Starting phenix.real_space_refine on Tue Aug 26 00:58:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pqx_17827/08_2025/8pqx_17827.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pqx_17827/08_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_17827/08_2025/8pqx_17827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pqx_17827/08_2025/8pqx_17827.map" model { file = "/net/cci-nas-00/data/ceres_data/8pqx_17827/08_2025/8pqx_17827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pqx_17827/08_2025/8pqx_17827.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASN:plan1': 9, 'ARG:plan': 17, 'ASP:plan': 15, 'GLU:plan': 17, 'GLN:plan1': 4, 'PHE:plan': 5, 'TYR:plan': 5, 'HIS:plan': 2} 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: {'ASN:plan1': 9, 'ARG:plan': 17, 'ASP:plan': 15, 'GLU:plan': 17, 'GLN:plan1': 4, 'PHE:plan': 5, 'TYR:plan': 5, 'HIS:plan': 2} 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: {'ASN:plan1': 9, 'ARG:plan': 17, 'ASP:plan': 15, 'GLU:plan': 17, 'GLN:plan1': 4, 'PHE:plan': 5, 'TYR:plan': 5, 'HIS:plan': 2} 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: {'ASN:plan1': 9, 'ARG:plan': 17, 'ASP:plan': 15, 'GLU:plan': 17, 'GLN:plan1': 4, 'PHE:plan': 5, 'TYR:plan': 5, 'HIS:plan': 2} 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: {'ASN:plan1': 9, 'ARG:plan': 17, 'ASP:plan': 15, 'GLU:plan': 17, 'GLN:plan1': 4, 'PHE:plan': 5, 'TYR:plan': 5, 'HIS:plan': 2} 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: {'ASN:plan1': 9, 'ARG:plan': 17, 'ASP:plan': 15, 'GLU:plan': 17, 'GLN:plan1': 4, 'PHE:plan': 5, 'TYR:plan': 5, 'HIS:plan': 2} 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: 7.84, per 1000 atoms: 0.24 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: 2.88 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.34 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: 6.73 Time building geometry restraints manager: 3.71 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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.570 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.970 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG F 313 TYR 0.006 0.001 TYR E 203 PHE 0.013 0.001 PHE A 230 TRP 0.006 0.001 TRP C 454 HIS 0.002 0.001 HIS D 384 Details of bonding type rmsd covalent geometry : bond 0.00294 (32488) covalent geometry : angle 0.61167 (44167) SS BOND : bond 0.01836 ( 6) SS BOND : angle 3.31701 ( 12) hydrogen bonds : bond 0.16041 ( 1576) hydrogen bonds : angle 6.04174 ( 4464) 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 : 1.147 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: 0.2375 time to fit residues: 315.5059 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 : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 0.2980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 0.8980 chunk 424 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 348 ASN A 602 ASN A 624 ASN A 641 GLN B 260 ASN B 460 ASN B 490 GLN B 494 GLN B 602 ASN B 616 ASN B 624 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 GLN D 602 ASN D 624 ASN E 327 GLN E 460 ASN E 490 GLN 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: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.205728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.176517 restraints weight = 42413.811| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 1.52 r_work: 0.3927 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3819 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 32500 Z= 0.166 Angle : 0.654 8.999 44179 Z= 0.327 Chirality : 0.046 0.209 5130 Planarity : 0.005 0.070 5916 Dihedral : 10.314 168.516 4901 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.68 % Favored : 93.30 % Rotamer: Outliers : 1.71 % Allowed : 9.74 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.13), residues: 4464 helix: 0.88 (0.12), residues: 1913 sheet: -1.62 (0.19), residues: 632 loop : -1.29 (0.15), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 365 TYR 0.014 0.002 TYR B 244 PHE 0.015 0.001 PHE B 503 TRP 0.006 0.001 TRP B 454 HIS 0.004 0.001 HIS D 384 Details of bonding type rmsd covalent geometry : bond 0.00368 (32488) covalent geometry : angle 0.65152 (44167) SS BOND : bond 0.01802 ( 6) SS BOND : angle 3.68023 ( 12) hydrogen bonds : bond 0.04808 ( 1576) hydrogen bonds : angle 5.24798 ( 4464) Misc. bond : bond 0.00343 ( 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 598 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 550 time to evaluate : 1.118 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: 0.7970 (mmtt) cc_final: 0.7713 (tttt) REVERT: A 307 ASP cc_start: 0.7197 (p0) cc_final: 0.6789 (t70) REVERT: A 322 ARG cc_start: 0.6509 (mtt90) cc_final: 0.6240 (mtm-85) REVERT: A 364 ASP cc_start: 0.4649 (m-30) cc_final: 0.4410 (t0) REVERT: A 484 ASP cc_start: 0.7138 (p0) cc_final: 0.6812 (m-30) REVERT: A 757 MET cc_start: 0.7183 (ppp) cc_final: 0.6174 (mtm) REVERT: B 239 ARG cc_start: 0.6507 (mtt180) cc_final: 0.6150 (mtt-85) REVERT: B 252 THR cc_start: 0.8884 (t) cc_final: 0.8504 (m) REVERT: B 357 LEU cc_start: 0.8921 (mm) cc_final: 0.8647 (mt) REVERT: C 252 THR cc_start: 0.9077 (t) cc_final: 0.8685 (m) REVERT: C 317 HIS cc_start: 0.3292 (t-90) cc_final: 0.2797 (m-70) REVERT: C 323 ARG cc_start: 0.8028 (ttp-170) cc_final: 0.7538 (ttm-80) REVERT: C 664 SER cc_start: 0.7403 (p) cc_final: 0.6789 (p) REVERT: C 678 MET cc_start: 0.5887 (mtp) cc_final: 0.5671 (mtp) REVERT: C 720 MET cc_start: -0.0848 (tpt) cc_final: -0.1587 (tpt) REVERT: C 740 MET cc_start: 0.7537 (mmp) cc_final: 0.6543 (mmm) REVERT: C 742 PHE cc_start: 0.6175 (OUTLIER) cc_final: 0.5667 (t80) REVERT: D 315 LYS cc_start: 0.6411 (tmtt) cc_final: 0.5337 (ttmt) REVERT: D 317 HIS cc_start: 0.4993 (t-90) cc_final: 0.4627 (m90) REVERT: D 508 MET cc_start: 0.3456 (mpp) cc_final: 0.3174 (tpp) REVERT: D 554 GLU cc_start: 0.6506 (mm-30) cc_final: 0.5718 (tp30) REVERT: D 565 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7239 (ttpp) REVERT: D 668 LYS cc_start: 0.6675 (mmtm) cc_final: 0.6274 (tttp) REVERT: D 740 MET cc_start: 0.7962 (mmp) cc_final: 0.7721 (mmm) REVERT: E 252 THR cc_start: 0.8855 (t) cc_final: 0.8456 (m) REVERT: E 505 LYS cc_start: 0.7277 (tptp) cc_final: 0.7040 (ttpt) REVERT: E 598 ASP cc_start: 0.7835 (m-30) cc_final: 0.7268 (m-30) REVERT: E 696 LYS cc_start: 0.7447 (ttpt) cc_final: 0.6979 (ttpp) REVERT: E 755 TYR cc_start: 0.6323 (m-80) cc_final: 0.5840 (m-80) REVERT: E 757 MET cc_start: 0.6442 (ppp) cc_final: 0.5633 (mtp) REVERT: F 236 LYS cc_start: 0.7024 (mmtt) cc_final: 0.6590 (mttp) REVERT: F 242 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.7840 (tt) REVERT: F 389 LYS cc_start: 0.6152 (tttt) cc_final: 0.5229 (mptt) REVERT: F 478 ASP cc_start: 0.7498 (t0) cc_final: 0.7234 (t0) REVERT: F 561 GLU cc_start: 0.7080 (pm20) cc_final: 0.6843 (mp0) REVERT: F 741 ARG cc_start: 0.6383 (mmp-170) cc_final: 0.6102 (mmp80) outliers start: 48 outliers final: 24 residues processed: 570 average time/residue: 0.2165 time to fit residues: 190.4984 Evaluate side-chains 476 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 449 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 387 ASN 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 561 GLU Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 565 LYS Chi-restraints excluded: chain D residue 642 LEU 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 460 ASN 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 120 optimal weight: 3.9990 chunk 204 optimal weight: 0.0050 chunk 413 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 277 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 297 optimal weight: 20.0000 chunk 159 optimal weight: 9.9990 chunk 246 optimal weight: 5.9990 chunk 422 optimal weight: 0.3980 overall best weight: 1.0800 ------------------------------------------------------------------------------- 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 ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 ASN C 348 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN C 624 ASN ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 692 GLN F 460 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.201848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 115)---------------| | r_work = 0.3992 r_free = 0.3992 target = 0.162975 restraints weight = 42395.888| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 2.71 r_work: 0.3807 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 32500 Z= 0.169 Angle : 0.635 7.321 44179 Z= 0.316 Chirality : 0.045 0.215 5130 Planarity : 0.005 0.074 5916 Dihedral : 10.268 178.283 4901 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.32 % Allowed : 11.92 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.13), residues: 4464 helix: 0.68 (0.12), residues: 1920 sheet: -1.54 (0.19), residues: 572 loop : -1.15 (0.15), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 365 TYR 0.014 0.002 TYR F 244 PHE 0.019 0.002 PHE C 360 TRP 0.007 0.001 TRP C 454 HIS 0.007 0.001 HIS E 340 Details of bonding type rmsd covalent geometry : bond 0.00391 (32488) covalent geometry : angle 0.63110 (44167) SS BOND : bond 0.01959 ( 6) SS BOND : angle 4.26207 ( 12) hydrogen bonds : bond 0.04233 ( 1576) hydrogen bonds : angle 5.15418 ( 4464) Misc. bond : bond 0.00375 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 483 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7703 (tttt) REVERT: A 307 ASP cc_start: 0.7121 (p0) cc_final: 0.6790 (t70) REVERT: A 364 ASP cc_start: 0.4885 (m-30) cc_final: 0.4577 (t0) REVERT: A 484 ASP cc_start: 0.7080 (p0) cc_final: 0.6708 (m-30) REVERT: A 757 MET cc_start: 0.7055 (ppp) cc_final: 0.6133 (mtm) REVERT: B 239 ARG cc_start: 0.6522 (mtt180) cc_final: 0.5979 (mtt-85) REVERT: B 252 THR cc_start: 0.8866 (t) cc_final: 0.8508 (m) REVERT: B 357 LEU cc_start: 0.9041 (mm) cc_final: 0.8764 (mt) REVERT: B 460 ASN cc_start: 0.5400 (OUTLIER) cc_final: 0.5148 (m110) REVERT: C 230 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.6846 (m-80) REVERT: C 252 THR cc_start: 0.9048 (t) cc_final: 0.8693 (m) REVERT: C 281 GLU cc_start: 0.7252 (tp30) cc_final: 0.6210 (tt0) REVERT: C 317 HIS cc_start: 0.3248 (t-90) cc_final: 0.2804 (m-70) REVERT: C 323 ARG cc_start: 0.7932 (ttp-170) cc_final: 0.7381 (ttm-80) REVERT: C 365 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6420 (mtm110) REVERT: C 664 SER cc_start: 0.7553 (p) cc_final: 0.7324 (p) REVERT: C 720 MET cc_start: -0.1018 (tpt) cc_final: -0.1619 (tpt) REVERT: C 740 MET cc_start: 0.7622 (mmp) cc_final: 0.6970 (mmm) REVERT: C 742 PHE cc_start: 0.6323 (OUTLIER) cc_final: 0.5817 (t80) REVERT: D 317 HIS cc_start: 0.4821 (t-90) cc_final: 0.4542 (m90) REVERT: D 554 GLU cc_start: 0.6807 (mm-30) cc_final: 0.6117 (tt0) REVERT: D 565 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7342 (ttpp) REVERT: D 668 LYS cc_start: 0.6917 (mmtm) cc_final: 0.6406 (tttp) REVERT: D 720 MET cc_start: 0.2653 (mmm) cc_final: 0.2227 (mmp) REVERT: D 740 MET cc_start: 0.8010 (mmp) cc_final: 0.7794 (mmm) REVERT: E 287 ARG cc_start: 0.6253 (mtm110) cc_final: 0.6027 (mtm110) REVERT: E 347 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8535 (m) REVERT: E 560 ARG cc_start: 0.7233 (tpt170) cc_final: 0.6709 (tpt-90) REVERT: E 561 GLU cc_start: 0.7112 (pt0) cc_final: 0.6802 (pt0) REVERT: E 696 LYS cc_start: 0.7383 (ttpt) cc_final: 0.6890 (ttpp) REVERT: E 755 TYR cc_start: 0.6354 (m-80) cc_final: 0.6084 (m-80) REVERT: E 757 MET cc_start: 0.6495 (ppp) cc_final: 0.5711 (mtp) REVERT: F 236 LYS cc_start: 0.7460 (mmtt) cc_final: 0.7157 (mttp) REVERT: F 242 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7892 (tt) REVERT: F 332 MET cc_start: 0.6847 (mtm) cc_final: 0.6606 (mtp) REVERT: F 389 LYS cc_start: 0.6386 (tttt) cc_final: 0.5260 (mptt) REVERT: F 478 ASP cc_start: 0.7586 (t0) cc_final: 0.7329 (t0) REVERT: F 561 GLU cc_start: 0.7062 (pm20) cc_final: 0.6704 (mp0) REVERT: F 741 ARG cc_start: 0.6344 (mmp-170) cc_final: 0.6004 (mmp80) outliers start: 65 outliers final: 32 residues processed: 510 average time/residue: 0.2005 time to fit residues: 159.0287 Evaluate side-chains 452 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 413 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 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 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 497 VAL Chi-restraints excluded: chain C residue 561 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 375 THR 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 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 119 optimal weight: 2.9990 chunk 326 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 347 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 chunk 329 optimal weight: 0.1980 chunk 325 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 309 optimal weight: 10.0000 chunk 178 optimal weight: 0.5980 chunk 139 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 ASN ** B 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 HIS D 404 HIS ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 HIS ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 490 GLN ** E 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN F 460 ASN F 533 ASN F 589 ASN F 660 ASN F 692 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.195000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.163366 restraints weight = 42426.718| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 1.58 r_work: 0.3755 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 32500 Z= 0.238 Angle : 0.710 8.093 44179 Z= 0.354 Chirality : 0.048 0.263 5130 Planarity : 0.005 0.063 5916 Dihedral : 10.490 167.573 4901 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.50 % Allowed : 14.60 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.13), residues: 4464 helix: 0.28 (0.12), residues: 1923 sheet: -1.75 (0.19), residues: 617 loop : -1.11 (0.15), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 465 TYR 0.019 0.002 TYR F 203 PHE 0.025 0.002 PHE C 360 TRP 0.010 0.002 TRP B 551 HIS 0.009 0.002 HIS D 404 Details of bonding type rmsd covalent geometry : bond 0.00557 (32488) covalent geometry : angle 0.70518 (44167) SS BOND : bond 0.02033 ( 6) SS BOND : angle 5.00809 ( 12) hydrogen bonds : bond 0.04451 ( 1576) hydrogen bonds : angle 5.29789 ( 4464) Misc. bond : bond 0.00490 ( 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: 70 poor density : 450 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8085 (mmtt) cc_final: 0.7615 (mmtm) REVERT: A 275 MET cc_start: 0.7466 (mtm) cc_final: 0.7148 (mtp) REVERT: A 307 ASP cc_start: 0.7508 (p0) cc_final: 0.7252 (t70) REVERT: A 327 GLN cc_start: 0.8038 (tp40) cc_final: 0.7827 (tp-100) REVERT: A 364 ASP cc_start: 0.5522 (m-30) cc_final: 0.5170 (t0) REVERT: A 757 MET cc_start: 0.6903 (ppp) cc_final: 0.6386 (mtm) REVERT: B 239 ARG cc_start: 0.6714 (mtt180) cc_final: 0.6194 (mtt-85) REVERT: B 252 THR cc_start: 0.9047 (t) cc_final: 0.8652 (m) REVERT: B 256 ARG cc_start: 0.7206 (ttm-80) cc_final: 0.6951 (mtt-85) REVERT: B 278 LEU cc_start: 0.7356 (mm) cc_final: 0.7140 (mp) REVERT: B 357 LEU cc_start: 0.9000 (mm) cc_final: 0.8703 (mt) REVERT: C 252 THR cc_start: 0.9063 (t) cc_final: 0.8746 (m) REVERT: C 281 GLU cc_start: 0.7566 (tp30) cc_final: 0.6425 (tt0) REVERT: C 365 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6995 (mtm110) REVERT: C 720 MET cc_start: -0.1387 (tpt) cc_final: -0.2102 (tpt) REVERT: C 740 MET cc_start: 0.7998 (mmp) cc_final: 0.7266 (mmm) REVERT: C 742 PHE cc_start: 0.6513 (OUTLIER) cc_final: 0.6068 (t80) REVERT: D 317 HIS cc_start: 0.4705 (t-90) cc_final: 0.4370 (m90) REVERT: D 404 HIS cc_start: 0.6424 (OUTLIER) cc_final: 0.5829 (t-90) REVERT: D 499 HIS cc_start: 0.7809 (m-70) cc_final: 0.7572 (m-70) REVERT: D 534 GLU cc_start: 0.6677 (tt0) cc_final: 0.6440 (tt0) REVERT: D 554 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6798 (tt0) REVERT: D 668 LYS cc_start: 0.7413 (mmtm) cc_final: 0.6867 (tttm) REVERT: D 720 MET cc_start: 0.3379 (mmm) cc_final: 0.2924 (mmp) REVERT: E 554 GLU cc_start: 0.6747 (mm-30) cc_final: 0.6437 (tt0) REVERT: E 677 LYS cc_start: 0.7596 (ttmm) cc_final: 0.7239 (tttm) REVERT: E 740 MET cc_start: 0.7188 (mmm) cc_final: 0.6878 (tpp) REVERT: E 755 TYR cc_start: 0.6950 (m-80) cc_final: 0.6588 (m-80) REVERT: E 757 MET cc_start: 0.6567 (ppp) cc_final: 0.5962 (mtp) REVERT: F 236 LYS cc_start: 0.7691 (mmtt) cc_final: 0.7379 (mttp) REVERT: F 242 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8411 (tt) REVERT: F 267 PHE cc_start: 0.8361 (t80) cc_final: 0.8123 (t80) REVERT: F 389 LYS cc_start: 0.6680 (tttt) cc_final: 0.5526 (mptt) REVERT: F 395 ASP cc_start: 0.5695 (p0) cc_final: 0.5486 (p0) outliers start: 70 outliers final: 41 residues processed: 487 average time/residue: 0.2113 time to fit residues: 159.9452 Evaluate side-chains 428 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 383 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 740 MET Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 550 MET 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 375 THR 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 556 GLU 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 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 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 295 optimal weight: 0.7980 chunk 317 optimal weight: 6.9990 chunk 2 optimal weight: 30.0000 chunk 85 optimal weight: 4.9990 chunk 339 optimal weight: 4.9990 chunk 9 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 chunk 316 optimal weight: 0.7980 chunk 248 optimal weight: 0.6980 chunk 148 optimal weight: 9.9990 chunk 143 optimal weight: 0.2980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 ASN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 GLN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 GLN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 GLN ** D 499 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.194543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.164470 restraints weight = 42370.152| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 1.61 r_work: 0.3745 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 32500 Z= 0.197 Angle : 0.656 7.795 44179 Z= 0.326 Chirality : 0.046 0.223 5130 Planarity : 0.005 0.063 5916 Dihedral : 10.323 166.395 4901 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.11 % Allowed : 16.99 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.13), residues: 4464 helix: 0.36 (0.12), residues: 1922 sheet: -1.78 (0.19), residues: 617 loop : -1.09 (0.15), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 487 TYR 0.018 0.002 TYR D 203 PHE 0.017 0.002 PHE E 267 TRP 0.010 0.002 TRP B 454 HIS 0.032 0.002 HIS D 404 Details of bonding type rmsd covalent geometry : bond 0.00457 (32488) covalent geometry : angle 0.65121 (44167) SS BOND : bond 0.02078 ( 6) SS BOND : angle 4.62901 ( 12) hydrogen bonds : bond 0.04234 ( 1576) hydrogen bonds : angle 5.20997 ( 4464) Misc. bond : bond 0.00472 ( 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 478 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 419 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8019 (mmtt) cc_final: 0.7475 (mmtm) REVERT: A 757 MET cc_start: 0.6776 (ppp) cc_final: 0.6429 (mtm) REVERT: B 239 ARG cc_start: 0.6508 (mtt180) cc_final: 0.6014 (mtt-85) REVERT: B 252 THR cc_start: 0.8954 (t) cc_final: 0.8564 (m) REVERT: B 256 ARG cc_start: 0.7112 (ttm-80) cc_final: 0.6888 (mtt-85) REVERT: B 357 LEU cc_start: 0.8955 (mm) cc_final: 0.8722 (mt) REVERT: B 628 ILE cc_start: 0.8661 (pt) cc_final: 0.8407 (pt) REVERT: C 230 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7373 (t80) REVERT: C 252 THR cc_start: 0.8986 (t) cc_final: 0.8699 (m) REVERT: C 281 GLU cc_start: 0.7327 (tp30) cc_final: 0.6321 (tt0) REVERT: C 340 HIS cc_start: 0.5411 (OUTLIER) cc_final: 0.5074 (t70) REVERT: C 365 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6815 (mtm110) REVERT: C 536 GLN cc_start: 0.6907 (mm110) cc_final: 0.6476 (mm-40) REVERT: C 561 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6728 (pt0) REVERT: C 720 MET cc_start: -0.1430 (tpt) cc_final: -0.2104 (tpt) REVERT: C 740 MET cc_start: 0.7795 (mmp) cc_final: 0.7110 (mmm) REVERT: D 360 PHE cc_start: 0.7659 (m-80) cc_final: 0.7390 (m-80) REVERT: D 508 MET cc_start: 0.3963 (mpp) cc_final: 0.3759 (tpp) REVERT: D 554 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6828 (tt0) REVERT: D 561 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6347 (pt0) REVERT: D 565 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7597 (ttpp) REVERT: D 668 LYS cc_start: 0.7353 (mmtm) cc_final: 0.6886 (tttm) REVERT: D 720 MET cc_start: 0.3662 (mmm) cc_final: 0.3229 (mmp) REVERT: D 740 MET cc_start: 0.7784 (mmm) cc_final: 0.7519 (mmm) REVERT: E 347 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8441 (m) REVERT: E 554 GLU cc_start: 0.6532 (mm-30) cc_final: 0.6185 (tt0) REVERT: E 586 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7388 (ptm-80) REVERT: E 607 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7425 (mm-30) REVERT: E 677 LYS cc_start: 0.7468 (ttmm) cc_final: 0.7118 (tttm) REVERT: E 740 MET cc_start: 0.7055 (mmm) cc_final: 0.6854 (tpp) REVERT: E 755 TYR cc_start: 0.6804 (m-80) cc_final: 0.6590 (m-80) REVERT: E 757 MET cc_start: 0.6426 (ppp) cc_final: 0.5948 (mtp) REVERT: F 236 LYS cc_start: 0.7569 (mmtt) cc_final: 0.7263 (mtmt) REVERT: F 242 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8201 (tt) REVERT: F 267 PHE cc_start: 0.8240 (t80) cc_final: 0.8038 (t80) REVERT: F 389 LYS cc_start: 0.6764 (tttt) cc_final: 0.5610 (mptt) REVERT: F 560 ARG cc_start: 0.7372 (tpt-90) cc_final: 0.6995 (ttp80) outliers start: 59 outliers final: 35 residues processed: 457 average time/residue: 0.1940 time to fit residues: 139.2817 Evaluate side-chains 420 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 377 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 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 624 ASN Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 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 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 E residue 316 THR 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 456 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 475 THR 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 368 optimal weight: 6.9990 chunk 381 optimal weight: 9.9990 chunk 338 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 375 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 86 optimal weight: 30.0000 chunk 244 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 390 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN A 589 ASN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 ASN ** B 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN D 270 ASN D 404 HIS ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN ** 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** E 490 GLN F 460 ASN F 536 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.187043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.156065 restraints weight = 42427.882| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 1.71 r_work: 0.3632 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.117 32500 Z= 0.356 Angle : 0.843 18.213 44179 Z= 0.424 Chirality : 0.051 0.236 5130 Planarity : 0.007 0.077 5916 Dihedral : 11.085 176.568 4901 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.07 % Allowed : 17.99 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.12), residues: 4464 helix: -0.27 (0.11), residues: 1949 sheet: -1.95 (0.19), residues: 614 loop : -1.34 (0.15), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 487 TYR 0.028 0.003 TYR A 203 PHE 0.027 0.003 PHE C 360 TRP 0.017 0.003 TRP B 454 HIS 0.017 0.002 HIS D 499 Details of bonding type rmsd covalent geometry : bond 0.00830 (32488) covalent geometry : angle 0.83372 (44167) SS BOND : bond 0.03710 ( 6) SS BOND : angle 7.77478 ( 12) hydrogen bonds : bond 0.05206 ( 1576) hydrogen bonds : angle 5.73630 ( 4464) Misc. bond : bond 0.00715 ( 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 496 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 410 time to evaluate : 1.142 Fit side-chains revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7640 (mmtm) REVERT: A 365 ARG cc_start: 0.6821 (OUTLIER) cc_final: 0.6398 (mmm-85) REVERT: B 239 ARG cc_start: 0.6515 (mtt180) cc_final: 0.6129 (mtt-85) REVERT: B 256 ARG cc_start: 0.7305 (ttm-80) cc_final: 0.6945 (mtt-85) REVERT: B 357 LEU cc_start: 0.9297 (mm) cc_final: 0.9078 (mt) REVERT: B 561 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7025 (pm20) REVERT: C 230 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7799 (t80) REVERT: C 260 ASN cc_start: 0.8100 (m-40) cc_final: 0.7743 (m110) REVERT: C 340 HIS cc_start: 0.5895 (OUTLIER) cc_final: 0.5393 (t70) REVERT: C 365 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7123 (mtm110) REVERT: C 561 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.7085 (pt0) REVERT: C 720 MET cc_start: -0.1399 (tpt) cc_final: -0.2030 (tpt) REVERT: D 534 GLU cc_start: 0.6810 (tt0) cc_final: 0.6601 (tt0) REVERT: D 554 GLU cc_start: 0.7772 (mm-30) cc_final: 0.6817 (mm-30) REVERT: D 561 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6649 (pt0) REVERT: D 668 LYS cc_start: 0.7738 (mmtm) cc_final: 0.7106 (tttm) REVERT: D 720 MET cc_start: 0.3818 (mmm) cc_final: 0.3388 (mmp) REVERT: D 740 MET cc_start: 0.7934 (mmm) cc_final: 0.7680 (mmm) REVERT: E 561 GLU cc_start: 0.6587 (mp0) cc_final: 0.6335 (mp0) REVERT: F 236 LYS cc_start: 0.7823 (mmtt) cc_final: 0.7499 (mttp) REVERT: F 256 ARG cc_start: 0.7288 (ttm-80) cc_final: 0.7059 (mtp-110) REVERT: F 268 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8207 (tp) REVERT: F 321 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.6060 (mp0) REVERT: F 323 ARG cc_start: 0.7238 (ttt180) cc_final: 0.6846 (ttt180) REVERT: F 502 LYS cc_start: 0.7005 (OUTLIER) cc_final: 0.6720 (ttmm) outliers start: 86 outliers final: 49 residues processed: 465 average time/residue: 0.2149 time to fit residues: 155.0986 Evaluate side-chains 415 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 356 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 347 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 425 LYS 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 373 ASP Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 347 THR 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 467 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 268 LEU 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 475 THR Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 316 THR 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 456 LEU Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 321 GLU 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 502 LYS Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 651 LYS Chi-restraints excluded: chain F residue 752 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 398 optimal weight: 0.5980 chunk 348 optimal weight: 0.0970 chunk 246 optimal weight: 0.8980 chunk 411 optimal weight: 9.9990 chunk 248 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 190 optimal weight: 9.9990 chunk 320 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 GLN B 317 HIS ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 HIS ** B 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS E 317 HIS E 351 ASN ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 490 GLN ** E 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.193165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.160818 restraints weight = 42115.134| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 1.64 r_work: 0.3741 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 32500 Z= 0.158 Angle : 0.670 15.611 44179 Z= 0.329 Chirality : 0.045 0.209 5130 Planarity : 0.005 0.069 5916 Dihedral : 10.454 170.607 4901 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.11 % Allowed : 20.09 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.12), residues: 4464 helix: 0.15 (0.12), residues: 1910 sheet: -1.87 (0.19), residues: 621 loop : -1.27 (0.15), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 700 TYR 0.018 0.002 TYR F 244 PHE 0.016 0.002 PHE D 302 TRP 0.044 0.002 TRP B 454 HIS 0.013 0.001 HIS D 499 Details of bonding type rmsd covalent geometry : bond 0.00362 (32488) covalent geometry : angle 0.66303 (44167) SS BOND : bond 0.02744 ( 6) SS BOND : angle 5.95343 ( 12) hydrogen bonds : bond 0.04279 ( 1576) hydrogen bonds : angle 5.27828 ( 4464) Misc. bond : bond 0.00459 ( 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 454 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 395 time to evaluate : 1.227 Fit side-chains revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7644 (mmtm) REVERT: A 678 MET cc_start: 0.5689 (OUTLIER) cc_final: 0.5045 (tpp) REVERT: B 239 ARG cc_start: 0.6647 (mtt180) cc_final: 0.6240 (mtt-85) REVERT: B 256 ARG cc_start: 0.7195 (ttm-80) cc_final: 0.6992 (mtt-85) REVERT: B 275 MET cc_start: 0.7585 (mtm) cc_final: 0.7314 (mmm) REVERT: B 357 LEU cc_start: 0.9185 (mm) cc_final: 0.8959 (mt) REVERT: B 360 PHE cc_start: 0.7215 (m-80) cc_final: 0.6965 (m-80) REVERT: C 230 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7663 (t80) REVERT: C 252 THR cc_start: 0.8985 (t) cc_final: 0.8683 (m) REVERT: C 340 HIS cc_start: 0.5608 (OUTLIER) cc_final: 0.5184 (t70) REVERT: C 536 GLN cc_start: 0.7005 (mm110) cc_final: 0.6536 (mm-40) REVERT: C 561 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6923 (pt0) REVERT: C 720 MET cc_start: -0.1237 (tpt) cc_final: -0.1668 (tpt) REVERT: C 740 MET cc_start: 0.7665 (tpp) cc_final: 0.7319 (mpp) REVERT: C 755 TYR cc_start: 0.5849 (m-80) cc_final: 0.5514 (m-80) REVERT: D 554 GLU cc_start: 0.7605 (mm-30) cc_final: 0.6552 (mt-10) REVERT: D 560 ARG cc_start: 0.7620 (tpt170) cc_final: 0.6988 (tpp80) REVERT: D 561 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6682 (pt0) REVERT: D 565 LYS cc_start: 0.7903 (ttpp) cc_final: 0.7580 (ttpp) REVERT: D 668 LYS cc_start: 0.7671 (mmtm) cc_final: 0.7051 (tttm) REVERT: D 720 MET cc_start: 0.3800 (mmm) cc_final: 0.3363 (mmp) REVERT: D 740 MET cc_start: 0.8067 (mmm) cc_final: 0.7808 (mmm) REVERT: E 554 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6303 (tt0) REVERT: E 561 GLU cc_start: 0.6663 (mp0) cc_final: 0.6448 (mp0) REVERT: E 607 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7553 (mm-30) REVERT: E 624 ASN cc_start: 0.7930 (m110) cc_final: 0.7593 (t0) REVERT: F 213 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8871 (mt) REVERT: F 236 LYS cc_start: 0.7960 (mmtt) cc_final: 0.7575 (mttp) REVERT: F 333 ASP cc_start: 0.7384 (m-30) cc_final: 0.7115 (m-30) REVERT: F 389 LYS cc_start: 0.7073 (tttt) cc_final: 0.5771 (mmmt) REVERT: F 502 LYS cc_start: 0.6856 (OUTLIER) cc_final: 0.6559 (ttmm) outliers start: 59 outliers final: 34 residues processed: 431 average time/residue: 0.2064 time to fit residues: 140.7216 Evaluate side-chains 399 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 358 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER 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 678 MET Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 373 ASP 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 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 748 SER Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 752 ILE Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 242 LEU 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 752 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 301 optimal weight: 30.0000 chunk 64 optimal weight: 3.9990 chunk 74 optimal weight: 40.0000 chunk 212 optimal weight: 4.9990 chunk 431 optimal weight: 0.9980 chunk 396 optimal weight: 2.9990 chunk 335 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 206 optimal weight: 0.5980 chunk 191 optimal weight: 1.9990 chunk 155 optimal weight: 30.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 GLN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN D 382 GLN ** D 460 ASN ** 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** ** E 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** 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 = 0.4331 r_free = 0.4331 target = 0.191171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.157628 restraints weight = 42414.042| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.67 r_work: 0.3719 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 32500 Z= 0.203 Angle : 0.697 21.748 44179 Z= 0.343 Chirality : 0.046 0.265 5130 Planarity : 0.005 0.076 5916 Dihedral : 10.456 177.051 4901 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.93 % Allowed : 20.91 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.12), residues: 4464 helix: 0.24 (0.12), residues: 1889 sheet: -1.69 (0.20), residues: 581 loop : -1.29 (0.14), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 560 TYR 0.020 0.002 TYR F 244 PHE 0.027 0.002 PHE C 267 TRP 0.022 0.002 TRP B 454 HIS 0.014 0.001 HIS D 499 Details of bonding type rmsd covalent geometry : bond 0.00473 (32488) covalent geometry : angle 0.68784 (44167) SS BOND : bond 0.02560 ( 6) SS BOND : angle 6.80897 ( 12) hydrogen bonds : bond 0.04308 ( 1576) hydrogen bonds : angle 5.28975 ( 4464) Misc. bond : bond 0.00519 ( 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 433 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 379 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7660 (mmtm) REVERT: A 678 MET cc_start: 0.5700 (OUTLIER) cc_final: 0.5159 (tpt) REVERT: B 239 ARG cc_start: 0.6752 (mtt180) cc_final: 0.6330 (mtt-85) REVERT: B 252 THR cc_start: 0.9043 (t) cc_final: 0.8643 (m) REVERT: B 256 ARG cc_start: 0.7304 (ttm-80) cc_final: 0.7061 (mtt-85) REVERT: B 357 LEU cc_start: 0.9225 (mm) cc_final: 0.9008 (mt) REVERT: B 560 ARG cc_start: 0.7474 (tpt170) cc_final: 0.7218 (ttt90) REVERT: C 230 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7742 (t80) REVERT: C 252 THR cc_start: 0.8967 (t) cc_final: 0.8720 (m) REVERT: C 340 HIS cc_start: 0.5669 (OUTLIER) cc_final: 0.5215 (t70) REVERT: C 360 PHE cc_start: 0.7563 (m-80) cc_final: 0.7154 (m-80) REVERT: C 561 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.7033 (pt0) REVERT: C 720 MET cc_start: -0.1227 (tpt) cc_final: -0.1738 (tpt) REVERT: C 740 MET cc_start: 0.7611 (tpp) cc_final: 0.7340 (mpp) REVERT: D 554 GLU cc_start: 0.7604 (mm-30) cc_final: 0.6522 (mt-10) REVERT: D 560 ARG cc_start: 0.7647 (tpt170) cc_final: 0.7198 (tpp80) REVERT: D 561 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6627 (pt0) REVERT: D 565 LYS cc_start: 0.7934 (ttpp) cc_final: 0.7678 (ttpp) REVERT: D 668 LYS cc_start: 0.7698 (mmtm) cc_final: 0.7069 (tttm) REVERT: D 696 LYS cc_start: 0.7483 (ttpt) cc_final: 0.7119 (tttm) REVERT: D 720 MET cc_start: 0.3754 (mmm) cc_final: 0.3330 (mmp) REVERT: E 554 GLU cc_start: 0.6812 (mm-30) cc_final: 0.5939 (mp0) REVERT: E 561 GLU cc_start: 0.6634 (mp0) cc_final: 0.6403 (mp0) REVERT: E 624 ASN cc_start: 0.7629 (m110) cc_final: 0.7076 (t0) REVERT: F 236 LYS cc_start: 0.8000 (mmtt) cc_final: 0.7632 (mttp) REVERT: F 389 LYS cc_start: 0.7120 (tttt) cc_final: 0.5810 (mmmt) outliers start: 54 outliers final: 39 residues processed: 411 average time/residue: 0.2135 time to fit residues: 139.0048 Evaluate side-chains 398 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 354 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 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 561 GLU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 460 ASN 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 748 SER Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 752 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 634 LEU Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain F residue 321 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 109 optimal weight: 1.9990 chunk 351 optimal weight: 0.5980 chunk 443 optimal weight: 7.9990 chunk 362 optimal weight: 1.9990 chunk 83 optimal weight: 40.0000 chunk 435 optimal weight: 5.9990 chunk 434 optimal weight: 0.0980 chunk 108 optimal weight: 0.8980 chunk 13 optimal weight: 50.0000 chunk 138 optimal weight: 1.9990 chunk 264 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN C 490 GLN D 382 GLN ** D 460 ASN ** 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 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** 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 = 0.4339 r_free = 0.4339 target = 0.191984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.160703 restraints weight = 42235.488| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 1.57 r_work: 0.3744 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 32500 Z= 0.176 Angle : 0.675 21.568 44179 Z= 0.332 Chirality : 0.045 0.275 5130 Planarity : 0.005 0.059 5916 Dihedral : 10.296 177.932 4901 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.00 % Allowed : 20.74 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.13), residues: 4464 helix: 0.32 (0.12), residues: 1881 sheet: -1.88 (0.19), residues: 615 loop : -1.23 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 560 TYR 0.020 0.002 TYR F 244 PHE 0.017 0.002 PHE C 360 TRP 0.023 0.002 TRP B 454 HIS 0.012 0.001 HIS D 499 Details of bonding type rmsd covalent geometry : bond 0.00410 (32488) covalent geometry : angle 0.66752 (44167) SS BOND : bond 0.02841 ( 6) SS BOND : angle 6.07784 ( 12) hydrogen bonds : bond 0.04189 ( 1576) hydrogen bonds : angle 5.20593 ( 4464) Misc. bond : bond 0.00484 ( 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 432 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 376 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8097 (mmtt) cc_final: 0.7626 (mmtm) REVERT: A 678 MET cc_start: 0.5554 (OUTLIER) cc_final: 0.5069 (tpt) REVERT: B 239 ARG cc_start: 0.6724 (mtt180) cc_final: 0.6172 (mtt-85) REVERT: B 252 THR cc_start: 0.9014 (t) cc_final: 0.8617 (m) REVERT: B 256 ARG cc_start: 0.7178 (ttm-80) cc_final: 0.6965 (mtt-85) REVERT: B 357 LEU cc_start: 0.9193 (mm) cc_final: 0.8972 (mt) REVERT: B 755 TYR cc_start: 0.7403 (m-80) cc_final: 0.7117 (m-80) REVERT: C 230 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7702 (t80) REVERT: C 252 THR cc_start: 0.8980 (t) cc_final: 0.8689 (m) REVERT: C 340 HIS cc_start: 0.5633 (OUTLIER) cc_final: 0.5102 (t70) REVERT: C 427 MET cc_start: 0.6517 (OUTLIER) cc_final: 0.5879 (tmm) REVERT: C 536 GLN cc_start: 0.7016 (mm110) cc_final: 0.6574 (mm-40) REVERT: C 720 MET cc_start: -0.1248 (tpt) cc_final: -0.1751 (tpt) REVERT: C 740 MET cc_start: 0.7633 (tpp) cc_final: 0.7343 (mpp) REVERT: D 427 MET cc_start: 0.5560 (tpp) cc_final: 0.5267 (tpt) REVERT: D 554 GLU cc_start: 0.7547 (mm-30) cc_final: 0.6571 (mt-10) REVERT: D 560 ARG cc_start: 0.7622 (tpt170) cc_final: 0.7194 (tpp80) REVERT: D 561 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6577 (pt0) REVERT: D 668 LYS cc_start: 0.7713 (mmtm) cc_final: 0.7069 (tttm) REVERT: D 696 LYS cc_start: 0.7434 (ttpt) cc_final: 0.7082 (tttm) REVERT: D 720 MET cc_start: 0.3808 (mmm) cc_final: 0.3356 (mmp) REVERT: E 554 GLU cc_start: 0.6779 (mm-30) cc_final: 0.6306 (tt0) REVERT: E 561 GLU cc_start: 0.6627 (mp0) cc_final: 0.6402 (mp0) REVERT: E 624 ASN cc_start: 0.7913 (m110) cc_final: 0.7403 (t0) REVERT: F 213 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8741 (mt) REVERT: F 236 LYS cc_start: 0.8061 (mmtt) cc_final: 0.7680 (mttp) REVERT: F 333 ASP cc_start: 0.7352 (m-30) cc_final: 0.7082 (m-30) REVERT: F 389 LYS cc_start: 0.7195 (tttt) cc_final: 0.5843 (mmmt) outliers start: 56 outliers final: 42 residues processed: 408 average time/residue: 0.1964 time to fit residues: 126.2154 Evaluate side-chains 402 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 354 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 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 561 GLU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 456 LEU 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 427 MET Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 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 321 GLU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 651 LYS Chi-restraints excluded: chain F residue 752 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 106 optimal weight: 3.9990 chunk 333 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 chunk 342 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 265 optimal weight: 0.9990 chunk 440 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 283 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.190758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.159207 restraints weight = 42359.475| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 1.57 r_work: 0.3727 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 32500 Z= 0.200 Angle : 0.694 21.464 44179 Z= 0.342 Chirality : 0.046 0.278 5130 Planarity : 0.005 0.076 5916 Dihedral : 10.313 177.538 4901 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.93 % Allowed : 21.09 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.13), residues: 4464 helix: 0.29 (0.12), residues: 1896 sheet: -1.69 (0.20), residues: 575 loop : -1.29 (0.14), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG F 560 TYR 0.024 0.002 TYR F 244 PHE 0.026 0.002 PHE C 267 TRP 0.019 0.002 TRP B 454 HIS 0.012 0.001 HIS D 499 Details of bonding type rmsd covalent geometry : bond 0.00466 (32488) covalent geometry : angle 0.68662 (44167) SS BOND : bond 0.02794 ( 6) SS BOND : angle 6.16781 ( 12) hydrogen bonds : bond 0.04266 ( 1576) hydrogen bonds : angle 5.23923 ( 4464) Misc. bond : bond 0.00511 ( 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 413 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 359 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8133 (mmtt) cc_final: 0.7647 (mmtm) REVERT: A 678 MET cc_start: 0.5641 (OUTLIER) cc_final: 0.5179 (tpt) REVERT: B 239 ARG cc_start: 0.6705 (mtt180) cc_final: 0.6167 (mtt-85) REVERT: B 252 THR cc_start: 0.9018 (t) cc_final: 0.8625 (m) REVERT: B 256 ARG cc_start: 0.7257 (ttm-80) cc_final: 0.7023 (mtt-85) REVERT: B 357 LEU cc_start: 0.9211 (mm) cc_final: 0.8977 (mt) REVERT: B 560 ARG cc_start: 0.7489 (tpt170) cc_final: 0.7274 (ttt90) REVERT: B 755 TYR cc_start: 0.7398 (m-80) cc_final: 0.7136 (m-80) REVERT: C 230 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7715 (t80) REVERT: C 252 THR cc_start: 0.9015 (t) cc_final: 0.8729 (m) REVERT: C 340 HIS cc_start: 0.5688 (OUTLIER) cc_final: 0.5137 (t70) REVERT: C 427 MET cc_start: 0.6587 (OUTLIER) cc_final: 0.5939 (tmm) REVERT: C 536 GLN cc_start: 0.6977 (mm110) cc_final: 0.6548 (mm-40) REVERT: C 720 MET cc_start: -0.1162 (tpt) cc_final: -0.1699 (tpt) REVERT: C 740 MET cc_start: 0.7584 (tpp) cc_final: 0.7317 (mpp) REVERT: D 348 ASN cc_start: 0.7625 (m-40) cc_final: 0.7311 (m-40) REVERT: D 358 ARG cc_start: 0.7825 (mpp80) cc_final: 0.7497 (mtp85) REVERT: D 427 MET cc_start: 0.5524 (tpp) cc_final: 0.5303 (tpt) REVERT: D 554 GLU cc_start: 0.7602 (mm-30) cc_final: 0.6596 (mt-10) REVERT: D 560 ARG cc_start: 0.7607 (tpt170) cc_final: 0.7160 (tpp80) REVERT: D 561 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6562 (pt0) REVERT: D 668 LYS cc_start: 0.7678 (mmtm) cc_final: 0.7054 (tttm) REVERT: D 696 LYS cc_start: 0.7471 (ttpt) cc_final: 0.7106 (tttm) REVERT: D 720 MET cc_start: 0.3778 (mmm) cc_final: 0.3572 (mmt) REVERT: E 554 GLU cc_start: 0.6758 (mm-30) cc_final: 0.6298 (tt0) REVERT: E 561 GLU cc_start: 0.6584 (mp0) cc_final: 0.6350 (mp0) REVERT: E 624 ASN cc_start: 0.8129 (m110) cc_final: 0.7676 (t0) REVERT: F 213 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8777 (mt) REVERT: F 333 ASP cc_start: 0.7385 (m-30) cc_final: 0.7139 (m-30) REVERT: F 389 LYS cc_start: 0.7177 (tttt) cc_final: 0.5772 (mmmt) outliers start: 54 outliers final: 44 residues processed: 392 average time/residue: 0.1806 time to fit residues: 112.1800 Evaluate side-chains 400 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 350 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 A residue 688 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 364 ASP 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 307 ASP Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 460 ASN 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 748 SER Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 752 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 E residue 761 THR Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 321 GLU 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 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 247 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 220 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 379 optimal weight: 50.0000 chunk 171 optimal weight: 1.9990 chunk 393 optimal weight: 0.9980 chunk 159 optimal weight: 10.0000 chunk 251 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN ** D 460 ASN ** 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** ** E 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.191109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.159024 restraints weight = 42181.339| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 1.62 r_work: 0.3734 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 32500 Z= 0.176 Angle : 0.678 20.032 44179 Z= 0.334 Chirality : 0.045 0.283 5130 Planarity : 0.005 0.060 5916 Dihedral : 10.194 176.169 4901 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.03 % Allowed : 21.13 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.13), residues: 4464 helix: 0.36 (0.12), residues: 1896 sheet: -1.82 (0.19), residues: 615 loop : -1.20 (0.15), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 560 TYR 0.022 0.002 TYR F 244 PHE 0.019 0.002 PHE B 290 TRP 0.019 0.002 TRP B 454 HIS 0.012 0.001 HIS D 499 Details of bonding type rmsd covalent geometry : bond 0.00411 (32488) covalent geometry : angle 0.66721 (44167) SS BOND : bond 0.03438 ( 6) SS BOND : angle 7.44505 ( 12) hydrogen bonds : bond 0.04157 ( 1576) hydrogen bonds : angle 5.16920 ( 4464) Misc. bond : bond 0.00478 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7924.20 seconds wall clock time: 136 minutes 20.87 seconds (8180.87 seconds total)