cc_start: 0.7879 (ttp-170) cc_final: 0.7316 (ttm-80) REVERT: C 365 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6388 (mtm110) REVERT: C 536 GLN cc_start: 0.6632 (mm110) cc_final: 0.6376 (mm-40) REVERT: C 720 MET cc_start: -0.1094 (tpt) cc_final: -0.1745 (tpt) REVERT: C 740 MET cc_start: 0.7655 (mmp) cc_final: 0.6996 (mmm) REVERT: C 742 PHE cc_start: 0.6333 (OUTLIER) cc_final: 0.5834 (t80) REVERT: D 554 GLU cc_start: 0.6876 (mm-30) cc_final: 0.6090 (tt0) REVERT: D 565 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7396 (ttpp) REVERT: D 668 LYS cc_start: 0.6943 (mmtm) cc_final: 0.6428 (tttp) REVERT: D 720 MET cc_start: 0.2712 (mmm) cc_final: 0.2266 (mmp) REVERT: D 740 MET cc_start: 0.8048 (mmp) cc_final: 0.7815 (mmm) REVERT: E 347 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8510 (m) REVERT: E 560 ARG cc_start: 0.7266 (tpt170) cc_final: 0.6725 (tpt-90) REVERT: E 561 GLU cc_start: 0.7156 (pt0) cc_final: 0.6882 (pt0) REVERT: E 696 LYS cc_start: 0.7523 (ttpt) cc_final: 0.6972 (ttpp) REVERT: E 755 TYR cc_start: 0.6430 (m-80) cc_final: 0.6148 (m-80) REVERT: E 757 MET cc_start: 0.6498 (ppp) cc_final: 0.5743 (mtp) REVERT: F 236 LYS cc_start: 0.7543 (mmtt) cc_final: 0.7211 (mttp) REVERT: F 242 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.7997 (tt) REVERT: F 244 TYR cc_start: 0.8009 (p90) cc_final: 0.7691 (p90) REVERT: F 267 PHE cc_start: 0.7981 (t80) cc_final: 0.7683 (t80) REVERT: F 332 MET cc_start: 0.6847 (mtm) cc_final: 0.6581 (mtp) REVERT: F 389 LYS cc_start: 0.6392 (tttt) cc_final: 0.5245 (mptt) REVERT: F 561 GLU cc_start: 0.7139 (pm20) cc_final: 0.6865 (mp0) REVERT: F 669 ASP cc_start: 0.6516 (t70) cc_final: 0.6311 (m-30) REVERT: F 741 ARG cc_start: 0.6261 (mmp-170) cc_final: 0.5900 (mmp80) outliers start: 61 outliers final: 34 residues processed: 502 average time/residue: 0.4874 time to fit residues: 380.6367 Evaluate side-chains 459 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 418 time to evaluate : 3.343 ------------------------------------------------------------------------------- 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: 0.6980 chunk 63 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 408 optimal weight: 6.9990 chunk 206 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 264 optimal weight: 6.9990 chunk 430 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 230 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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** ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.199063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.166100 restraints weight = 42174.263| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 1.59 r_work: 0.3831 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 32500 Z= 0.165 Angle : 0.621 9.669 44179 Z= 0.308 Chirality : 0.045 0.254 5130 Planarity : 0.005 0.057 5916 Dihedral : 10.169 168.952 4901 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.25 % Allowed : 14.17 % Favored : 83.58 % 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: -0.67 (0.13), residues: 4464 helix: 0.59 (0.12), residues: 1919 sheet: -1.60 (0.20), residues: 572 loop : -1.03 (0.15), residues: 1973 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 0.012 0.002 TYR C 755 ARG 0.010 0.001 ARG D 487 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 1576) hydrogen bonds : angle 5.04896 ( 4464) SS BOND : bond 0.02185 ( 6) SS BOND : angle 4.12153 ( 12) covalent geometry : bond 0.00379 (32488) covalent geometry : angle 0.61777 (44167) Misc. bond : bond 0.00385 ( 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 520 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 457 time to evaluate : 3.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8087 (mmtt) cc_final: 0.7801 (tttt) REVERT: A 307 ASP cc_start: 0.7576 (p0) cc_final: 0.7322 (t70) REVERT: A 327 GLN cc_start: 0.7856 (tp40) cc_final: 0.7561 (tp-100) REVERT: A 364 ASP cc_start: 0.5049 (m-30) cc_final: 0.4835 (t0) REVERT: A 449 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.6706 (tpt) REVERT: A 484 ASP cc_start: 0.7181 (p0) cc_final: 0.6801 (m-30) REVERT: A 757 MET cc_start: 0.7018 (ppp) cc_final: 0.6296 (mtm) REVERT: B 239 ARG cc_start: 0.6641 (mtt180) cc_final: 0.6131 (mtt-85) REVERT: B 252 THR cc_start: 0.8970 (t) cc_final: 0.8647 (m) REVERT: B 288 LYS cc_start: 0.7809 (mtmm) cc_final: 0.7551 (ttpt) REVERT: B 357 LEU cc_start: 0.8976 (mm) cc_final: 0.8690 (mt) REVERT: B 460 ASN cc_start: 0.5728 (OUTLIER) cc_final: 0.5405 (m110) REVERT: B 504 LEU cc_start: 0.8111 (tp) cc_final: 0.7841 (mt) REVERT: B 755 TYR cc_start: 0.7397 (m-80) cc_final: 0.7121 (m-80) REVERT: C 230 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.6849 (m-80) REVERT: C 252 THR cc_start: 0.9069 (t) cc_final: 0.8746 (m) REVERT: C 281 GLU cc_start: 0.7393 (tp30) cc_final: 0.6327 (tt0) REVERT: C 323 ARG cc_start: 0.8042 (ttp-170) cc_final: 0.7505 (ttm-80) REVERT: C 365 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6595 (mtm110) REVERT: C 550 MET cc_start: 0.8176 (mtm) cc_final: 0.7924 (mtm) REVERT: C 720 MET cc_start: -0.1298 (tpt) cc_final: -0.2068 (tpt) REVERT: C 740 MET cc_start: 0.7782 (mmp) cc_final: 0.7009 (mmm) REVERT: C 742 PHE cc_start: 0.6274 (OUTLIER) cc_final: 0.5779 (t80) REVERT: D 404 HIS cc_start: 0.6281 (OUTLIER) cc_final: 0.5691 (t-90) REVERT: D 554 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6472 (tt0) REVERT: D 565 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7397 (ttpp) REVERT: D 668 LYS cc_start: 0.7054 (mmtm) cc_final: 0.6683 (tttm) REVERT: D 720 MET cc_start: 0.3115 (mmm) cc_final: 0.2681 (mmp) REVERT: D 740 MET cc_start: 0.8161 (mmp) cc_final: 0.7948 (mmm) REVERT: E 347 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8488 (m) REVERT: E 554 GLU cc_start: 0.6602 (mm-30) cc_final: 0.6265 (tt0) REVERT: E 560 ARG cc_start: 0.7434 (tpt170) cc_final: 0.6940 (tpt-90) REVERT: E 677 LYS cc_start: 0.7570 (ttmm) cc_final: 0.7244 (tttm) REVERT: E 755 TYR cc_start: 0.6507 (m-80) cc_final: 0.6205 (m-80) REVERT: E 757 MET cc_start: 0.6341 (ppp) cc_final: 0.5816 (mtp) REVERT: F 236 LYS cc_start: 0.7605 (mmtt) cc_final: 0.7328 (mttp) REVERT: F 242 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8196 (tt) REVERT: F 244 TYR cc_start: 0.8079 (p90) cc_final: 0.7857 (p90) REVERT: F 327 GLN cc_start: 0.7387 (tp40) cc_final: 0.7112 (tp-100) REVERT: F 389 LYS cc_start: 0.6570 (tttt) cc_final: 0.5439 (mptt) REVERT: F 560 ARG cc_start: 0.7205 (tpt170) cc_final: 0.6892 (ttp80) REVERT: F 561 GLU cc_start: 0.7326 (pm20) cc_final: 0.6988 (mp0) REVERT: F 741 ARG cc_start: 0.6287 (mmp-170) cc_final: 0.5885 (mmp80) REVERT: F 755 TYR cc_start: 0.7100 (m-80) cc_final: 0.6766 (m-80) outliers start: 63 outliers final: 37 residues processed: 488 average time/residue: 0.4823 time to fit residues: 364.2915 Evaluate side-chains 445 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 399 time to evaluate : 3.689 ------------------------------------------------------------------------------- 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 449 MET Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 561 GLU 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 624 ASN Chi-restraints excluded: chain B residue 663 LYS 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 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 404 HIS Chi-restraints excluded: chain D residue 468 VAL 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 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: 2.9990 chunk 369 optimal weight: 0.6980 chunk 148 optimal weight: 10.0000 chunk 348 optimal weight: 0.0030 chunk 120 optimal weight: 3.9990 chunk 234 optimal weight: 30.0000 chunk 77 optimal weight: 50.0000 chunk 44 optimal weight: 0.0070 chunk 416 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 246 optimal weight: 5.9990 overall best weight: 1.5412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN B 260 ASN B 327 GLN B 460 ASN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 ASN 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 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 460 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.195719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.165188 restraints weight = 42275.766| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 1.55 r_work: 0.3775 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 32500 Z= 0.197 Angle : 0.648 8.161 44179 Z= 0.322 Chirality : 0.046 0.215 5130 Planarity : 0.005 0.059 5916 Dihedral : 10.185 165.847 4901 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.46 % Allowed : 15.81 % Favored : 81.73 % 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: -0.78 (0.13), residues: 4464 helix: 0.47 (0.12), residues: 1923 sheet: -1.72 (0.19), residues: 617 loop : -1.03 (0.15), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 551 HIS 0.036 0.002 HIS D 404 PHE 0.023 0.002 PHE C 267 TYR 0.018 0.002 TYR C 755 ARG 0.010 0.001 ARG D 487 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 1576) hydrogen bonds : angle 5.10497 ( 4464) SS BOND : bond 0.02110 ( 6) SS BOND : angle 4.68977 ( 12) covalent geometry : bond 0.00457 (32488) covalent geometry : angle 0.64377 (44167) Misc. bond : bond 0.00426 ( 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 496 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 427 time to evaluate : 3.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8069 (mmtt) cc_final: 0.7494 (mmtm) REVERT: A 307 ASP cc_start: 0.7727 (p0) cc_final: 0.7397 (t70) REVERT: A 358 ARG cc_start: 0.7945 (mtp180) cc_final: 0.7742 (mtm180) REVERT: A 364 ASP cc_start: 0.5250 (m-30) cc_final: 0.4980 (t0) REVERT: A 442 MET cc_start: 0.3718 (OUTLIER) cc_final: 0.3000 (tmm) REVERT: A 757 MET cc_start: 0.6922 (ppp) cc_final: 0.6275 (mtt) REVERT: B 239 ARG cc_start: 0.6816 (mtt180) cc_final: 0.6297 (mtt-85) REVERT: B 252 THR cc_start: 0.9056 (t) cc_final: 0.8645 (m) REVERT: B 357 LEU cc_start: 0.9016 (mm) cc_final: 0.8751 (mt) REVERT: B 460 ASN cc_start: 0.5747 (OUTLIER) cc_final: 0.5411 (m110) REVERT: B 504 LEU cc_start: 0.8179 (tp) cc_final: 0.7865 (mt) REVERT: C 230 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7326 (t80) REVERT: C 252 THR cc_start: 0.9078 (t) cc_final: 0.8771 (m) REVERT: C 323 ARG cc_start: 0.8004 (ttp-170) cc_final: 0.7461 (ttm-80) REVERT: C 365 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6858 (mtm110) REVERT: C 492 LEU cc_start: 0.8669 (mt) cc_final: 0.8440 (mp) REVERT: C 720 MET cc_start: -0.1352 (tpt) cc_final: -0.1981 (tpt) REVERT: C 740 MET cc_start: 0.7829 (mmp) cc_final: 0.7084 (mmm) REVERT: C 742 PHE cc_start: 0.6450 (OUTLIER) cc_final: 0.6029 (t80) REVERT: D 203 TYR cc_start: 0.8032 (m-80) cc_final: 0.7804 (m-80) REVERT: D 554 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6726 (tt0) REVERT: D 565 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7597 (ttpp) REVERT: D 668 LYS cc_start: 0.7352 (mmtm) cc_final: 0.6842 (tttm) REVERT: D 720 MET cc_start: 0.3501 (mmm) cc_final: 0.3078 (mmm) REVERT: D 740 MET cc_start: 0.8279 (mmp) cc_final: 0.8078 (mmm) REVERT: E 268 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7915 (tp) REVERT: E 347 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8534 (m) REVERT: E 554 GLU cc_start: 0.6691 (mm-30) cc_final: 0.6308 (tt0) REVERT: E 560 ARG cc_start: 0.7602 (tpt170) cc_final: 0.7153 (tpt-90) REVERT: E 607 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7470 (mm-30) REVERT: E 677 LYS cc_start: 0.7504 (ttmm) cc_final: 0.7130 (tttm) REVERT: E 755 TYR cc_start: 0.6810 (m-80) cc_final: 0.6482 (m-80) REVERT: E 757 MET cc_start: 0.6482 (ppp) cc_final: 0.5904 (mtp) REVERT: F 236 LYS cc_start: 0.7571 (mmtt) cc_final: 0.7208 (mtmt) REVERT: F 242 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8434 (tt) REVERT: F 389 LYS cc_start: 0.6594 (tttt) cc_final: 0.5419 (mptt) REVERT: F 561 GLU cc_start: 0.7599 (pm20) cc_final: 0.7295 (mp0) REVERT: F 755 TYR cc_start: 0.7296 (m-80) cc_final: 0.6946 (m-80) outliers start: 69 outliers final: 42 residues processed: 464 average time/residue: 0.4684 time to fit residues: 338.9506 Evaluate side-chains 439 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 388 time to evaluate : 3.369 ------------------------------------------------------------------------------- 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 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 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 468 VAL 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 629 ILE Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain E residue 268 LEU 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 433 GLU Chi-restraints excluded: chain E residue 456 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 468 VAL Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 608 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: 6.9990 chunk 411 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 352 optimal weight: 3.9990 chunk 390 optimal weight: 0.5980 chunk 72 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 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 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 404 HIS ** 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 F 533 ASN F 589 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.193011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.163149 restraints weight = 42466.908| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 1.62 r_work: 0.3734 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 32500 Z= 0.228 Angle : 0.681 8.357 44179 Z= 0.339 Chirality : 0.047 0.327 5130 Planarity : 0.005 0.061 5916 Dihedral : 10.311 168.853 4901 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.82 % Allowed : 16.67 % Favored : 80.51 % 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: -0.93 (0.13), residues: 4464 helix: 0.30 (0.12), residues: 1920 sheet: -1.73 (0.19), residues: 621 loop : -1.07 (0.15), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 551 HIS 0.007 0.001 HIS E 340 PHE 0.020 0.002 PHE C 360 TYR 0.018 0.002 TYR A 203 ARG 0.010 0.001 ARG D 487 Details of bonding type rmsd hydrogen bonds : bond 0.04317 ( 1576) hydrogen bonds : angle 5.22648 ( 4464) SS BOND : bond 0.02160 ( 6) SS BOND : angle 5.06524 ( 12) covalent geometry : bond 0.00528 (32488) covalent geometry : angle 0.67599 (44167) Misc. bond : bond 0.00493 ( 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 499 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 420 time to evaluate : 3.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8093 (mmtt) cc_final: 0.7620 (mmtm) REVERT: A 307 ASP cc_start: 0.7731 (p0) cc_final: 0.7342 (t70) REVERT: A 364 ASP cc_start: 0.5672 (m-30) cc_final: 0.5363 (t0) REVERT: A 442 MET cc_start: 0.3445 (mpp) cc_final: 0.2815 (tmm) REVERT: A 757 MET cc_start: 0.6890 (ppp) cc_final: 0.6469 (mtt) REVERT: B 239 ARG cc_start: 0.6849 (mtt180) cc_final: 0.6308 (mtt-85) REVERT: B 357 LEU cc_start: 0.9207 (mm) cc_final: 0.8923 (mt) REVERT: B 460 ASN cc_start: 0.6242 (OUTLIER) cc_final: 0.5989 (m-40) REVERT: B 504 LEU cc_start: 0.8138 (tp) cc_final: 0.7843 (mt) REVERT: B 628 ILE cc_start: 0.8709 (pt) cc_final: 0.8503 (pt) REVERT: C 230 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7547 (t80) REVERT: C 340 HIS cc_start: 0.5586 (OUTLIER) cc_final: 0.5238 (t70) REVERT: C 365 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6936 (mtm110) REVERT: C 464 LEU cc_start: 0.3967 (tp) cc_final: 0.3522 (tp) REVERT: C 720 MET cc_start: -0.1302 (tpt) cc_final: -0.1841 (tpt) REVERT: C 740 MET cc_start: 0.7920 (mmp) cc_final: 0.7195 (mmm) REVERT: D 554 GLU cc_start: 0.7425 (mm-30) cc_final: 0.6505 (mm-30) REVERT: D 561 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6605 (pt0) REVERT: D 565 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7640 (ttpp) REVERT: D 668 LYS cc_start: 0.7529 (mmtm) cc_final: 0.6971 (tttm) REVERT: D 720 MET cc_start: 0.3485 (mmm) cc_final: 0.3133 (mmp) REVERT: D 740 MET cc_start: 0.8424 (mmp) cc_final: 0.8199 (mmm) REVERT: E 347 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8564 (m) REVERT: E 433 GLU cc_start: 0.0812 (OUTLIER) cc_final: 0.0151 (mm-30) REVERT: E 586 ARG cc_start: 0.7988 (ttp80) cc_final: 0.7741 (ttp80) REVERT: E 607 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7554 (mm-30) REVERT: E 677 LYS cc_start: 0.7505 (ttmm) cc_final: 0.7167 (tttm) REVERT: F 236 LYS cc_start: 0.7759 (mmtt) cc_final: 0.7371 (mttp) REVERT: F 242 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8562 (tt) REVERT: F 389 LYS cc_start: 0.6776 (tttt) cc_final: 0.5572 (mptt) REVERT: F 502 LYS cc_start: 0.6913 (OUTLIER) cc_final: 0.6554 (ttmm) REVERT: F 561 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: F 730 GLU cc_start: 0.7335 (pm20) cc_final: 0.7078 (pm20) outliers start: 79 outliers final: 49 residues processed: 467 average time/residue: 0.4686 time to fit residues: 343.1611 Evaluate side-chains 439 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 379 time to evaluate : 3.388 ------------------------------------------------------------------------------- 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 688 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 275 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 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 497 VAL 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 D residue 690 ILE Chi-restraints excluded: chain D residue 752 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 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 213 LEU 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 502 LYS Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 598 ASP 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: 0.5980 chunk 268 optimal weight: 3.9990 chunk 15 optimal weight: 0.0970 chunk 312 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 431 optimal weight: 0.7980 chunk 169 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 443 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 405 optimal weight: 0.0770 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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 460 ASN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 558 ASN 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** ** E 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 HIS F 533 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.195950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.163443 restraints weight = 41985.114| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 1.54 r_work: 0.3807 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 32500 Z= 0.139 Angle : 0.627 9.901 44179 Z= 0.307 Chirality : 0.044 0.223 5130 Planarity : 0.005 0.088 5916 Dihedral : 9.901 164.589 4901 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.39 % Allowed : 17.67 % Favored : 79.94 % 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: -0.73 (0.13), residues: 4464 helix: 0.57 (0.12), residues: 1889 sheet: -1.56 (0.20), residues: 582 loop : -1.12 (0.14), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 454 HIS 0.008 0.001 HIS E 340 PHE 0.016 0.001 PHE B 290 TYR 0.023 0.002 TYR F 244 ARG 0.012 0.001 ARG D 487 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 1576) hydrogen bonds : angle 5.00123 ( 4464) SS BOND : bond 0.02228 ( 6) SS BOND : angle 4.31336 ( 12) covalent geometry : bond 0.00317 (32488) covalent geometry : angle 0.62325 (44167) Misc. bond : bond 0.00382 ( 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 490 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 423 time to evaluate : 3.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7454 (mmtm) REVERT: A 307 ASP cc_start: 0.7584 (p0) cc_final: 0.7253 (t70) REVERT: A 442 MET cc_start: 0.3491 (mpp) cc_final: 0.2941 (tmm) REVERT: A 678 MET cc_start: 0.5563 (OUTLIER) cc_final: 0.4839 (tpp) REVERT: A 740 MET cc_start: 0.7511 (mmp) cc_final: 0.7295 (mmt) REVERT: A 757 MET cc_start: 0.6840 (ppp) cc_final: 0.6420 (mtt) REVERT: B 239 ARG cc_start: 0.6672 (mtt180) cc_final: 0.6316 (mtt-85) REVERT: B 275 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6815 (mmm) REVERT: B 357 LEU cc_start: 0.9110 (mm) cc_final: 0.8844 (mt) REVERT: B 504 LEU cc_start: 0.7985 (tp) cc_final: 0.7724 (mt) REVERT: B 561 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6916 (pm20) REVERT: B 628 ILE cc_start: 0.8690 (pt) cc_final: 0.8436 (pt) REVERT: B 755 TYR cc_start: 0.7352 (m-80) cc_final: 0.7135 (m-80) REVERT: C 230 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.7441 (t80) REVERT: C 252 THR cc_start: 0.9002 (t) cc_final: 0.8674 (m) REVERT: C 323 ARG cc_start: 0.7855 (ttp-170) cc_final: 0.7218 (ttm-80) REVERT: C 365 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6827 (mtm-85) REVERT: C 720 MET cc_start: -0.1242 (tpt) cc_final: -0.1731 (tpt) REVERT: C 740 MET cc_start: 0.7843 (mmp) cc_final: 0.7086 (mmm) REVERT: C 755 TYR cc_start: 0.5805 (m-80) cc_final: 0.5457 (m-80) REVERT: D 397 GLU cc_start: 0.7765 (tp30) cc_final: 0.7372 (pm20) REVERT: D 420 LEU cc_start: 0.8311 (mm) cc_final: 0.8076 (mm) REVERT: D 554 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6214 (mt-10) REVERT: D 565 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7583 (ttpp) REVERT: D 668 LYS cc_start: 0.7408 (mmtm) cc_final: 0.6873 (tttm) REVERT: D 720 MET cc_start: 0.3575 (mmm) cc_final: 0.3233 (mmp) REVERT: D 740 MET cc_start: 0.8353 (mmp) cc_final: 0.8063 (mmm) REVERT: E 554 GLU cc_start: 0.6515 (mm-30) cc_final: 0.5884 (mp0) REVERT: E 561 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6874 (mp0) REVERT: E 624 ASN cc_start: 0.7329 (m-40) cc_final: 0.6872 (t0) REVERT: E 677 LYS cc_start: 0.7462 (ttmm) cc_final: 0.7118 (tttm) REVERT: E 757 MET cc_start: 0.6955 (tmm) cc_final: 0.6066 (mtp) REVERT: F 213 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8861 (mt) REVERT: F 236 LYS cc_start: 0.7768 (mmtt) cc_final: 0.7448 (mttp) REVERT: F 327 GLN cc_start: 0.7460 (tp40) cc_final: 0.7191 (tp-100) REVERT: F 333 ASP cc_start: 0.7224 (m-30) cc_final: 0.6863 (m-30) REVERT: F 389 LYS cc_start: 0.6785 (tttt) cc_final: 0.5476 (mmmt) REVERT: F 560 ARG cc_start: 0.7173 (tpt-90) cc_final: 0.6760 (ttp80) outliers start: 67 outliers final: 39 residues processed: 463 average time/residue: 0.4652 time to fit residues: 343.1465 Evaluate side-chains 431 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 385 time to evaluate : 3.935 ------------------------------------------------------------------------------- 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 490 GLN Chi-restraints excluded: chain A residue 497 VAL 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 B residue 275 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 561 GLU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 373 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 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 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 475 THR Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 353 ILE 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 752 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 242 optimal weight: 0.8980 chunk 426 optimal weight: 1.9990 chunk 384 optimal weight: 20.0000 chunk 45 optimal weight: 0.0570 chunk 366 optimal weight: 6.9990 chunk 340 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 406 optimal weight: 0.6980 chunk 20 optimal weight: 0.0670 chunk 215 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 624 ASN F 460 ASN F 692 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.196908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.163087 restraints weight = 42098.144| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 1.65 r_work: 0.3810 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 32500 Z= 0.138 Angle : 0.619 9.365 44179 Z= 0.302 Chirality : 0.044 0.222 5130 Planarity : 0.005 0.081 5916 Dihedral : 9.687 166.768 4901 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.93 % Allowed : 19.06 % Favored : 79.01 % 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: -0.64 (0.13), residues: 4464 helix: 0.70 (0.12), residues: 1856 sheet: -1.47 (0.20), residues: 582 loop : -1.11 (0.14), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 454 HIS 0.008 0.001 HIS E 340 PHE 0.019 0.001 PHE A 506 TYR 0.022 0.002 TYR F 244 ARG 0.012 0.001 ARG D 487 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 1576) hydrogen bonds : angle 4.90372 ( 4464) SS BOND : bond 0.02077 ( 6) SS BOND : angle 4.20108 ( 12) covalent geometry : bond 0.00316 (32488) covalent geometry : angle 0.61495 (44167) Misc. bond : bond 0.00366 ( 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 467 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 413 time to evaluate : 3.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8059 (mmtt) cc_final: 0.7457 (mmtm) REVERT: A 307 ASP cc_start: 0.7628 (p0) cc_final: 0.7253 (t70) REVERT: A 442 MET cc_start: 0.3529 (mpp) cc_final: 0.3014 (tmm) REVERT: A 678 MET cc_start: 0.5562 (OUTLIER) cc_final: 0.4824 (tpp) REVERT: A 740 MET cc_start: 0.7492 (mmp) cc_final: 0.7286 (mmt) REVERT: A 757 MET cc_start: 0.6733 (ppp) cc_final: 0.6315 (mtt) REVERT: B 239 ARG cc_start: 0.6767 (mtt180) cc_final: 0.6341 (mtt-85) REVERT: B 275 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6887 (mmm) REVERT: B 288 LYS cc_start: 0.7920 (mtmm) cc_final: 0.7611 (ttpt) REVERT: B 357 LEU cc_start: 0.9094 (mm) cc_final: 0.8824 (mt) REVERT: B 504 LEU cc_start: 0.7932 (tp) cc_final: 0.7693 (mt) REVERT: B 560 ARG cc_start: 0.7347 (tpt170) cc_final: 0.7016 (ttt90) REVERT: B 561 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6970 (pm20) REVERT: B 628 ILE cc_start: 0.8654 (pt) cc_final: 0.8409 (pt) REVERT: C 230 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7470 (t80) REVERT: C 252 THR cc_start: 0.9007 (t) cc_final: 0.8695 (m) REVERT: C 323 ARG cc_start: 0.7842 (ttp-170) cc_final: 0.7440 (ttm-80) REVERT: C 427 MET cc_start: 0.6288 (OUTLIER) cc_final: 0.5436 (tmm) REVERT: C 720 MET cc_start: -0.1167 (tpt) cc_final: -0.1686 (tpt) REVERT: C 740 MET cc_start: 0.7824 (mmp) cc_final: 0.7056 (mmm) REVERT: D 397 GLU cc_start: 0.7631 (tp30) cc_final: 0.7217 (pm20) REVERT: D 398 GLN cc_start: 0.6915 (tt0) cc_final: 0.6304 (tt0) REVERT: D 420 LEU cc_start: 0.8241 (mm) cc_final: 0.8040 (mm) REVERT: D 554 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6217 (mt-10) REVERT: D 560 ARG cc_start: 0.7442 (tpt170) cc_final: 0.7024 (tpp80) REVERT: D 565 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7531 (ttpp) REVERT: D 668 LYS cc_start: 0.7398 (mmtm) cc_final: 0.6885 (tttm) REVERT: D 720 MET cc_start: 0.3576 (mmm) cc_final: 0.3229 (mmp) REVERT: D 740 MET cc_start: 0.8303 (mmp) cc_final: 0.8013 (mmm) REVERT: E 554 GLU cc_start: 0.6496 (mm-30) cc_final: 0.5868 (mp0) REVERT: E 607 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7458 (mm-30) REVERT: E 677 LYS cc_start: 0.7417 (ttmm) cc_final: 0.7071 (tttm) REVERT: F 236 LYS cc_start: 0.7760 (mmtt) cc_final: 0.7426 (mttp) REVERT: F 327 GLN cc_start: 0.7487 (tp40) cc_final: 0.7224 (tp-100) REVERT: F 333 ASP cc_start: 0.7179 (m-30) cc_final: 0.6843 (m-30) REVERT: F 389 LYS cc_start: 0.6878 (tttt) cc_final: 0.5559 (mmmt) REVERT: F 607 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7544 (mm-30) REVERT: F 755 TYR cc_start: 0.7221 (m-80) cc_final: 0.6947 (m-80) outliers start: 54 outliers final: 38 residues processed: 442 average time/residue: 0.4568 time to fit residues: 316.8872 Evaluate side-chains 431 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 387 time to evaluate : 3.737 ------------------------------------------------------------------------------- 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 611 MET Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain B residue 275 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 561 GLU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 464 LEU 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 748 SER 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 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 353 ILE 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 678 MET 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: 8.9990 chunk 271 optimal weight: 2.9990 chunk 192 optimal weight: 0.0870 chunk 141 optimal weight: 0.5980 chunk 89 optimal weight: 20.0000 chunk 130 optimal weight: 2.9990 chunk 359 optimal weight: 5.9990 chunk 345 optimal weight: 2.9990 chunk 189 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 overall best weight: 1.9364 ------------------------------------------------------------------------------- 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 499 HIS ** 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** D 558 ASN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.4333 r_free = 0.4333 target = 0.191340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.163244 restraints weight = 42248.876| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 1.60 r_work: 0.3714 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 32500 Z= 0.232 Angle : 0.708 11.851 44179 Z= 0.351 Chirality : 0.047 0.264 5130 Planarity : 0.006 0.076 5916 Dihedral : 10.071 172.333 4901 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.03 % Allowed : 19.45 % 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: -0.91 (0.13), residues: 4464 helix: 0.35 (0.12), residues: 1895 sheet: -1.44 (0.20), residues: 581 loop : -1.22 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 454 HIS 0.008 0.001 HIS E 340 PHE 0.025 0.002 PHE E 267 TYR 0.025 0.002 TYR F 244 ARG 0.014 0.001 ARG F 560 Details of bonding type rmsd hydrogen bonds : bond 0.04345 ( 1576) hydrogen bonds : angle 5.19357 ( 4464) SS BOND : bond 0.02042 ( 6) SS BOND : angle 5.22552 ( 12) covalent geometry : bond 0.00543 (32488) covalent geometry : angle 0.70299 (44167) Misc. bond : bond 0.00503 ( 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 434 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 377 time to evaluate : 3.824 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: 0.7991 (mmtt) cc_final: 0.7506 (mmtm) REVERT: A 307 ASP cc_start: 0.7456 (p0) cc_final: 0.7229 (t70) REVERT: A 442 MET cc_start: 0.3571 (mpp) cc_final: 0.3237 (tmm) REVERT: B 239 ARG cc_start: 0.6557 (mtt180) cc_final: 0.6106 (mtt-85) REVERT: B 357 LEU cc_start: 0.9188 (mm) cc_final: 0.8943 (mt) REVERT: B 504 LEU cc_start: 0.7927 (tp) cc_final: 0.7674 (mt) REVERT: B 628 ILE cc_start: 0.8704 (pt) cc_final: 0.8500 (pt) REVERT: C 230 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7575 (t80) REVERT: C 252 THR cc_start: 0.9023 (t) cc_final: 0.8692 (m) REVERT: C 278 LEU cc_start: 0.7361 (mm) cc_final: 0.7087 (mm) REVERT: C 340 HIS cc_start: 0.5564 (OUTLIER) cc_final: 0.5153 (t70) REVERT: C 427 MET cc_start: 0.6410 (OUTLIER) cc_final: 0.5766 (tmm) REVERT: C 611 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6732 (ttm) REVERT: C 720 MET cc_start: -0.1211 (tpt) cc_final: -0.1740 (tpt) REVERT: C 740 MET cc_start: 0.7791 (mmp) cc_final: 0.7048 (mmm) REVERT: D 397 GLU cc_start: 0.7530 (tp30) cc_final: 0.7205 (pm20) REVERT: D 398 GLN cc_start: 0.6799 (tt0) cc_final: 0.6458 (tt0) REVERT: D 554 GLU cc_start: 0.7331 (mm-30) cc_final: 0.6398 (mm-30) REVERT: D 560 ARG cc_start: 0.7451 (tpt170) cc_final: 0.7039 (tpp80) REVERT: D 565 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7561 (ttpp) REVERT: D 668 LYS cc_start: 0.7562 (mmtm) cc_final: 0.7015 (tttm) REVERT: D 720 MET cc_start: 0.3844 (mmm) cc_final: 0.3441 (mmp) REVERT: D 740 MET cc_start: 0.8256 (mmp) cc_final: 0.8009 (mmm) REVERT: E 554 GLU cc_start: 0.6738 (mm-30) cc_final: 0.6345 (tt0) REVERT: E 677 LYS cc_start: 0.7347 (ttmm) cc_final: 0.7074 (tttm) REVERT: F 236 LYS cc_start: 0.7793 (mmtt) cc_final: 0.7519 (mttp) REVERT: F 242 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8441 (tt) outliers start: 57 outliers final: 40 residues processed: 413 average time/residue: 0.4595 time to fit residues: 301.0678 Evaluate side-chains 405 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 359 time to evaluate : 3.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 740 MET Chi-restraints excluded: chain B residue 277 LYS 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 375 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 340 HIS 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 561 GLU Chi-restraints excluded: chain C residue 611 MET 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 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 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 342 ILE 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 508 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: 1.9990 chunk 394 optimal weight: 0.8980 chunk 170 optimal weight: 0.1980 chunk 403 optimal weight: 0.4980 chunk 3 optimal weight: 50.0000 chunk 151 optimal weight: 50.0000 chunk 338 optimal weight: 3.9990 chunk 91 optimal weight: 30.0000 chunk 373 optimal weight: 30.0000 chunk 365 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 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 ** 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 ** 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 = 0.4342 r_free = 0.4342 target = 0.192167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.159474 restraints weight = 42324.490| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 1.61 r_work: 0.3737 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 32500 Z= 0.196 Angle : 0.673 12.634 44179 Z= 0.332 Chirality : 0.046 0.235 5130 Planarity : 0.005 0.080 5916 Dihedral : 9.972 169.113 4901 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.00 % Allowed : 19.41 % Favored : 78.59 % 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: -0.94 (0.13), residues: 4464 helix: 0.37 (0.12), residues: 1891 sheet: -1.59 (0.20), residues: 611 loop : -1.20 (0.15), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 454 HIS 0.011 0.001 HIS E 340 PHE 0.021 0.002 PHE C 267 TYR 0.024 0.002 TYR F 244 ARG 0.012 0.001 ARG F 560 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 1576) hydrogen bonds : angle 5.11231 ( 4464) SS BOND : bond 0.02019 ( 6) SS BOND : angle 4.75035 ( 12) covalent geometry : bond 0.00459 (32488) covalent geometry : angle 0.66902 (44167) Misc. bond : bond 0.00461 ( 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 431 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 375 time to evaluate : 3.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7552 (mmtm) REVERT: A 442 MET cc_start: 0.3537 (mpp) cc_final: 0.3289 (tmm) REVERT: A 678 MET cc_start: 0.5721 (OUTLIER) cc_final: 0.5163 (tpt) REVERT: A 740 MET cc_start: 0.7458 (mmp) cc_final: 0.7223 (mmt) REVERT: B 239 ARG cc_start: 0.6650 (mtt180) cc_final: 0.6166 (mtt-85) REVERT: B 357 LEU cc_start: 0.9175 (mm) cc_final: 0.8919 (mt) REVERT: B 504 LEU cc_start: 0.7986 (tp) cc_final: 0.7695 (mt) REVERT: B 560 ARG cc_start: 0.7395 (tpt170) cc_final: 0.7181 (ttt90) REVERT: B 628 ILE cc_start: 0.8688 (pt) cc_final: 0.8480 (pt) REVERT: B 663 LYS cc_start: 0.5859 (OUTLIER) cc_final: 0.5324 (pttp) REVERT: C 230 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7654 (t80) REVERT: C 252 THR cc_start: 0.9019 (t) cc_final: 0.8722 (m) REVERT: C 323 ARG cc_start: 0.7851 (ttp-170) cc_final: 0.7410 (ttm-80) REVERT: C 340 HIS cc_start: 0.5587 (OUTLIER) cc_final: 0.5245 (t70) REVERT: C 397 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6931 (mt-10) REVERT: C 427 MET cc_start: 0.6475 (OUTLIER) cc_final: 0.5807 (tmm) REVERT: C 611 MET cc_start: 0.7065 (OUTLIER) cc_final: 0.6862 (ttm) REVERT: C 720 MET cc_start: -0.1195 (tpt) cc_final: -0.1651 (tpt) REVERT: C 740 MET cc_start: 0.7931 (mmp) cc_final: 0.7193 (mmm) REVERT: D 554 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6432 (mm-30) REVERT: D 560 ARG cc_start: 0.7561 (tpt170) cc_final: 0.7189 (tpp80) REVERT: D 561 GLU cc_start: 0.7034 (pt0) cc_final: 0.6708 (mt-10) REVERT: D 565 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7673 (ttpp) REVERT: D 668 LYS cc_start: 0.7687 (mmtm) cc_final: 0.7054 (tttm) REVERT: D 720 MET cc_start: 0.3684 (mmm) cc_final: 0.3308 (mmp) REVERT: D 740 MET cc_start: 0.8347 (mmp) cc_final: 0.8100 (mmm) REVERT: E 554 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6304 (tt0) REVERT: E 677 LYS cc_start: 0.7484 (ttmm) cc_final: 0.7078 (tttm) REVERT: F 236 LYS cc_start: 0.8003 (mmtt) cc_final: 0.7599 (mttp) REVERT: F 242 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8551 (tt) outliers start: 56 outliers final: 40 residues processed: 409 average time/residue: 0.4810 time to fit residues: 310.2068 Evaluate side-chains 401 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 353 time to evaluate : 3.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER 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 490 GLN 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 B residue 277 LYS 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 375 THR Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 340 HIS 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 464 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 230 PHE 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 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 342 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 245 optimal weight: 0.6980 chunk 363 optimal weight: 2.9990 chunk 358 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 439 optimal weight: 9.9990 chunk 229 optimal weight: 10.0000 chunk 151 optimal weight: 50.0000 chunk 72 optimal weight: 10.0000 chunk 422 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 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 ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.193518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.160479 restraints weight = 42145.657| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 1.60 r_work: 0.3772 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 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 0.079 32500 Z= 0.159 Angle : 0.648 12.302 44179 Z= 0.318 Chirality : 0.045 0.246 5130 Planarity : 0.005 0.087 5916 Dihedral : 9.747 168.125 4901 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.96 % Allowed : 19.52 % 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: -0.80 (0.13), residues: 4464 helix: 0.49 (0.12), residues: 1897 sheet: -1.54 (0.20), residues: 611 loop : -1.14 (0.15), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 454 HIS 0.009 0.001 HIS E 340 PHE 0.018 0.002 PHE C 360 TYR 0.023 0.002 TYR F 244 ARG 0.013 0.001 ARG F 560 Details of bonding type rmsd hydrogen bonds : bond 0.03982 ( 1576) hydrogen bonds : angle 4.98857 ( 4464) SS BOND : bond 0.02133 ( 6) SS BOND : angle 4.45692 ( 12) covalent geometry : bond 0.00371 (32488) covalent geometry : angle 0.64428 (44167) Misc. bond : bond 0.00405 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19118.53 seconds wall clock time: 330 minutes 18.11 seconds (19818.11 seconds total)