Starting phenix.real_space_refine on Fri Jul 26 07:10:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqx_17827/07_2024/8pqx_17827.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqx_17827/07_2024/8pqx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqx_17827/07_2024/8pqx_17827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqx_17827/07_2024/8pqx_17827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqx_17827/07_2024/8pqx_17827.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqx_17827/07_2024/8pqx_17827.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 25 5.49 5 S 138 5.16 5 C 19836 2.51 5 N 5808 2.21 5 O 6231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 1.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 32038 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5285 Classifications: {'peptide': 746} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 704} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 586 Unresolved non-hydrogen angles: 744 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 316 Chain: "B" Number of atoms: 5285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5285 Classifications: {'peptide': 746} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 704} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 586 Unresolved non-hydrogen angles: 744 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 316 Chain: "C" Number of atoms: 5285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5285 Classifications: {'peptide': 746} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 704} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 586 Unresolved non-hydrogen angles: 744 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 316 Chain: "D" Number of atoms: 5285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5285 Classifications: {'peptide': 746} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 704} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 586 Unresolved non-hydrogen angles: 744 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 316 Chain: "E" Number of atoms: 5285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5285 Classifications: {'peptide': 746} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 704} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 586 Unresolved non-hydrogen angles: 744 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 316 Chain: "F" Number of atoms: 5285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5285 Classifications: {'peptide': 746} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 704} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 586 Unresolved non-hydrogen angles: 744 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 316 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.49, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 13.49 Conformation dependent library (CDL) restraints added in 6.3 seconds 8928 Ramachandran restraints generated. 4464 Oldfield, 0 Emsley, 4464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8376 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 35 sheets defined 50.4% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.51 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: 14.00 Time building geometry restraints manager: 14.69 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: 99.75 - 107.70: 1326 107.70 - 115.65: 19950 115.65 - 123.60: 22165 123.60 - 131.55: 683 131.55 - 139.50: 43 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 21 through 766 or resid 902)) selection = (chain 'B' and (resid 21 through 766 or resid 902)) selection = (chain 'C' and (resid 21 through 766 or resid 902)) selection = (chain 'D' and (resid 21 through 766 or resid 902)) selection = (chain 'E' and (resid 21 through 766 or resid 902)) selection = (chain 'F' and (resid 21 through 766 or resid 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 1.350 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 88.790 Find NCS groups from input model: 2.770 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.300 ------------------------------------------------------------------------------- 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 32488 Z= 0.197 Angle : 0.612 8.796 44167 Z= 0.321 Chirality : 0.043 0.274 5130 Planarity : 0.003 0.048 5916 Dihedral : 14.113 150.181 11567 Min Nonbonded Distance : 0.565 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.06 % Favored : 91.89 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.13), residues: 4464 helix: 1.14 (0.12), residues: 1921 sheet: -1.75 (0.20), residues: 587 loop : -1.72 (0.15), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 454 HIS 0.002 0.001 HIS D 384 PHE 0.013 0.001 PHE A 230 TYR 0.006 0.001 TYR E 203 ARG 0.003 0.000 ARG F 313 *********************** 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 fitting. rotamer outliers: 0 poor density : 891 time to evaluate : 3.376 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: 0.5390 time to fit residues: 715.4864 Evaluate side-chains 534 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 534 time to evaluate : 3.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 20.0000 chunk 336 optimal weight: 6.9990 chunk 186 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 227 optimal weight: 20.0000 chunk 179 optimal weight: 5.9990 chunk 348 optimal weight: 0.7980 chunk 134 optimal weight: 0.0870 chunk 211 optimal weight: 0.8980 chunk 259 optimal weight: 5.9990 chunk 403 optimal weight: 0.8980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 327 GLN A 348 ASN ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 ASN A 641 GLN ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN B 460 ASN B 494 GLN B 602 ASN B 616 ASN B 624 ASN C 460 ASN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN E 460 ASN E 538 ASN ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5193 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 32488 Z= 0.224 Angle : 0.628 7.800 44167 Z= 0.312 Chirality : 0.045 0.212 5130 Planarity : 0.005 0.069 5916 Dihedral : 10.092 154.660 4901 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.78 % Allowed : 10.10 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.13), residues: 4464 helix: 0.92 (0.12), residues: 1914 sheet: -1.55 (0.19), residues: 602 loop : -1.26 (0.15), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 454 HIS 0.005 0.001 HIS E 340 PHE 0.015 0.001 PHE B 503 TYR 0.014 0.002 TYR B 244 ARG 0.006 0.000 ARG E 365 *********************** 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 606 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 556 time to evaluate : 3.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8020 (mmtt) cc_final: 0.7277 (tttt) REVERT: A 265 PHE cc_start: 0.7258 (t80) cc_final: 0.6799 (t80) REVERT: A 281 GLU cc_start: 0.5647 (tp30) cc_final: 0.5144 (mm-30) REVERT: A 288 LYS cc_start: 0.6532 (mtmm) cc_final: 0.6308 (pttm) REVERT: A 304 ASP cc_start: 0.6234 (p0) cc_final: 0.5544 (t0) REVERT: A 307 ASP cc_start: 0.7167 (p0) cc_final: 0.5764 (t70) REVERT: A 319 GLU cc_start: 0.4982 (tm-30) cc_final: 0.4576 (tp30) REVERT: A 364 ASP cc_start: 0.5093 (m-30) cc_final: 0.3916 (t0) REVERT: A 366 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6044 (mp0) REVERT: A 401 ASN cc_start: 0.7411 (m-40) cc_final: 0.6724 (t0) REVERT: A 410 ASP cc_start: 0.7418 (t0) cc_final: 0.6532 (m-30) REVERT: A 450 ASP cc_start: 0.7050 (m-30) cc_final: 0.6387 (p0) REVERT: A 484 ASP cc_start: 0.7113 (p0) cc_final: 0.6458 (m-30) REVERT: A 534 GLU cc_start: 0.6564 (tt0) cc_final: 0.5960 (tt0) REVERT: A 554 GLU cc_start: 0.5915 (mm-30) cc_final: 0.5561 (mm-30) REVERT: A 635 ARG cc_start: 0.6104 (mmm-85) cc_final: 0.5699 (mmt90) REVERT: A 651 LYS cc_start: 0.7501 (mppt) cc_final: 0.7249 (mttm) REVERT: A 720 MET cc_start: -0.0126 (tpt) cc_final: -0.0519 (mmp) REVERT: A 730 GLU cc_start: 0.6681 (mt-10) cc_final: 0.6359 (pm20) REVERT: A 744 ARG cc_start: 0.3354 (mtt90) cc_final: 0.3063 (ptp-170) REVERT: A 757 MET cc_start: 0.6940 (ppp) cc_final: 0.5597 (mtm) REVERT: B 239 ARG cc_start: 0.5908 (mtt180) cc_final: 0.5287 (mtt-85) REVERT: B 252 THR cc_start: 0.8104 (t) cc_final: 0.7494 (m) REVERT: B 265 PHE cc_start: 0.7301 (t80) cc_final: 0.6834 (t80) REVERT: B 288 LYS cc_start: 0.7332 (mtmm) cc_final: 0.6832 (ttpp) REVERT: B 304 ASP cc_start: 0.7004 (p0) cc_final: 0.6481 (t0) REVERT: B 354 ASP cc_start: 0.7848 (t70) cc_final: 0.7521 (t0) REVERT: B 478 ASP cc_start: 0.7535 (t0) cc_final: 0.6890 (m-30) REVERT: B 488 GLU cc_start: 0.6588 (tp30) cc_final: 0.6333 (tp30) REVERT: B 504 LEU cc_start: 0.8029 (tp) cc_final: 0.7654 (mt) REVERT: B 663 LYS cc_start: 0.5922 (pttp) cc_final: 0.4986 (pttm) REVERT: C 241 ILE cc_start: 0.7133 (mt) cc_final: 0.6831 (mt) REVERT: C 252 THR cc_start: 0.8095 (t) cc_final: 0.7586 (m) REVERT: C 265 PHE cc_start: 0.6846 (t80) cc_final: 0.6561 (t80) REVERT: C 267 PHE cc_start: 0.7333 (t80) cc_final: 0.6908 (t80) REVERT: C 273 GLU cc_start: 0.6619 (tp30) cc_final: 0.5632 (pt0) REVERT: C 305 GLU cc_start: 0.6865 (mm-30) cc_final: 0.6353 (mt-10) REVERT: C 317 HIS cc_start: 0.3217 (t-90) cc_final: 0.2615 (m-70) REVERT: C 323 ARG cc_start: 0.6258 (ttp-170) cc_final: 0.5605 (ttm-80) REVERT: C 365 ARG cc_start: 0.6062 (OUTLIER) cc_final: 0.5686 (mtm110) REVERT: C 450 ASP cc_start: 0.7782 (m-30) cc_final: 0.7288 (t0) REVERT: C 536 GLN cc_start: 0.6840 (mm110) cc_final: 0.6303 (mm-40) REVERT: C 550 MET cc_start: 0.6953 (mtm) cc_final: 0.6736 (mtp) REVERT: C 558 ASN cc_start: 0.6748 (m110) cc_final: 0.6229 (t0) REVERT: C 586 ARG cc_start: 0.6723 (ttp80) cc_final: 0.6501 (ptm-80) REVERT: C 664 SER cc_start: 0.8014 (p) cc_final: 0.7149 (p) REVERT: C 720 MET cc_start: -0.0195 (tpt) cc_final: -0.0544 (tpt) REVERT: C 740 MET cc_start: 0.7066 (mmp) cc_final: 0.6140 (mmm) REVERT: C 742 PHE cc_start: 0.6936 (OUTLIER) cc_final: 0.6304 (t80) REVERT: C 748 SER cc_start: 0.6329 (t) cc_final: 0.5979 (t) REVERT: D 267 PHE cc_start: 0.7402 (t80) cc_final: 0.6942 (t80) REVERT: D 315 LYS cc_start: 0.6258 (tmtt) cc_final: 0.5764 (tmtt) REVERT: D 317 HIS cc_start: 0.4541 (t-90) cc_final: 0.3854 (m90) REVERT: D 340 HIS cc_start: 0.5339 (t70) cc_final: 0.4946 (t70) REVERT: D 487 ARG cc_start: 0.7229 (ttp80) cc_final: 0.6874 (mtm110) REVERT: D 490 GLN cc_start: 0.7359 (mt0) cc_final: 0.6891 (mt0) REVERT: D 499 HIS cc_start: 0.7337 (m90) cc_final: 0.7066 (m-70) REVERT: D 502 LYS cc_start: 0.6822 (mmtp) cc_final: 0.6467 (mmmm) REVERT: D 506 PHE cc_start: 0.6266 (m-80) cc_final: 0.6051 (m-80) REVERT: D 543 LYS cc_start: 0.6924 (mttp) cc_final: 0.6325 (mmtt) REVERT: D 554 GLU cc_start: 0.6129 (mm-30) cc_final: 0.4868 (tp30) REVERT: D 556 GLU cc_start: 0.5980 (pt0) cc_final: 0.5406 (mp0) REVERT: D 578 GLU cc_start: 0.6966 (tp30) cc_final: 0.6077 (mp0) REVERT: D 668 LYS cc_start: 0.6936 (mmtm) cc_final: 0.6014 (tttp) REVERT: D 708 ARG cc_start: 0.5351 (ttp80) cc_final: 0.5144 (tmm160) REVERT: D 740 MET cc_start: 0.7197 (mmp) cc_final: 0.6892 (mmm) REVERT: E 210 ARG cc_start: 0.6575 (tpp-160) cc_final: 0.6295 (mtm110) REVERT: E 252 THR cc_start: 0.7974 (t) cc_final: 0.7428 (m) REVERT: E 267 PHE cc_start: 0.7305 (t80) cc_final: 0.6888 (t80) REVERT: E 273 GLU cc_start: 0.6527 (tp30) cc_final: 0.5606 (mt-10) REVERT: E 288 LYS cc_start: 0.6821 (mtmm) cc_final: 0.6268 (mtpp) REVERT: E 292 GLU cc_start: 0.6775 (mt-10) cc_final: 0.6521 (mp0) REVERT: E 304 ASP cc_start: 0.6536 (p0) cc_final: 0.6134 (t0) REVERT: E 340 HIS cc_start: 0.5475 (t70) cc_final: 0.5172 (t70) REVERT: E 359 ARG cc_start: 0.6771 (ttt180) cc_final: 0.6453 (ttp-170) REVERT: E 483 GLU cc_start: 0.7235 (tp30) cc_final: 0.6839 (mp0) REVERT: E 484 ASP cc_start: 0.7267 (p0) cc_final: 0.6854 (t70) REVERT: E 505 LYS cc_start: 0.7510 (tptp) cc_final: 0.6931 (ttpt) REVERT: E 529 LYS cc_start: 0.6200 (mtpp) cc_final: 0.5880 (mttt) REVERT: E 543 LYS cc_start: 0.7383 (mttp) cc_final: 0.7099 (mttm) REVERT: E 554 GLU cc_start: 0.6373 (mm-30) cc_final: 0.6079 (tt0) REVERT: E 558 ASN cc_start: 0.7473 (m110) cc_final: 0.7208 (m110) REVERT: E 560 ARG cc_start: 0.5958 (tpt170) cc_final: 0.5567 (tpt170) REVERT: E 564 ASP cc_start: 0.7247 (m-30) cc_final: 0.6888 (m-30) REVERT: E 598 ASP cc_start: 0.6347 (m-30) cc_final: 0.5781 (m-30) REVERT: E 696 LYS cc_start: 0.6824 (ttpt) cc_final: 0.6301 (ttpp) REVERT: E 757 MET cc_start: 0.6993 (ppp) cc_final: 0.5499 (mtp) REVERT: F 221 GLU cc_start: 0.6379 (tp30) cc_final: 0.6004 (tp30) REVERT: F 236 LYS cc_start: 0.7044 (mmtt) cc_final: 0.6301 (mttp) REVERT: F 242 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6212 (tt) REVERT: F 244 TYR cc_start: 0.6959 (p90) cc_final: 0.6617 (p90) REVERT: F 288 LYS cc_start: 0.7538 (mtmm) cc_final: 0.6999 (pptt) REVERT: F 291 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7105 (mm-30) REVERT: F 304 ASP cc_start: 0.6600 (p0) cc_final: 0.6275 (t0) REVERT: F 389 LYS cc_start: 0.5394 (tttt) cc_final: 0.4450 (mptt) REVERT: F 392 ASP cc_start: 0.6724 (p0) cc_final: 0.6357 (t0) REVERT: F 410 ASP cc_start: 0.7457 (t0) cc_final: 0.6914 (m-30) REVERT: F 465 ARG cc_start: 0.6099 (ptm160) cc_final: 0.5268 (ptp-170) REVERT: F 478 ASP cc_start: 0.8083 (t0) cc_final: 0.7794 (t0) REVERT: F 487 ARG cc_start: 0.7086 (ttp80) cc_final: 0.6848 (ptp90) REVERT: F 502 LYS cc_start: 0.7086 (mmtp) cc_final: 0.6736 (ttmm) REVERT: F 561 GLU cc_start: 0.6817 (pm20) cc_final: 0.6263 (mp0) REVERT: F 568 GLN cc_start: 0.7364 (mm-40) cc_final: 0.6887 (mt0) REVERT: F 578 GLU cc_start: 0.6622 (tp30) cc_final: 0.5821 (tt0) REVERT: F 624 ASN cc_start: 0.6660 (m-40) cc_final: 0.6309 (m-40) REVERT: F 669 ASP cc_start: 0.6786 (t70) cc_final: 0.6258 (m-30) REVERT: F 741 ARG cc_start: 0.5995 (mmp-170) cc_final: 0.5660 (mmp80) REVERT: F 758 PHE cc_start: 0.6553 (t80) cc_final: 0.6273 (t80) outliers start: 50 outliers final: 28 residues processed: 578 average time/residue: 0.4684 time to fit residues: 416.6055 Evaluate side-chains 508 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 477 time to evaluate : 3.692 ------------------------------------------------------------------------------- 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 457 SER Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain B residue 307 ASP 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 365 ARG Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 649 ASP Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain D residue 484 ASP 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 224 optimal weight: 30.0000 chunk 125 optimal weight: 0.6980 chunk 335 optimal weight: 0.7980 chunk 274 optimal weight: 0.6980 chunk 111 optimal weight: 0.0870 chunk 403 optimal weight: 1.9990 chunk 436 optimal weight: 0.9980 chunk 359 optimal weight: 1.9990 chunk 400 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 324 optimal weight: 3.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 460 ASN B 558 ASN B 624 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN D 624 ASN D 692 GLN ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN F 460 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5220 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 32488 Z= 0.207 Angle : 0.589 7.331 44167 Z= 0.291 Chirality : 0.044 0.196 5130 Planarity : 0.004 0.071 5916 Dihedral : 9.830 155.698 4901 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.21 % Allowed : 11.03 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.13), residues: 4464 helix: 0.88 (0.12), residues: 1915 sheet: -1.43 (0.19), residues: 572 loop : -1.15 (0.15), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 454 HIS 0.006 0.001 HIS E 406 PHE 0.020 0.001 PHE C 360 TYR 0.010 0.001 TYR D 244 ARG 0.009 0.000 ARG F 465 *********************** 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 577 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 515 time to evaluate : 3.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8038 (mmtt) cc_final: 0.7282 (tttt) REVERT: A 265 PHE cc_start: 0.7322 (t80) cc_final: 0.6863 (t80) REVERT: A 281 GLU cc_start: 0.5705 (tp30) cc_final: 0.5173 (mm-30) REVERT: A 304 ASP cc_start: 0.6250 (p0) cc_final: 0.5511 (t0) REVERT: A 307 ASP cc_start: 0.7044 (p0) cc_final: 0.5684 (t70) REVERT: A 322 ARG cc_start: 0.6377 (mtm-85) cc_final: 0.6152 (mtt-85) REVERT: A 364 ASP cc_start: 0.5197 (m-30) cc_final: 0.4122 (t0) REVERT: A 366 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6102 (mp0) REVERT: A 387 ASN cc_start: 0.6729 (OUTLIER) cc_final: 0.6245 (m-40) REVERT: A 401 ASN cc_start: 0.7489 (m-40) cc_final: 0.6742 (t0) REVERT: A 410 ASP cc_start: 0.7505 (t0) cc_final: 0.6580 (m-30) REVERT: A 450 ASP cc_start: 0.7056 (m-30) cc_final: 0.6396 (p0) REVERT: A 484 ASP cc_start: 0.7258 (p0) cc_final: 0.6415 (m-30) REVERT: A 534 GLU cc_start: 0.6562 (tt0) cc_final: 0.5955 (tt0) REVERT: A 554 GLU cc_start: 0.5928 (mm-30) cc_final: 0.5569 (mm-30) REVERT: A 635 ARG cc_start: 0.6048 (mmm-85) cc_final: 0.5546 (mmt90) REVERT: A 651 LYS cc_start: 0.7513 (mppt) cc_final: 0.7251 (mttm) REVERT: A 720 MET cc_start: -0.0123 (tpt) cc_final: -0.0561 (mmp) REVERT: A 730 GLU cc_start: 0.6734 (mt-10) cc_final: 0.6338 (pm20) REVERT: A 757 MET cc_start: 0.6993 (ppp) cc_final: 0.5713 (mtm) REVERT: B 239 ARG cc_start: 0.5932 (mtt180) cc_final: 0.5099 (mtt-85) REVERT: B 252 THR cc_start: 0.8087 (t) cc_final: 0.7484 (m) REVERT: B 265 PHE cc_start: 0.7268 (t80) cc_final: 0.6812 (t80) REVERT: B 288 LYS cc_start: 0.7443 (mtmm) cc_final: 0.6923 (ttpp) REVERT: B 304 ASP cc_start: 0.7111 (p0) cc_final: 0.6518 (t0) REVERT: B 354 ASP cc_start: 0.7841 (t70) cc_final: 0.7547 (t0) REVERT: B 397 GLU cc_start: 0.7223 (tp30) cc_final: 0.6514 (mp0) REVERT: B 460 ASN cc_start: 0.5315 (OUTLIER) cc_final: 0.4923 (m110) REVERT: B 478 ASP cc_start: 0.7559 (t0) cc_final: 0.6880 (m-30) REVERT: B 504 LEU cc_start: 0.8092 (tp) cc_final: 0.7700 (mt) REVERT: B 556 GLU cc_start: 0.6199 (mp0) cc_final: 0.5924 (mp0) REVERT: C 252 THR cc_start: 0.8132 (t) cc_final: 0.7639 (m) REVERT: C 265 PHE cc_start: 0.6892 (t80) cc_final: 0.6631 (t80) REVERT: C 273 GLU cc_start: 0.6666 (tp30) cc_final: 0.5680 (pt0) REVERT: C 281 GLU cc_start: 0.7002 (tp30) cc_final: 0.5869 (tt0) REVERT: C 305 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6303 (mt-10) REVERT: C 317 HIS cc_start: 0.2946 (t-90) cc_final: 0.2454 (m-70) REVERT: C 323 ARG cc_start: 0.6194 (ttp-170) cc_final: 0.5554 (ttm-80) REVERT: C 365 ARG cc_start: 0.5937 (OUTLIER) cc_final: 0.5652 (mtm110) REVERT: C 450 ASP cc_start: 0.7750 (m-30) cc_final: 0.7161 (t0) REVERT: C 506 PHE cc_start: 0.7102 (m-80) cc_final: 0.6875 (m-80) REVERT: C 536 GLN cc_start: 0.6807 (mm110) cc_final: 0.6183 (mm-40) REVERT: C 558 ASN cc_start: 0.6781 (m110) cc_final: 0.6169 (t0) REVERT: C 586 ARG cc_start: 0.6716 (ttp80) cc_final: 0.6475 (ptm-80) REVERT: C 624 ASN cc_start: 0.7158 (m-40) cc_final: 0.6911 (m-40) REVERT: C 686 ASP cc_start: 0.6768 (t0) cc_final: 0.6537 (t0) REVERT: C 720 MET cc_start: -0.0359 (tpt) cc_final: -0.0742 (tpt) REVERT: C 740 MET cc_start: 0.7108 (mmp) cc_final: 0.6171 (mmm) REVERT: C 742 PHE cc_start: 0.6906 (OUTLIER) cc_final: 0.6320 (t80) REVERT: D 267 PHE cc_start: 0.7462 (t80) cc_final: 0.6920 (t80) REVERT: D 315 LYS cc_start: 0.6228 (tmtt) cc_final: 0.5524 (tmtt) REVERT: D 317 HIS cc_start: 0.4428 (t-90) cc_final: 0.3934 (m90) REVERT: D 340 HIS cc_start: 0.5380 (t70) cc_final: 0.5018 (t70) REVERT: D 462 SER cc_start: 0.6614 (m) cc_final: 0.6226 (p) REVERT: D 487 ARG cc_start: 0.7215 (ttp80) cc_final: 0.6858 (mtm110) REVERT: D 490 GLN cc_start: 0.7435 (mt0) cc_final: 0.6985 (mt0) REVERT: D 499 HIS cc_start: 0.7381 (m90) cc_final: 0.7056 (m90) REVERT: D 502 LYS cc_start: 0.6742 (mmtp) cc_final: 0.6501 (mmmm) REVERT: D 543 LYS cc_start: 0.6979 (mttp) cc_final: 0.6365 (mmtt) REVERT: D 554 GLU cc_start: 0.6163 (mm-30) cc_final: 0.4970 (tt0) REVERT: D 556 GLU cc_start: 0.5980 (pt0) cc_final: 0.5469 (mp0) REVERT: D 578 GLU cc_start: 0.6979 (tp30) cc_final: 0.6109 (mp0) REVERT: D 668 LYS cc_start: 0.7045 (mmtm) cc_final: 0.6137 (tttp) REVERT: D 708 ARG cc_start: 0.5390 (ttp80) cc_final: 0.5159 (tmm160) REVERT: D 720 MET cc_start: 0.2129 (mmm) cc_final: 0.1920 (mmp) REVERT: D 740 MET cc_start: 0.7388 (mmp) cc_final: 0.7094 (mmm) REVERT: E 203 TYR cc_start: 0.7487 (m-80) cc_final: 0.7231 (m-80) REVERT: E 210 ARG cc_start: 0.6588 (tpp-160) cc_final: 0.6252 (mtm110) REVERT: E 252 THR cc_start: 0.7970 (t) cc_final: 0.7378 (m) REVERT: E 267 PHE cc_start: 0.7348 (t80) cc_final: 0.6972 (t80) REVERT: E 273 GLU cc_start: 0.6486 (tp30) cc_final: 0.5567 (mt-10) REVERT: E 288 LYS cc_start: 0.6794 (mtmm) cc_final: 0.6263 (mtpp) REVERT: E 291 GLU cc_start: 0.7531 (mt-10) cc_final: 0.6912 (mm-30) REVERT: E 292 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6707 (mp0) REVERT: E 304 ASP cc_start: 0.6575 (p0) cc_final: 0.6230 (t0) REVERT: E 340 HIS cc_start: 0.5462 (t70) cc_final: 0.5218 (t70) REVERT: E 359 ARG cc_start: 0.6702 (ttt180) cc_final: 0.6214 (ttp-170) REVERT: E 373 ASP cc_start: 0.6993 (OUTLIER) cc_final: 0.6743 (p0) REVERT: E 483 GLU cc_start: 0.7363 (tp30) cc_final: 0.6924 (mp0) REVERT: E 484 ASP cc_start: 0.7206 (p0) cc_final: 0.6890 (t70) REVERT: E 505 LYS cc_start: 0.7574 (tptp) cc_final: 0.7167 (ptmt) REVERT: E 529 LYS cc_start: 0.6267 (mtpp) cc_final: 0.5878 (mtmt) REVERT: E 543 LYS cc_start: 0.7386 (mttp) cc_final: 0.6838 (mmmt) REVERT: E 558 ASN cc_start: 0.7531 (m110) cc_final: 0.7199 (m110) REVERT: E 560 ARG cc_start: 0.6029 (tpt170) cc_final: 0.5174 (tpt-90) REVERT: E 561 GLU cc_start: 0.7159 (pt0) cc_final: 0.6717 (pt0) REVERT: E 564 ASP cc_start: 0.7228 (m-30) cc_final: 0.6854 (m-30) REVERT: E 598 ASP cc_start: 0.6553 (m-30) cc_final: 0.6213 (m-30) REVERT: E 674 PHE cc_start: 0.7260 (t80) cc_final: 0.7033 (t80) REVERT: E 677 LYS cc_start: 0.7560 (ttmm) cc_final: 0.7122 (tttm) REVERT: E 696 LYS cc_start: 0.6815 (ttpt) cc_final: 0.6266 (ttpp) REVERT: E 757 MET cc_start: 0.6900 (ppp) cc_final: 0.5520 (mtp) REVERT: F 221 GLU cc_start: 0.6392 (tp30) cc_final: 0.5838 (tp30) REVERT: F 236 LYS cc_start: 0.7188 (mmtt) cc_final: 0.6357 (mttp) REVERT: F 242 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6521 (tt) REVERT: F 244 TYR cc_start: 0.6978 (p90) cc_final: 0.6602 (p90) REVERT: F 288 LYS cc_start: 0.7529 (mtmm) cc_final: 0.7006 (pptt) REVERT: F 291 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7079 (mm-30) REVERT: F 389 LYS cc_start: 0.5547 (tttt) cc_final: 0.4532 (mptt) REVERT: F 392 ASP cc_start: 0.6632 (p0) cc_final: 0.6277 (t0) REVERT: F 410 ASP cc_start: 0.7434 (t0) cc_final: 0.7111 (m-30) REVERT: F 465 ARG cc_start: 0.6289 (ptm160) cc_final: 0.5357 (ptp-170) REVERT: F 487 ARG cc_start: 0.7445 (ttp80) cc_final: 0.7097 (ptp90) REVERT: F 502 LYS cc_start: 0.6995 (mmtp) cc_final: 0.6739 (ttmm) REVERT: F 560 ARG cc_start: 0.5645 (tpt170) cc_final: 0.4720 (ttp80) REVERT: F 561 GLU cc_start: 0.6906 (pm20) cc_final: 0.6107 (mp0) REVERT: F 567 ARG cc_start: 0.6230 (ttp80) cc_final: 0.5385 (ttm-80) REVERT: F 568 GLN cc_start: 0.7446 (mm-40) cc_final: 0.6938 (mt0) REVERT: F 578 GLU cc_start: 0.6571 (tp30) cc_final: 0.5773 (tt0) REVERT: F 624 ASN cc_start: 0.6574 (m-40) cc_final: 0.6168 (m-40) REVERT: F 669 ASP cc_start: 0.6891 (t70) cc_final: 0.6257 (m-30) REVERT: F 741 ARG cc_start: 0.5981 (mmp-170) cc_final: 0.5625 (mmp80) REVERT: F 758 PHE cc_start: 0.6497 (t80) cc_final: 0.6095 (t80) outliers start: 62 outliers final: 34 residues processed: 541 average time/residue: 0.5282 time to fit residues: 447.0476 Evaluate side-chains 504 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 464 time to evaluate : 3.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 649 ASP Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 484 ASP 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 373 ASP Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 353 ILE 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 752 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 0.0980 chunk 303 optimal weight: 20.0000 chunk 209 optimal weight: 3.9990 chunk 44 optimal weight: 0.0270 chunk 192 optimal weight: 0.4980 chunk 271 optimal weight: 3.9990 chunk 405 optimal weight: 4.9990 chunk 429 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 384 optimal weight: 30.0000 chunk 115 optimal weight: 9.9990 overall best weight: 1.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN A 538 ASN A 624 ASN A 750 ASN B 348 ASN B 384 HIS ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5333 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 32488 Z= 0.336 Angle : 0.667 10.189 44167 Z= 0.330 Chirality : 0.047 0.270 5130 Planarity : 0.005 0.060 5916 Dihedral : 10.104 163.312 4901 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.78 % Allowed : 13.28 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.13), residues: 4464 helix: 0.54 (0.12), residues: 1920 sheet: -1.64 (0.19), residues: 632 loop : -1.04 (0.15), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 454 HIS 0.008 0.002 HIS C 340 PHE 0.024 0.002 PHE C 360 TYR 0.016 0.002 TYR A 203 ARG 0.006 0.001 ARG A 362 *********************** 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 571 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 493 time to evaluate : 3.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8131 (mmtt) cc_final: 0.6965 (mmtm) REVERT: A 265 PHE cc_start: 0.7415 (t80) cc_final: 0.6973 (t80) REVERT: A 281 GLU cc_start: 0.5728 (tp30) cc_final: 0.5246 (mm-30) REVERT: A 287 ARG cc_start: 0.6196 (mtt180) cc_final: 0.5800 (mtp-110) REVERT: A 288 LYS cc_start: 0.7107 (mtmm) cc_final: 0.6786 (pttm) REVERT: A 304 ASP cc_start: 0.6318 (p0) cc_final: 0.5736 (t0) REVERT: A 307 ASP cc_start: 0.7258 (p0) cc_final: 0.6018 (t70) REVERT: A 327 GLN cc_start: 0.6389 (tp40) cc_final: 0.5994 (tp-100) REVERT: A 364 ASP cc_start: 0.5671 (m-30) cc_final: 0.4692 (t0) REVERT: A 387 ASN cc_start: 0.6987 (OUTLIER) cc_final: 0.6678 (m-40) REVERT: A 401 ASN cc_start: 0.7591 (m-40) cc_final: 0.6692 (t0) REVERT: A 410 ASP cc_start: 0.7650 (t0) cc_final: 0.6700 (m-30) REVERT: A 450 ASP cc_start: 0.7151 (m-30) cc_final: 0.6595 (p0) REVERT: A 534 GLU cc_start: 0.6460 (tt0) cc_final: 0.5957 (tt0) REVERT: A 554 GLU cc_start: 0.6210 (mm-30) cc_final: 0.5758 (mm-30) REVERT: A 556 GLU cc_start: 0.4694 (pt0) cc_final: 0.4397 (pm20) REVERT: A 635 ARG cc_start: 0.6069 (mmm-85) cc_final: 0.5400 (mmt90) REVERT: A 651 LYS cc_start: 0.7571 (mppt) cc_final: 0.7241 (mmtp) REVERT: A 720 MET cc_start: -0.0046 (tpt) cc_final: -0.0563 (mmt) REVERT: A 730 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6307 (pm20) REVERT: A 757 MET cc_start: 0.7019 (ppp) cc_final: 0.5924 (mtm) REVERT: B 239 ARG cc_start: 0.5971 (mtt180) cc_final: 0.5177 (mtt-85) REVERT: B 252 THR cc_start: 0.8197 (t) cc_final: 0.7484 (m) REVERT: B 256 ARG cc_start: 0.6459 (ttm-80) cc_final: 0.5962 (mtt-85) REVERT: B 265 PHE cc_start: 0.7146 (t80) cc_final: 0.6646 (t80) REVERT: B 304 ASP cc_start: 0.6995 (p0) cc_final: 0.6441 (t0) REVERT: B 397 GLU cc_start: 0.7338 (tp30) cc_final: 0.6766 (mp0) REVERT: B 460 ASN cc_start: 0.6065 (OUTLIER) cc_final: 0.5583 (m-40) REVERT: B 478 ASP cc_start: 0.7492 (t0) cc_final: 0.6855 (m-30) REVERT: B 504 LEU cc_start: 0.8107 (tp) cc_final: 0.7668 (mt) REVERT: B 740 MET cc_start: 0.7339 (mmm) cc_final: 0.7093 (mmm) REVERT: C 230 PHE cc_start: 0.6881 (OUTLIER) cc_final: 0.5880 (m-80) REVERT: C 265 PHE cc_start: 0.6977 (t80) cc_final: 0.6721 (t80) REVERT: C 267 PHE cc_start: 0.7751 (t80) cc_final: 0.7425 (t80) REVERT: C 273 GLU cc_start: 0.6855 (tp30) cc_final: 0.5741 (pt0) REVERT: C 305 GLU cc_start: 0.6777 (mm-30) cc_final: 0.6158 (mt-10) REVERT: C 401 ASN cc_start: 0.6253 (m-40) cc_final: 0.5923 (m110) REVERT: C 450 ASP cc_start: 0.7896 (m-30) cc_final: 0.7186 (t0) REVERT: C 558 ASN cc_start: 0.6879 (m110) cc_final: 0.6108 (t0) REVERT: C 577 ASP cc_start: 0.7167 (t0) cc_final: 0.6799 (t70) REVERT: C 624 ASN cc_start: 0.7443 (m-40) cc_final: 0.7146 (m110) REVERT: C 686 ASP cc_start: 0.6911 (t0) cc_final: 0.6673 (t0) REVERT: C 720 MET cc_start: -0.0812 (tpt) cc_final: -0.1161 (tpt) REVERT: C 742 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6439 (t80) REVERT: D 236 LYS cc_start: 0.6244 (mmtt) cc_final: 0.5491 (mmtm) REVERT: D 265 PHE cc_start: 0.6821 (t80) cc_final: 0.6566 (t80) REVERT: D 315 LYS cc_start: 0.6384 (tmtt) cc_final: 0.5815 (tmtt) REVERT: D 317 HIS cc_start: 0.4427 (t-90) cc_final: 0.3789 (m90) REVERT: D 340 HIS cc_start: 0.5317 (t70) cc_final: 0.5008 (t70) REVERT: D 382 GLN cc_start: 0.6898 (mt0) cc_final: 0.6676 (mp10) REVERT: D 398 GLN cc_start: 0.7289 (tt0) cc_final: 0.6938 (tm-30) REVERT: D 462 SER cc_start: 0.6964 (m) cc_final: 0.6738 (p) REVERT: D 499 HIS cc_start: 0.7478 (m90) cc_final: 0.7238 (m90) REVERT: D 534 GLU cc_start: 0.6228 (tt0) cc_final: 0.5709 (tt0) REVERT: D 543 LYS cc_start: 0.6900 (mttp) cc_final: 0.6234 (mmtt) REVERT: D 554 GLU cc_start: 0.6249 (mm-30) cc_final: 0.5015 (tt0) REVERT: D 556 GLU cc_start: 0.6217 (pt0) cc_final: 0.5718 (pm20) REVERT: D 578 GLU cc_start: 0.7159 (tp30) cc_final: 0.6581 (mt-10) REVERT: D 668 LYS cc_start: 0.7312 (mmtm) cc_final: 0.6477 (tttm) REVERT: D 708 ARG cc_start: 0.5383 (ttp80) cc_final: 0.4997 (tmm160) REVERT: E 210 ARG cc_start: 0.6596 (tpp-160) cc_final: 0.6165 (mtm110) REVERT: E 268 LEU cc_start: 0.8485 (tp) cc_final: 0.8256 (tp) REVERT: E 273 GLU cc_start: 0.6609 (tp30) cc_final: 0.5615 (mt-10) REVERT: E 291 GLU cc_start: 0.7510 (mt-10) cc_final: 0.6500 (mm-30) REVERT: E 321 GLU cc_start: 0.6576 (mp0) cc_final: 0.5995 (mp0) REVERT: E 340 HIS cc_start: 0.5556 (t70) cc_final: 0.5353 (t70) REVERT: E 373 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6815 (p0) REVERT: E 483 GLU cc_start: 0.7575 (tp30) cc_final: 0.7027 (mp0) REVERT: E 484 ASP cc_start: 0.7227 (p0) cc_final: 0.7001 (t70) REVERT: E 505 LYS cc_start: 0.7439 (tptp) cc_final: 0.7017 (ptmt) REVERT: E 529 LYS cc_start: 0.6556 (mtpp) cc_final: 0.6124 (mtmt) REVERT: E 543 LYS cc_start: 0.7304 (mttp) cc_final: 0.6822 (mttm) REVERT: E 560 ARG cc_start: 0.6121 (tpt170) cc_final: 0.5807 (tpt170) REVERT: E 561 GLU cc_start: 0.7268 (pt0) cc_final: 0.6974 (pt0) REVERT: E 677 LYS cc_start: 0.7514 (ttmm) cc_final: 0.7127 (tttm) REVERT: E 696 LYS cc_start: 0.6856 (ttpt) cc_final: 0.6651 (ttpp) REVERT: E 738 GLU cc_start: 0.4931 (tp30) cc_final: 0.4700 (tp30) REVERT: E 757 MET cc_start: 0.6823 (ppp) cc_final: 0.5450 (mtp) REVERT: F 210 ARG cc_start: 0.6372 (tpp-160) cc_final: 0.5971 (ttp80) REVERT: F 221 GLU cc_start: 0.6574 (tp30) cc_final: 0.6320 (tp30) REVERT: F 236 LYS cc_start: 0.7647 (mmtt) cc_final: 0.6755 (mttp) REVERT: F 242 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7288 (tt) REVERT: F 244 TYR cc_start: 0.7075 (p90) cc_final: 0.6728 (p90) REVERT: F 268 LEU cc_start: 0.8382 (tp) cc_final: 0.8061 (tp) REVERT: F 288 LYS cc_start: 0.7708 (mtmm) cc_final: 0.7327 (mtmt) REVERT: F 291 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7147 (mt-10) REVERT: F 327 GLN cc_start: 0.5365 (tp40) cc_final: 0.4758 (tp-100) REVERT: F 365 ARG cc_start: 0.5668 (mtm180) cc_final: 0.5065 (mtt180) REVERT: F 389 LYS cc_start: 0.5792 (tttt) cc_final: 0.4663 (mptt) REVERT: F 392 ASP cc_start: 0.6784 (p0) cc_final: 0.6358 (t0) REVERT: F 395 ASP cc_start: 0.5468 (p0) cc_final: 0.5162 (p0) REVERT: F 410 ASP cc_start: 0.7488 (t0) cc_final: 0.7222 (m-30) REVERT: F 487 ARG cc_start: 0.7421 (ttp80) cc_final: 0.7089 (ptp90) REVERT: F 502 LYS cc_start: 0.7134 (mmtp) cc_final: 0.6780 (ttmm) REVERT: F 561 GLU cc_start: 0.6885 (pm20) cc_final: 0.6528 (mp0) REVERT: F 568 GLN cc_start: 0.7481 (mm-40) cc_final: 0.7222 (mm-40) REVERT: F 578 GLU cc_start: 0.6658 (tp30) cc_final: 0.5835 (tt0) REVERT: F 611 MET cc_start: 0.6812 (ttp) cc_final: 0.6575 (ttm) REVERT: F 624 ASN cc_start: 0.6751 (m-40) cc_final: 0.6230 (m-40) REVERT: F 669 ASP cc_start: 0.6774 (t70) cc_final: 0.6117 (m-30) outliers start: 78 outliers final: 45 residues processed: 536 average time/residue: 0.4728 time to fit residues: 389.8941 Evaluate side-chains 484 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 433 time to evaluate : 3.601 ------------------------------------------------------------------------------- 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 373 ASP Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 307 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 373 ASP Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 649 ASP Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 475 THR 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 373 ASP 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 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 357 optimal weight: 0.0670 chunk 243 optimal weight: 0.6980 chunk 6 optimal weight: 40.0000 chunk 319 optimal weight: 0.5980 chunk 177 optimal weight: 9.9990 chunk 366 optimal weight: 0.0020 chunk 296 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 219 optimal weight: 0.9980 chunk 385 optimal weight: 30.0000 chunk 108 optimal weight: 0.7980 overall best weight: 0.4326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN A 624 ASN ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS ** E 443 ASN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5291 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 32488 Z= 0.194 Angle : 0.584 8.130 44167 Z= 0.286 Chirality : 0.044 0.200 5130 Planarity : 0.004 0.062 5916 Dihedral : 9.680 157.558 4901 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.21 % Allowed : 15.63 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.13), residues: 4464 helix: 0.73 (0.12), residues: 1890 sheet: -1.55 (0.19), residues: 572 loop : -0.99 (0.15), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 454 HIS 0.012 0.001 HIS D 404 PHE 0.018 0.001 PHE E 267 TYR 0.009 0.001 TYR D 244 ARG 0.010 0.000 ARG E 625 *********************** 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 540 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 478 time to evaluate : 3.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8065 (mmtt) cc_final: 0.7288 (tttt) REVERT: A 265 PHE cc_start: 0.7372 (t80) cc_final: 0.6949 (t80) REVERT: A 281 GLU cc_start: 0.5783 (tp30) cc_final: 0.5203 (mm-30) REVERT: A 304 ASP cc_start: 0.6303 (p0) cc_final: 0.5687 (t0) REVERT: A 307 ASP cc_start: 0.7234 (p0) cc_final: 0.5980 (t70) REVERT: A 327 GLN cc_start: 0.6284 (tp40) cc_final: 0.6028 (tp-100) REVERT: A 364 ASP cc_start: 0.5475 (m-30) cc_final: 0.4570 (t0) REVERT: A 387 ASN cc_start: 0.6887 (OUTLIER) cc_final: 0.6656 (m-40) REVERT: A 401 ASN cc_start: 0.7559 (m-40) cc_final: 0.6637 (t0) REVERT: A 410 ASP cc_start: 0.7592 (t0) cc_final: 0.6638 (m-30) REVERT: A 442 MET cc_start: 0.3451 (OUTLIER) cc_final: 0.2896 (tmm) REVERT: A 450 ASP cc_start: 0.7129 (m-30) cc_final: 0.6572 (p0) REVERT: A 534 GLU cc_start: 0.6410 (tt0) cc_final: 0.5901 (tt0) REVERT: A 554 GLU cc_start: 0.6062 (mm-30) cc_final: 0.5756 (mm-30) REVERT: A 635 ARG cc_start: 0.6013 (mmm-85) cc_final: 0.5391 (mmt90) REVERT: A 651 LYS cc_start: 0.7558 (mppt) cc_final: 0.7236 (mmtp) REVERT: A 720 MET cc_start: -0.0005 (tpt) cc_final: -0.0514 (mmt) REVERT: A 730 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6346 (pm20) REVERT: A 757 MET cc_start: 0.7005 (ppp) cc_final: 0.5966 (mtm) REVERT: B 239 ARG cc_start: 0.5759 (mtt180) cc_final: 0.5029 (mtt-85) REVERT: B 244 TYR cc_start: 0.6881 (p90) cc_final: 0.6661 (p90) REVERT: B 252 THR cc_start: 0.8104 (t) cc_final: 0.7391 (m) REVERT: B 256 ARG cc_start: 0.6418 (ttm-80) cc_final: 0.5902 (mtt-85) REVERT: B 265 PHE cc_start: 0.7167 (t80) cc_final: 0.6693 (t80) REVERT: B 288 LYS cc_start: 0.7643 (mtmm) cc_final: 0.7049 (ttpt) REVERT: B 304 ASP cc_start: 0.7021 (p0) cc_final: 0.6466 (t0) REVERT: B 397 GLU cc_start: 0.7423 (tp30) cc_final: 0.6834 (mp0) REVERT: B 478 ASP cc_start: 0.7449 (t0) cc_final: 0.6834 (m-30) REVERT: B 504 LEU cc_start: 0.8102 (tp) cc_final: 0.7645 (mt) REVERT: B 561 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6464 (pm20) REVERT: B 634 LEU cc_start: 0.6999 (mt) cc_final: 0.6672 (mt) REVERT: C 230 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.5823 (m-80) REVERT: C 265 PHE cc_start: 0.6994 (t80) cc_final: 0.6731 (t80) REVERT: C 273 GLU cc_start: 0.6819 (tp30) cc_final: 0.5725 (pt0) REVERT: C 305 GLU cc_start: 0.6724 (mm-30) cc_final: 0.6101 (mt-10) REVERT: C 323 ARG cc_start: 0.6112 (ttp-170) cc_final: 0.5395 (ttm-80) REVERT: C 401 ASN cc_start: 0.6165 (m-40) cc_final: 0.5836 (m110) REVERT: C 450 ASP cc_start: 0.7946 (m-30) cc_final: 0.7580 (m-30) REVERT: C 536 GLN cc_start: 0.6905 (mm110) cc_final: 0.6180 (mm-40) REVERT: C 558 ASN cc_start: 0.6873 (m110) cc_final: 0.6144 (t0) REVERT: C 586 ARG cc_start: 0.6850 (ttp80) cc_final: 0.6498 (ptm-80) REVERT: C 624 ASN cc_start: 0.7213 (m-40) cc_final: 0.6856 (m110) REVERT: C 662 ARG cc_start: 0.7603 (ptp90) cc_final: 0.7385 (ttp-170) REVERT: C 686 ASP cc_start: 0.6876 (t0) cc_final: 0.6628 (t0) REVERT: C 720 MET cc_start: -0.0863 (tpt) cc_final: -0.1217 (tpt) REVERT: C 740 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.6891 (mpp) REVERT: C 742 PHE cc_start: 0.6915 (OUTLIER) cc_final: 0.6300 (t80) REVERT: D 236 LYS cc_start: 0.6178 (mmtt) cc_final: 0.5482 (mmtm) REVERT: D 265 PHE cc_start: 0.6698 (t80) cc_final: 0.6462 (t80) REVERT: D 315 LYS cc_start: 0.6324 (tmtt) cc_final: 0.5723 (tmtt) REVERT: D 317 HIS cc_start: 0.4528 (t-90) cc_final: 0.3859 (m90) REVERT: D 340 HIS cc_start: 0.5277 (t70) cc_final: 0.4960 (t70) REVERT: D 358 ARG cc_start: 0.6663 (mtp180) cc_final: 0.6408 (mtm180) REVERT: D 462 SER cc_start: 0.6602 (m) cc_final: 0.6327 (p) REVERT: D 543 LYS cc_start: 0.6922 (mttp) cc_final: 0.6196 (mmtt) REVERT: D 554 GLU cc_start: 0.6156 (mm-30) cc_final: 0.4896 (tt0) REVERT: D 556 GLU cc_start: 0.5978 (pt0) cc_final: 0.5501 (pm20) REVERT: D 578 GLU cc_start: 0.6971 (tp30) cc_final: 0.6147 (mp0) REVERT: D 668 LYS cc_start: 0.7235 (mmtm) cc_final: 0.6356 (tttm) REVERT: D 708 ARG cc_start: 0.5444 (ttp80) cc_final: 0.5036 (tmm160) REVERT: D 734 ASP cc_start: 0.7267 (t0) cc_final: 0.6983 (t0) REVERT: E 210 ARG cc_start: 0.6609 (tpp-160) cc_final: 0.6158 (mtm110) REVERT: E 273 GLU cc_start: 0.6516 (tp30) cc_final: 0.6144 (tt0) REVERT: E 291 GLU cc_start: 0.7506 (mt-10) cc_final: 0.6784 (mm-30) REVERT: E 292 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6451 (pt0) REVERT: E 340 HIS cc_start: 0.5368 (t70) cc_final: 0.5161 (t70) REVERT: E 373 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6855 (p0) REVERT: E 483 GLU cc_start: 0.7562 (tp30) cc_final: 0.7020 (mp0) REVERT: E 484 ASP cc_start: 0.7206 (p0) cc_final: 0.6937 (t70) REVERT: E 505 LYS cc_start: 0.7434 (tptp) cc_final: 0.7001 (ptmt) REVERT: E 529 LYS cc_start: 0.6489 (mtpp) cc_final: 0.6074 (mtmt) REVERT: E 543 LYS cc_start: 0.7254 (mttp) cc_final: 0.6783 (mttm) REVERT: E 554 GLU cc_start: 0.6555 (mm-30) cc_final: 0.6071 (tt0) REVERT: E 560 ARG cc_start: 0.6015 (tpt170) cc_final: 0.5796 (tpt170) REVERT: E 561 GLU cc_start: 0.7251 (pt0) cc_final: 0.6963 (pt0) REVERT: E 578 GLU cc_start: 0.6703 (tp30) cc_final: 0.5866 (mt-10) REVERT: E 677 LYS cc_start: 0.7483 (ttmm) cc_final: 0.7098 (tttm) REVERT: E 757 MET cc_start: 0.6779 (ppp) cc_final: 0.5452 (mtp) REVERT: F 210 ARG cc_start: 0.6321 (tpp-160) cc_final: 0.5944 (ttp80) REVERT: F 221 GLU cc_start: 0.6395 (tp30) cc_final: 0.5931 (tp30) REVERT: F 236 LYS cc_start: 0.7613 (mmtt) cc_final: 0.6707 (mttp) REVERT: F 244 TYR cc_start: 0.7029 (p90) cc_final: 0.6762 (p90) REVERT: F 268 LEU cc_start: 0.8149 (tp) cc_final: 0.7866 (tp) REVERT: F 288 LYS cc_start: 0.7660 (mtmm) cc_final: 0.7307 (mttm) REVERT: F 291 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7109 (mt-10) REVERT: F 327 GLN cc_start: 0.5295 (tp40) cc_final: 0.4708 (tp-100) REVERT: F 358 ARG cc_start: 0.7185 (mtp-110) cc_final: 0.6921 (mtp-110) REVERT: F 365 ARG cc_start: 0.5692 (mtm180) cc_final: 0.4958 (mtt180) REVERT: F 378 LEU cc_start: 0.7584 (tt) cc_final: 0.7280 (mt) REVERT: F 389 LYS cc_start: 0.5707 (tttt) cc_final: 0.4544 (mptt) REVERT: F 392 ASP cc_start: 0.6784 (p0) cc_final: 0.6335 (t0) REVERT: F 395 ASP cc_start: 0.5507 (p0) cc_final: 0.5249 (p0) REVERT: F 410 ASP cc_start: 0.7510 (t0) cc_final: 0.7079 (m-30) REVERT: F 465 ARG cc_start: 0.6672 (ptt180) cc_final: 0.5919 (ptp-170) REVERT: F 487 ARG cc_start: 0.7365 (ttp80) cc_final: 0.7040 (ptp90) REVERT: F 502 LYS cc_start: 0.7084 (mmtp) cc_final: 0.6762 (ttmm) REVERT: F 560 ARG cc_start: 0.6082 (tpt170) cc_final: 0.5166 (ttp80) REVERT: F 561 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6457 (mp0) REVERT: F 568 GLN cc_start: 0.7499 (mm-40) cc_final: 0.7281 (mm-40) REVERT: F 578 GLU cc_start: 0.6643 (tp30) cc_final: 0.5943 (tt0) REVERT: F 611 MET cc_start: 0.6692 (ttp) cc_final: 0.6231 (ptp) REVERT: F 624 ASN cc_start: 0.6579 (m-40) cc_final: 0.6158 (m-40) REVERT: F 669 ASP cc_start: 0.6689 (OUTLIER) cc_final: 0.6119 (m-30) outliers start: 62 outliers final: 36 residues processed: 514 average time/residue: 0.4775 time to fit residues: 379.5593 Evaluate side-chains 483 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 438 time to evaluate : 3.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 457 SER 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 640 ASP Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 649 ASP Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 690 ILE Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 598 ASP Chi-restraints excluded: chain F residue 669 ASP 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 144 optimal weight: 6.9990 chunk 386 optimal weight: 2.9990 chunk 84 optimal weight: 0.0060 chunk 251 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 429 optimal weight: 0.1980 chunk 356 optimal weight: 0.8980 chunk 198 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 225 optimal weight: 50.0000 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN C 421 GLN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS ** E 443 ASN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5309 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 32488 Z= 0.220 Angle : 0.585 8.642 44167 Z= 0.284 Chirality : 0.044 0.203 5130 Planarity : 0.004 0.054 5916 Dihedral : 9.573 160.135 4901 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.46 % Allowed : 16.20 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.13), residues: 4464 helix: 0.85 (0.12), residues: 1860 sheet: -1.59 (0.19), residues: 632 loop : -0.98 (0.15), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 551 HIS 0.010 0.001 HIS D 404 PHE 0.020 0.001 PHE F 267 TYR 0.010 0.001 TYR D 244 ARG 0.008 0.000 ARG E 625 *********************** 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 537 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 468 time to evaluate : 3.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8083 (mmtt) cc_final: 0.7322 (tttt) REVERT: A 265 PHE cc_start: 0.7382 (t80) cc_final: 0.7003 (t80) REVERT: A 281 GLU cc_start: 0.5796 (tp30) cc_final: 0.5209 (mm-30) REVERT: A 304 ASP cc_start: 0.6249 (p0) cc_final: 0.5870 (t0) REVERT: A 307 ASP cc_start: 0.7308 (p0) cc_final: 0.5934 (t70) REVERT: A 322 ARG cc_start: 0.6195 (mtt-85) cc_final: 0.5369 (mpt-90) REVERT: A 364 ASP cc_start: 0.5492 (m-30) cc_final: 0.4583 (t0) REVERT: A 401 ASN cc_start: 0.7506 (m-40) cc_final: 0.6590 (t0) REVERT: A 410 ASP cc_start: 0.7604 (t0) cc_final: 0.6644 (m-30) REVERT: A 442 MET cc_start: 0.3246 (OUTLIER) cc_final: 0.2776 (tmm) REVERT: A 450 ASP cc_start: 0.7137 (m-30) cc_final: 0.6594 (p0) REVERT: A 554 GLU cc_start: 0.6206 (mm-30) cc_final: 0.5889 (mm-30) REVERT: A 635 ARG cc_start: 0.6027 (mmm-85) cc_final: 0.5371 (mmt90) REVERT: A 651 LYS cc_start: 0.7574 (mppt) cc_final: 0.7247 (mmtp) REVERT: A 720 MET cc_start: -0.0003 (tpt) cc_final: -0.0513 (mmt) REVERT: A 730 GLU cc_start: 0.6907 (mt-10) cc_final: 0.6319 (pm20) REVERT: A 757 MET cc_start: 0.6980 (ppp) cc_final: 0.5976 (mtm) REVERT: B 239 ARG cc_start: 0.5756 (mtt180) cc_final: 0.4764 (mtt-85) REVERT: B 252 THR cc_start: 0.8108 (t) cc_final: 0.7405 (m) REVERT: B 256 ARG cc_start: 0.6466 (ttm-80) cc_final: 0.6007 (mtt-85) REVERT: B 265 PHE cc_start: 0.7166 (t80) cc_final: 0.6673 (t80) REVERT: B 304 ASP cc_start: 0.7018 (p0) cc_final: 0.6478 (t0) REVERT: B 382 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7398 (mm-40) REVERT: B 478 ASP cc_start: 0.7433 (t0) cc_final: 0.6816 (m-30) REVERT: B 504 LEU cc_start: 0.8095 (tp) cc_final: 0.7631 (mt) REVERT: B 634 LEU cc_start: 0.7046 (mt) cc_final: 0.6732 (mt) REVERT: C 230 PHE cc_start: 0.6805 (OUTLIER) cc_final: 0.5933 (m-80) REVERT: C 265 PHE cc_start: 0.7023 (t80) cc_final: 0.6760 (t80) REVERT: C 267 PHE cc_start: 0.7583 (t80) cc_final: 0.7298 (t80) REVERT: C 273 GLU cc_start: 0.6820 (tp30) cc_final: 0.5712 (pt0) REVERT: C 305 GLU cc_start: 0.6652 (mm-30) cc_final: 0.6033 (mt-10) REVERT: C 323 ARG cc_start: 0.6079 (ttp-170) cc_final: 0.5342 (ttm-80) REVERT: C 397 GLU cc_start: 0.6655 (mp0) cc_final: 0.6295 (mp0) REVERT: C 401 ASN cc_start: 0.6168 (m-40) cc_final: 0.5836 (m110) REVERT: C 450 ASP cc_start: 0.7955 (m-30) cc_final: 0.7599 (m-30) REVERT: C 536 GLN cc_start: 0.6883 (mm110) cc_final: 0.6159 (mm-40) REVERT: C 540 ILE cc_start: 0.8067 (mt) cc_final: 0.7825 (mp) REVERT: C 558 ASN cc_start: 0.6975 (m110) cc_final: 0.6168 (t0) REVERT: C 586 ARG cc_start: 0.6841 (ttp80) cc_final: 0.6440 (ptm-80) REVERT: C 624 ASN cc_start: 0.7295 (m-40) cc_final: 0.6925 (m110) REVERT: C 662 ARG cc_start: 0.7629 (ptp90) cc_final: 0.7408 (ttp-170) REVERT: C 686 ASP cc_start: 0.6944 (t0) cc_final: 0.6713 (t0) REVERT: C 720 MET cc_start: -0.0813 (tpt) cc_final: -0.1144 (tpt) REVERT: C 740 MET cc_start: 0.7384 (tpp) cc_final: 0.6695 (mpp) REVERT: C 742 PHE cc_start: 0.6822 (OUTLIER) cc_final: 0.6291 (t80) REVERT: D 236 LYS cc_start: 0.6220 (mmtt) cc_final: 0.5505 (mmtm) REVERT: D 267 PHE cc_start: 0.7345 (t80) cc_final: 0.6668 (t80) REVERT: D 315 LYS cc_start: 0.6375 (tmtt) cc_final: 0.5718 (tmtt) REVERT: D 317 HIS cc_start: 0.4558 (t-90) cc_final: 0.3874 (m90) REVERT: D 340 HIS cc_start: 0.5308 (t70) cc_final: 0.5073 (t70) REVERT: D 543 LYS cc_start: 0.6897 (mttp) cc_final: 0.6277 (mtmt) REVERT: D 554 GLU cc_start: 0.6195 (mm-30) cc_final: 0.4779 (tt0) REVERT: D 556 GLU cc_start: 0.6003 (pt0) cc_final: 0.5473 (mp0) REVERT: D 578 GLU cc_start: 0.7007 (tp30) cc_final: 0.6333 (mp0) REVERT: D 663 LYS cc_start: 0.6426 (ttpt) cc_final: 0.6210 (ttpt) REVERT: D 668 LYS cc_start: 0.7344 (mmtm) cc_final: 0.6494 (tttm) REVERT: D 708 ARG cc_start: 0.5473 (ttp80) cc_final: 0.5056 (tmm160) REVERT: D 734 ASP cc_start: 0.7278 (t0) cc_final: 0.6960 (t0) REVERT: E 210 ARG cc_start: 0.6598 (tpp-160) cc_final: 0.6136 (mtm110) REVERT: E 267 PHE cc_start: 0.7685 (t80) cc_final: 0.7479 (t80) REVERT: E 273 GLU cc_start: 0.6619 (tp30) cc_final: 0.6255 (tt0) REVERT: E 291 GLU cc_start: 0.7491 (mt-10) cc_final: 0.6745 (mm-30) REVERT: E 373 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6878 (p0) REVERT: E 402 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.5689 (mt-10) REVERT: E 483 GLU cc_start: 0.7571 (tp30) cc_final: 0.7019 (mp0) REVERT: E 484 ASP cc_start: 0.7186 (p0) cc_final: 0.6932 (t70) REVERT: E 505 LYS cc_start: 0.7445 (tptp) cc_final: 0.7006 (ptmt) REVERT: E 529 LYS cc_start: 0.6499 (mtpp) cc_final: 0.6078 (mtmt) REVERT: E 543 LYS cc_start: 0.7282 (mttp) cc_final: 0.6792 (mttm) REVERT: E 554 GLU cc_start: 0.6578 (mm-30) cc_final: 0.6038 (tt0) REVERT: E 560 ARG cc_start: 0.5926 (tpt170) cc_final: 0.5649 (tpt170) REVERT: E 561 GLU cc_start: 0.7193 (pt0) cc_final: 0.6450 (mp0) REVERT: E 578 GLU cc_start: 0.6782 (tp30) cc_final: 0.5907 (mt-10) REVERT: E 625 ARG cc_start: 0.6218 (mtp85) cc_final: 0.5547 (mtp180) REVERT: E 635 ARG cc_start: 0.6533 (mtp85) cc_final: 0.5665 (mtm-85) REVERT: E 677 LYS cc_start: 0.7459 (ttmm) cc_final: 0.7062 (tttm) REVERT: E 738 GLU cc_start: 0.4930 (tp30) cc_final: 0.4690 (tp30) REVERT: E 757 MET cc_start: 0.6799 (ppp) cc_final: 0.5440 (mtp) REVERT: F 210 ARG cc_start: 0.6386 (tpp-160) cc_final: 0.6001 (ttp80) REVERT: F 221 GLU cc_start: 0.6445 (tp30) cc_final: 0.6014 (tp30) REVERT: F 236 LYS cc_start: 0.7611 (mmtt) cc_final: 0.6731 (mttp) REVERT: F 242 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7251 (tt) REVERT: F 268 LEU cc_start: 0.8181 (tp) cc_final: 0.7909 (tp) REVERT: F 288 LYS cc_start: 0.7647 (mtmm) cc_final: 0.7307 (mttm) REVERT: F 291 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7087 (mt-10) REVERT: F 327 GLN cc_start: 0.5346 (tp40) cc_final: 0.4727 (tp-100) REVERT: F 358 ARG cc_start: 0.7279 (mtp-110) cc_final: 0.7037 (mtp-110) REVERT: F 365 ARG cc_start: 0.5819 (mtm180) cc_final: 0.4985 (mtt180) REVERT: F 378 LEU cc_start: 0.7613 (tt) cc_final: 0.7300 (mt) REVERT: F 392 ASP cc_start: 0.6701 (p0) cc_final: 0.6241 (t0) REVERT: F 395 ASP cc_start: 0.5438 (p0) cc_final: 0.5188 (p0) REVERT: F 410 ASP cc_start: 0.7520 (t0) cc_final: 0.7089 (m-30) REVERT: F 487 ARG cc_start: 0.7384 (ttp80) cc_final: 0.7053 (ptp90) REVERT: F 502 LYS cc_start: 0.7131 (mmtp) cc_final: 0.6783 (ttmm) REVERT: F 560 ARG cc_start: 0.6167 (tpt170) cc_final: 0.5315 (ttp80) REVERT: F 561 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6492 (mp0) REVERT: F 568 GLN cc_start: 0.7477 (mm-40) cc_final: 0.7220 (mm-40) REVERT: F 578 GLU cc_start: 0.6614 (tp30) cc_final: 0.5909 (tt0) REVERT: F 611 MET cc_start: 0.6682 (OUTLIER) cc_final: 0.6342 (ptp) REVERT: F 624 ASN cc_start: 0.6619 (m-40) cc_final: 0.6193 (m-40) REVERT: F 669 ASP cc_start: 0.6666 (OUTLIER) cc_final: 0.6101 (m-30) outliers start: 69 outliers final: 46 residues processed: 504 average time/residue: 0.4678 time to fit residues: 365.9098 Evaluate side-chains 496 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 441 time to evaluate : 3.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 457 SER 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 640 ASP Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 689 GLU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 649 ASP Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 410 ASP Chi-restraints excluded: chain E residue 475 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 353 ILE 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 561 GLU Chi-restraints excluded: chain F residue 598 ASP Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 669 ASP 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 414 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 313 optimal weight: 2.9990 chunk 243 optimal weight: 0.9980 chunk 361 optimal weight: 3.9990 chunk 239 optimal weight: 9.9990 chunk 427 optimal weight: 0.8980 chunk 267 optimal weight: 0.7980 chunk 260 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN A 750 ASN B 460 ASN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN F 460 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5333 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 32488 Z= 0.254 Angle : 0.601 7.456 44167 Z= 0.293 Chirality : 0.044 0.324 5130 Planarity : 0.004 0.055 5916 Dihedral : 9.573 162.537 4901 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.71 % Allowed : 16.70 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.13), residues: 4464 helix: 0.79 (0.12), residues: 1864 sheet: -1.57 (0.19), residues: 632 loop : -0.99 (0.15), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 551 HIS 0.007 0.001 HIS D 404 PHE 0.036 0.002 PHE E 267 TYR 0.015 0.002 TYR F 244 ARG 0.007 0.000 ARG E 625 *********************** 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 537 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 461 time to evaluate : 3.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8088 (mmtt) cc_final: 0.6939 (mmtm) REVERT: A 261 GLU cc_start: 0.6198 (mm-30) cc_final: 0.5769 (tp30) REVERT: A 281 GLU cc_start: 0.5760 (tp30) cc_final: 0.5243 (mm-30) REVERT: A 288 LYS cc_start: 0.7302 (mtmm) cc_final: 0.6992 (pttm) REVERT: A 304 ASP cc_start: 0.6232 (p0) cc_final: 0.5916 (t0) REVERT: A 307 ASP cc_start: 0.7249 (p0) cc_final: 0.5889 (t70) REVERT: A 322 ARG cc_start: 0.6293 (mtt-85) cc_final: 0.5444 (mpt-90) REVERT: A 364 ASP cc_start: 0.5675 (m-30) cc_final: 0.4725 (t0) REVERT: A 401 ASN cc_start: 0.7523 (m-40) cc_final: 0.6581 (t0) REVERT: A 410 ASP cc_start: 0.7612 (t0) cc_final: 0.6673 (m-30) REVERT: A 442 MET cc_start: 0.3250 (mpp) cc_final: 0.2842 (tmm) REVERT: A 450 ASP cc_start: 0.7066 (m-30) cc_final: 0.6510 (p0) REVERT: A 534 GLU cc_start: 0.6394 (tt0) cc_final: 0.5904 (tt0) REVERT: A 554 GLU cc_start: 0.6193 (mm-30) cc_final: 0.5877 (mm-30) REVERT: A 635 ARG cc_start: 0.6057 (mmm-85) cc_final: 0.5367 (mmt90) REVERT: A 651 LYS cc_start: 0.7596 (mppt) cc_final: 0.7253 (mmtp) REVERT: A 678 MET cc_start: 0.5959 (OUTLIER) cc_final: 0.4948 (tpp) REVERT: A 720 MET cc_start: -0.0052 (tpt) cc_final: -0.0602 (mmt) REVERT: A 730 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6320 (pm20) REVERT: A 757 MET cc_start: 0.6942 (ppp) cc_final: 0.5961 (mtm) REVERT: B 239 ARG cc_start: 0.5818 (mtt180) cc_final: 0.4676 (mtt-85) REVERT: B 252 THR cc_start: 0.8113 (t) cc_final: 0.7403 (m) REVERT: B 256 ARG cc_start: 0.6492 (ttm-80) cc_final: 0.5977 (mtt-85) REVERT: B 265 PHE cc_start: 0.7182 (t80) cc_final: 0.6673 (t80) REVERT: B 275 MET cc_start: 0.7281 (mtm) cc_final: 0.7032 (mtm) REVERT: B 288 LYS cc_start: 0.7753 (mtmm) cc_final: 0.7133 (ttpt) REVERT: B 304 ASP cc_start: 0.6997 (p0) cc_final: 0.6498 (t0) REVERT: B 478 ASP cc_start: 0.7425 (t0) cc_final: 0.6791 (m-30) REVERT: B 504 LEU cc_start: 0.8122 (tp) cc_final: 0.7653 (mt) REVERT: B 561 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6637 (pm20) REVERT: C 265 PHE cc_start: 0.7021 (t80) cc_final: 0.6758 (t80) REVERT: C 267 PHE cc_start: 0.7643 (t80) cc_final: 0.7371 (t80) REVERT: C 273 GLU cc_start: 0.6791 (tp30) cc_final: 0.5633 (pt0) REVERT: C 305 GLU cc_start: 0.6635 (mm-30) cc_final: 0.6032 (mt-10) REVERT: C 323 ARG cc_start: 0.6087 (ttp-170) cc_final: 0.5348 (ttm-80) REVERT: C 360 PHE cc_start: 0.7569 (m-80) cc_final: 0.7334 (m-80) REVERT: C 397 GLU cc_start: 0.6651 (mp0) cc_final: 0.6165 (mp0) REVERT: C 401 ASN cc_start: 0.6238 (m-40) cc_final: 0.5903 (m110) REVERT: C 427 MET cc_start: 0.6094 (OUTLIER) cc_final: 0.5783 (tmm) REVERT: C 450 ASP cc_start: 0.7983 (m-30) cc_final: 0.7644 (m-30) REVERT: C 536 GLN cc_start: 0.6875 (mm110) cc_final: 0.6151 (mm-40) REVERT: C 558 ASN cc_start: 0.6946 (m110) cc_final: 0.6106 (t0) REVERT: C 624 ASN cc_start: 0.7333 (m-40) cc_final: 0.6963 (m110) REVERT: C 662 ARG cc_start: 0.7566 (ptp90) cc_final: 0.7276 (ttp-170) REVERT: C 686 ASP cc_start: 0.6911 (t0) cc_final: 0.6635 (t0) REVERT: C 720 MET cc_start: -0.0816 (tpt) cc_final: -0.1117 (tpt) REVERT: D 236 LYS cc_start: 0.6231 (mmtt) cc_final: 0.5542 (mmtm) REVERT: D 267 PHE cc_start: 0.7293 (t80) cc_final: 0.6983 (t80) REVERT: D 315 LYS cc_start: 0.6378 (tmtt) cc_final: 0.5688 (tmtt) REVERT: D 317 HIS cc_start: 0.4608 (t-90) cc_final: 0.3904 (m90) REVERT: D 340 HIS cc_start: 0.5348 (t70) cc_final: 0.5145 (t70) REVERT: D 382 GLN cc_start: 0.6875 (mt0) cc_final: 0.6625 (mp10) REVERT: D 397 GLU cc_start: 0.6962 (mp0) cc_final: 0.6369 (pm20) REVERT: D 398 GLN cc_start: 0.7413 (tt0) cc_final: 0.6490 (tm-30) REVERT: D 410 ASP cc_start: 0.6844 (m-30) cc_final: 0.6628 (m-30) REVERT: D 462 SER cc_start: 0.6570 (m) cc_final: 0.6289 (p) REVERT: D 543 LYS cc_start: 0.6887 (mttp) cc_final: 0.6275 (mtmt) REVERT: D 554 GLU cc_start: 0.6190 (mm-30) cc_final: 0.4931 (tt0) REVERT: D 556 GLU cc_start: 0.6007 (pt0) cc_final: 0.5525 (pm20) REVERT: D 578 GLU cc_start: 0.7036 (tp30) cc_final: 0.6356 (mp0) REVERT: D 668 LYS cc_start: 0.7425 (mmtm) cc_final: 0.6442 (tttm) REVERT: D 708 ARG cc_start: 0.5410 (ttp80) cc_final: 0.4984 (tmm160) REVERT: D 734 ASP cc_start: 0.7275 (t0) cc_final: 0.6944 (t0) REVERT: E 273 GLU cc_start: 0.6638 (tp30) cc_final: 0.6280 (tt0) REVERT: E 291 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6240 (mm-30) REVERT: E 340 HIS cc_start: 0.5465 (t70) cc_final: 0.5147 (t-170) REVERT: E 373 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6902 (p0) REVERT: E 483 GLU cc_start: 0.7576 (tp30) cc_final: 0.6992 (mp0) REVERT: E 505 LYS cc_start: 0.7425 (tptp) cc_final: 0.6980 (ptmt) REVERT: E 543 LYS cc_start: 0.7296 (mttp) cc_final: 0.7027 (mttm) REVERT: E 554 GLU cc_start: 0.6609 (mm-30) cc_final: 0.5886 (tt0) REVERT: E 560 ARG cc_start: 0.5946 (tpt170) cc_final: 0.5384 (tpt-90) REVERT: E 561 GLU cc_start: 0.7220 (pt0) cc_final: 0.6330 (mp0) REVERT: E 578 GLU cc_start: 0.6812 (tp30) cc_final: 0.5958 (mt-10) REVERT: E 607 GLU cc_start: 0.6727 (mm-30) cc_final: 0.5927 (mm-30) REVERT: E 625 ARG cc_start: 0.6232 (mtp85) cc_final: 0.5636 (mtp180) REVERT: E 677 LYS cc_start: 0.7455 (ttmm) cc_final: 0.7060 (tttm) REVERT: E 738 GLU cc_start: 0.5009 (tp30) cc_final: 0.4782 (tp30) REVERT: E 757 MET cc_start: 0.6822 (ppp) cc_final: 0.5524 (mtp) REVERT: F 210 ARG cc_start: 0.6348 (tpp-160) cc_final: 0.5960 (ttp80) REVERT: F 230 PHE cc_start: 0.6607 (t80) cc_final: 0.6371 (t80) REVERT: F 236 LYS cc_start: 0.7572 (mmtt) cc_final: 0.6720 (mttp) REVERT: F 242 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7376 (tt) REVERT: F 268 LEU cc_start: 0.8234 (tp) cc_final: 0.7935 (tp) REVERT: F 288 LYS cc_start: 0.7741 (mtmm) cc_final: 0.7364 (mttm) REVERT: F 291 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7099 (mt-10) REVERT: F 327 GLN cc_start: 0.5339 (tp40) cc_final: 0.4694 (tp-100) REVERT: F 365 ARG cc_start: 0.5836 (mtm180) cc_final: 0.5059 (mtt180) REVERT: F 378 LEU cc_start: 0.7601 (tt) cc_final: 0.7239 (mt) REVERT: F 392 ASP cc_start: 0.6750 (p0) cc_final: 0.6285 (t0) REVERT: F 395 ASP cc_start: 0.5439 (p0) cc_final: 0.5181 (p0) REVERT: F 487 ARG cc_start: 0.7400 (ttp80) cc_final: 0.7073 (ptp90) REVERT: F 502 LYS cc_start: 0.7167 (mmtp) cc_final: 0.6826 (ttmm) REVERT: F 560 ARG cc_start: 0.6227 (tpt170) cc_final: 0.5406 (ttp80) REVERT: F 561 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6434 (mp0) REVERT: F 578 GLU cc_start: 0.6604 (tp30) cc_final: 0.6193 (tt0) REVERT: F 624 ASN cc_start: 0.6644 (m-40) cc_final: 0.5667 (p0) REVERT: F 669 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.6052 (m-30) REVERT: F 756 GLU cc_start: 0.6844 (pt0) cc_final: 0.6624 (mt-10) outliers start: 76 outliers final: 51 residues processed: 503 average time/residue: 0.4717 time to fit residues: 366.8428 Evaluate side-chains 503 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 445 time to evaluate : 3.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 491 GLU 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 640 ASP Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 319 GLU 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 561 GLU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 649 ASP Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 353 ILE 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 561 GLU Chi-restraints excluded: chain F residue 598 ASP Chi-restraints excluded: chain F residue 669 ASP 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 264 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 255 optimal weight: 0.6980 chunk 128 optimal weight: 0.5980 chunk 84 optimal weight: 0.0670 chunk 82 optimal weight: 30.0000 chunk 272 optimal weight: 0.5980 chunk 291 optimal weight: 8.9990 chunk 211 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 336 optimal weight: 2.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 ASN F 460 ASN F 660 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5317 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 32488 Z= 0.199 Angle : 0.581 9.383 44167 Z= 0.281 Chirality : 0.044 0.236 5130 Planarity : 0.004 0.088 5916 Dihedral : 9.368 161.325 4901 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.46 % Allowed : 17.27 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.13), residues: 4464 helix: 0.89 (0.12), residues: 1857 sheet: -1.50 (0.19), residues: 632 loop : -0.98 (0.15), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 454 HIS 0.007 0.001 HIS D 404 PHE 0.019 0.001 PHE F 267 TYR 0.014 0.001 TYR F 244 ARG 0.008 0.000 ARG A 349 *********************** 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 518 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 449 time to evaluate : 3.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8065 (mmtt) cc_final: 0.6877 (mmtm) REVERT: A 281 GLU cc_start: 0.5845 (tp30) cc_final: 0.5267 (mm-30) REVERT: A 304 ASP cc_start: 0.6214 (p0) cc_final: 0.5910 (t0) REVERT: A 307 ASP cc_start: 0.7215 (p0) cc_final: 0.5903 (t70) REVERT: A 322 ARG cc_start: 0.6365 (mtt-85) cc_final: 0.5598 (mpt-90) REVERT: A 324 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6734 (mm) REVERT: A 364 ASP cc_start: 0.5597 (m-30) cc_final: 0.4707 (t0) REVERT: A 401 ASN cc_start: 0.7499 (m-40) cc_final: 0.6541 (t0) REVERT: A 410 ASP cc_start: 0.7592 (t0) cc_final: 0.6609 (m-30) REVERT: A 442 MET cc_start: 0.3243 (mpp) cc_final: 0.2840 (tmm) REVERT: A 450 ASP cc_start: 0.7172 (m-30) cc_final: 0.6605 (p0) REVERT: A 554 GLU cc_start: 0.6174 (mm-30) cc_final: 0.5855 (mm-30) REVERT: A 635 ARG cc_start: 0.6053 (mmm-85) cc_final: 0.5330 (mmt90) REVERT: A 651 LYS cc_start: 0.7596 (mppt) cc_final: 0.7236 (mmtp) REVERT: A 720 MET cc_start: -0.0067 (tpt) cc_final: -0.0619 (mmt) REVERT: A 730 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6290 (pm20) REVERT: A 757 MET cc_start: 0.6927 (ppp) cc_final: 0.5970 (mtm) REVERT: B 239 ARG cc_start: 0.5776 (mtt180) cc_final: 0.4707 (mtt-85) REVERT: B 252 THR cc_start: 0.8061 (t) cc_final: 0.7346 (m) REVERT: B 256 ARG cc_start: 0.6455 (ttm-80) cc_final: 0.5957 (mtt-85) REVERT: B 265 PHE cc_start: 0.7172 (t80) cc_final: 0.6661 (t80) REVERT: B 288 LYS cc_start: 0.7755 (mtmm) cc_final: 0.7137 (ttpt) REVERT: B 304 ASP cc_start: 0.6989 (p0) cc_final: 0.6485 (t0) REVERT: B 478 ASP cc_start: 0.7373 (t0) cc_final: 0.6781 (m-30) REVERT: B 504 LEU cc_start: 0.8095 (tp) cc_final: 0.7640 (mt) REVERT: B 561 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6613 (pm20) REVERT: C 230 PHE cc_start: 0.6778 (OUTLIER) cc_final: 0.5958 (m-80) REVERT: C 265 PHE cc_start: 0.7038 (t80) cc_final: 0.6774 (t80) REVERT: C 267 PHE cc_start: 0.7573 (t80) cc_final: 0.7315 (t80) REVERT: C 273 GLU cc_start: 0.6764 (tp30) cc_final: 0.5604 (pt0) REVERT: C 305 GLU cc_start: 0.6578 (mm-30) cc_final: 0.6002 (mt-10) REVERT: C 323 ARG cc_start: 0.6094 (ttp-170) cc_final: 0.5353 (ttm-80) REVERT: C 397 GLU cc_start: 0.6602 (mp0) cc_final: 0.6073 (mp0) REVERT: C 401 ASN cc_start: 0.6258 (m-40) cc_final: 0.5924 (m110) REVERT: C 427 MET cc_start: 0.6080 (OUTLIER) cc_final: 0.5768 (tmm) REVERT: C 450 ASP cc_start: 0.7970 (m-30) cc_final: 0.7641 (m-30) REVERT: C 536 GLN cc_start: 0.6898 (mm110) cc_final: 0.6159 (mm-40) REVERT: C 540 ILE cc_start: 0.8023 (mt) cc_final: 0.7802 (mp) REVERT: C 558 ASN cc_start: 0.6918 (m110) cc_final: 0.6098 (t0) REVERT: C 586 ARG cc_start: 0.6848 (ttp80) cc_final: 0.6462 (ptm-80) REVERT: C 624 ASN cc_start: 0.7187 (m-40) cc_final: 0.6809 (m110) REVERT: C 662 ARG cc_start: 0.7626 (ptp90) cc_final: 0.7413 (ttp-170) REVERT: C 686 ASP cc_start: 0.6801 (t70) cc_final: 0.6518 (t0) REVERT: C 720 MET cc_start: -0.0725 (tpt) cc_final: -0.1024 (tpt) REVERT: C 740 MET cc_start: 0.7423 (tpp) cc_final: 0.6708 (mpp) REVERT: D 236 LYS cc_start: 0.6270 (mmtt) cc_final: 0.5563 (mmtm) REVERT: D 315 LYS cc_start: 0.6349 (tmtt) cc_final: 0.5703 (tmtt) REVERT: D 317 HIS cc_start: 0.4576 (t-90) cc_final: 0.3890 (m-70) REVERT: D 358 ARG cc_start: 0.6591 (mtp180) cc_final: 0.6297 (mtm180) REVERT: D 365 ARG cc_start: 0.6391 (mtt90) cc_final: 0.5913 (mmm-85) REVERT: D 397 GLU cc_start: 0.6888 (mp0) cc_final: 0.6348 (pm20) REVERT: D 398 GLN cc_start: 0.7387 (tt0) cc_final: 0.6461 (tm-30) REVERT: D 410 ASP cc_start: 0.6864 (m-30) cc_final: 0.6618 (m-30) REVERT: D 543 LYS cc_start: 0.6894 (mttp) cc_final: 0.6276 (mtmt) REVERT: D 554 GLU cc_start: 0.6207 (mm-30) cc_final: 0.4746 (tt0) REVERT: D 556 GLU cc_start: 0.5941 (pt0) cc_final: 0.5425 (mp0) REVERT: D 578 GLU cc_start: 0.7002 (tp30) cc_final: 0.6343 (mp0) REVERT: D 668 LYS cc_start: 0.7438 (mmtm) cc_final: 0.6465 (tttm) REVERT: D 708 ARG cc_start: 0.5402 (ttp80) cc_final: 0.4984 (tmm160) REVERT: D 734 ASP cc_start: 0.7214 (t0) cc_final: 0.6880 (t0) REVERT: E 267 PHE cc_start: 0.6604 (t80) cc_final: 0.6382 (t80) REVERT: E 273 GLU cc_start: 0.6638 (tp30) cc_final: 0.6267 (tt0) REVERT: E 291 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6168 (mm-30) REVERT: E 373 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6877 (p0) REVERT: E 483 GLU cc_start: 0.7521 (tp30) cc_final: 0.6992 (mp0) REVERT: E 505 LYS cc_start: 0.7222 (tptp) cc_final: 0.6831 (ptmt) REVERT: E 543 LYS cc_start: 0.7283 (mttp) cc_final: 0.7010 (mttm) REVERT: E 554 GLU cc_start: 0.6573 (mm-30) cc_final: 0.5823 (tt0) REVERT: E 560 ARG cc_start: 0.5897 (tpt170) cc_final: 0.5380 (tpt-90) REVERT: E 561 GLU cc_start: 0.7148 (pt0) cc_final: 0.6319 (mp0) REVERT: E 578 GLU cc_start: 0.6781 (tp30) cc_final: 0.5941 (mt-10) REVERT: E 607 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6002 (mm-30) REVERT: E 635 ARG cc_start: 0.6167 (mtp85) cc_final: 0.5402 (mtm-85) REVERT: E 677 LYS cc_start: 0.7477 (ttmm) cc_final: 0.7100 (tttm) REVERT: E 738 GLU cc_start: 0.5021 (tp30) cc_final: 0.4767 (tp30) REVERT: E 757 MET cc_start: 0.6847 (ppp) cc_final: 0.5539 (mtp) REVERT: E 758 PHE cc_start: 0.6248 (t80) cc_final: 0.6048 (t80) REVERT: F 210 ARG cc_start: 0.6339 (tpp-160) cc_final: 0.5958 (ttp80) REVERT: F 230 PHE cc_start: 0.6623 (t80) cc_final: 0.6359 (t80) REVERT: F 236 LYS cc_start: 0.7592 (mmtt) cc_final: 0.6733 (mttp) REVERT: F 268 LEU cc_start: 0.8151 (tp) cc_final: 0.7874 (tp) REVERT: F 288 LYS cc_start: 0.7673 (mtmm) cc_final: 0.7362 (mttm) REVERT: F 291 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7090 (mt-10) REVERT: F 327 GLN cc_start: 0.5306 (tp40) cc_final: 0.4681 (tp-100) REVERT: F 365 ARG cc_start: 0.5862 (mtm180) cc_final: 0.5058 (mtt180) REVERT: F 378 LEU cc_start: 0.7550 (tt) cc_final: 0.7232 (mt) REVERT: F 392 ASP cc_start: 0.6714 (p0) cc_final: 0.6234 (t0) REVERT: F 395 ASP cc_start: 0.5426 (p0) cc_final: 0.5184 (p0) REVERT: F 487 ARG cc_start: 0.7373 (ttp80) cc_final: 0.7043 (ptp90) REVERT: F 502 LYS cc_start: 0.7124 (mmtp) cc_final: 0.6823 (ttmm) REVERT: F 560 ARG cc_start: 0.6189 (tpt170) cc_final: 0.5382 (ttp80) REVERT: F 561 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6450 (mp0) REVERT: F 567 ARG cc_start: 0.6116 (ttp80) cc_final: 0.5390 (ttm-80) REVERT: F 578 GLU cc_start: 0.6648 (tp30) cc_final: 0.6243 (tt0) REVERT: F 624 ASN cc_start: 0.6527 (m-40) cc_final: 0.5560 (p0) REVERT: F 669 ASP cc_start: 0.6667 (t70) cc_final: 0.6046 (m-30) outliers start: 69 outliers final: 52 residues processed: 490 average time/residue: 0.4677 time to fit residues: 353.7700 Evaluate side-chains 493 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 435 time to evaluate : 3.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 ILE 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 457 SER Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 491 GLU 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 640 ASP Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 319 GLU 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 501 ASP Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 649 ASP Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 353 ILE 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 561 GLU Chi-restraints excluded: chain F residue 598 ASP Chi-restraints excluded: chain F residue 651 LYS Chi-restraints excluded: chain F residue 752 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 0.5980 chunk 409 optimal weight: 0.7980 chunk 374 optimal weight: 1.9990 chunk 398 optimal weight: 0.9980 chunk 240 optimal weight: 4.9990 chunk 173 optimal weight: 0.6980 chunk 313 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 360 optimal weight: 8.9990 chunk 377 optimal weight: 9.9990 chunk 397 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5326 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 32488 Z= 0.217 Angle : 0.589 8.989 44167 Z= 0.286 Chirality : 0.044 0.232 5130 Planarity : 0.004 0.072 5916 Dihedral : 9.308 164.012 4901 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.32 % Allowed : 17.74 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.13), residues: 4464 helix: 0.88 (0.12), residues: 1877 sheet: -1.41 (0.19), residues: 622 loop : -1.00 (0.15), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 454 HIS 0.012 0.001 HIS D 340 PHE 0.015 0.001 PHE D 302 TYR 0.015 0.002 TYR F 244 ARG 0.007 0.000 ARG E 625 *********************** 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 505 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 440 time to evaluate : 3.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8070 (mmtt) cc_final: 0.6888 (mmtm) REVERT: A 281 GLU cc_start: 0.5868 (tp30) cc_final: 0.5294 (mm-30) REVERT: A 304 ASP cc_start: 0.6227 (p0) cc_final: 0.5946 (t0) REVERT: A 307 ASP cc_start: 0.7233 (p0) cc_final: 0.5919 (t70) REVERT: A 322 ARG cc_start: 0.6446 (mtt-85) cc_final: 0.5708 (mpt-90) REVERT: A 364 ASP cc_start: 0.5624 (m-30) cc_final: 0.4752 (t0) REVERT: A 401 ASN cc_start: 0.7484 (m-40) cc_final: 0.6525 (t0) REVERT: A 410 ASP cc_start: 0.7595 (t0) cc_final: 0.6621 (m-30) REVERT: A 442 MET cc_start: 0.3347 (mpp) cc_final: 0.2989 (tmm) REVERT: A 450 ASP cc_start: 0.7100 (m-30) cc_final: 0.6531 (p0) REVERT: A 534 GLU cc_start: 0.6428 (tt0) cc_final: 0.5932 (tt0) REVERT: A 554 GLU cc_start: 0.6145 (mm-30) cc_final: 0.5823 (mm-30) REVERT: A 635 ARG cc_start: 0.5980 (mmm-85) cc_final: 0.5245 (mmt90) REVERT: A 651 LYS cc_start: 0.7594 (mppt) cc_final: 0.7207 (mmtp) REVERT: A 678 MET cc_start: 0.5887 (OUTLIER) cc_final: 0.4862 (tpp) REVERT: A 720 MET cc_start: -0.0034 (tpt) cc_final: -0.0597 (mmt) REVERT: A 730 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6261 (pm20) REVERT: A 757 MET cc_start: 0.6931 (ppp) cc_final: 0.5978 (mtm) REVERT: B 239 ARG cc_start: 0.5740 (mtt180) cc_final: 0.4717 (mtt-85) REVERT: B 252 THR cc_start: 0.8061 (t) cc_final: 0.7347 (m) REVERT: B 256 ARG cc_start: 0.6432 (ttm-80) cc_final: 0.5917 (mtt-85) REVERT: B 265 PHE cc_start: 0.7163 (t80) cc_final: 0.6598 (t80) REVERT: B 275 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6677 (mmm) REVERT: B 288 LYS cc_start: 0.7767 (mtmm) cc_final: 0.7148 (ttpt) REVERT: B 304 ASP cc_start: 0.6975 (p0) cc_final: 0.6489 (t0) REVERT: B 478 ASP cc_start: 0.7374 (t0) cc_final: 0.6782 (m-30) REVERT: B 504 LEU cc_start: 0.8054 (tp) cc_final: 0.7597 (mt) REVERT: B 561 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6650 (pm20) REVERT: C 265 PHE cc_start: 0.7040 (t80) cc_final: 0.6771 (t80) REVERT: C 267 PHE cc_start: 0.7599 (t80) cc_final: 0.7352 (t80) REVERT: C 273 GLU cc_start: 0.6766 (tp30) cc_final: 0.5601 (pt0) REVERT: C 305 GLU cc_start: 0.6665 (mm-30) cc_final: 0.6078 (mt-10) REVERT: C 323 ARG cc_start: 0.6061 (ttp-170) cc_final: 0.5313 (ttm-80) REVERT: C 397 GLU cc_start: 0.6626 (mp0) cc_final: 0.6103 (mp0) REVERT: C 401 ASN cc_start: 0.6250 (m-40) cc_final: 0.5937 (m110) REVERT: C 427 MET cc_start: 0.6027 (OUTLIER) cc_final: 0.5718 (tmm) REVERT: C 450 ASP cc_start: 0.7989 (m-30) cc_final: 0.7651 (m-30) REVERT: C 536 GLN cc_start: 0.6860 (mm110) cc_final: 0.6107 (mm-40) REVERT: C 540 ILE cc_start: 0.8031 (mt) cc_final: 0.7805 (mp) REVERT: C 558 ASN cc_start: 0.6927 (m110) cc_final: 0.6059 (t0) REVERT: C 586 ARG cc_start: 0.6849 (ttp80) cc_final: 0.6431 (ptm-80) REVERT: C 624 ASN cc_start: 0.7225 (m-40) cc_final: 0.6843 (m110) REVERT: C 662 ARG cc_start: 0.7621 (ptp90) cc_final: 0.7412 (ttp-170) REVERT: C 686 ASP cc_start: 0.6862 (t70) cc_final: 0.6566 (t0) REVERT: C 720 MET cc_start: -0.0652 (tpt) cc_final: -0.0932 (tpt) REVERT: C 740 MET cc_start: 0.7419 (tpp) cc_final: 0.6709 (mpp) REVERT: D 317 HIS cc_start: 0.4597 (t-90) cc_final: 0.3931 (m-70) REVERT: D 358 ARG cc_start: 0.6696 (mtp180) cc_final: 0.6391 (mtm180) REVERT: D 365 ARG cc_start: 0.6398 (mtt90) cc_final: 0.6002 (mmm-85) REVERT: D 397 GLU cc_start: 0.6905 (mp0) cc_final: 0.6365 (pm20) REVERT: D 398 GLN cc_start: 0.7453 (tt0) cc_final: 0.6329 (tt0) REVERT: D 410 ASP cc_start: 0.6827 (m-30) cc_final: 0.6560 (m-30) REVERT: D 543 LYS cc_start: 0.6871 (mttp) cc_final: 0.6259 (mtmt) REVERT: D 554 GLU cc_start: 0.6225 (mm-30) cc_final: 0.4730 (tt0) REVERT: D 556 GLU cc_start: 0.5895 (pt0) cc_final: 0.5400 (mp0) REVERT: D 560 ARG cc_start: 0.6018 (tpt170) cc_final: 0.5193 (tpp80) REVERT: D 578 GLU cc_start: 0.6998 (tp30) cc_final: 0.6348 (mp0) REVERT: D 668 LYS cc_start: 0.7471 (mmtm) cc_final: 0.6487 (tttm) REVERT: D 708 ARG cc_start: 0.5400 (ttp80) cc_final: 0.4978 (tmm160) REVERT: D 734 ASP cc_start: 0.7189 (t0) cc_final: 0.6836 (t0) REVERT: E 265 PHE cc_start: 0.7737 (t80) cc_final: 0.7289 (t80) REVERT: E 273 GLU cc_start: 0.6662 (tp30) cc_final: 0.6278 (tt0) REVERT: E 291 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6135 (mm-30) REVERT: E 373 ASP cc_start: 0.7177 (OUTLIER) cc_final: 0.6869 (p0) REVERT: E 402 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.5955 (mt-10) REVERT: E 483 GLU cc_start: 0.7537 (tp30) cc_final: 0.6991 (mp0) REVERT: E 505 LYS cc_start: 0.7178 (tptp) cc_final: 0.6815 (ptmt) REVERT: E 543 LYS cc_start: 0.7292 (mttp) cc_final: 0.7023 (mttm) REVERT: E 554 GLU cc_start: 0.6576 (mm-30) cc_final: 0.5822 (tt0) REVERT: E 560 ARG cc_start: 0.5944 (tpt170) cc_final: 0.5445 (tpt-90) REVERT: E 561 GLU cc_start: 0.7215 (pt0) cc_final: 0.6368 (mp0) REVERT: E 578 GLU cc_start: 0.6775 (tp30) cc_final: 0.5950 (mt-10) REVERT: E 607 GLU cc_start: 0.6890 (mm-30) cc_final: 0.6045 (mm-30) REVERT: E 625 ARG cc_start: 0.6170 (mtp85) cc_final: 0.5576 (mtp180) REVERT: E 635 ARG cc_start: 0.6210 (mtp85) cc_final: 0.5430 (mtm-85) REVERT: E 677 LYS cc_start: 0.7454 (ttmm) cc_final: 0.7047 (tttm) REVERT: E 738 GLU cc_start: 0.5052 (tp30) cc_final: 0.4832 (tp30) REVERT: E 757 MET cc_start: 0.6866 (ppp) cc_final: 0.5550 (mtp) REVERT: E 758 PHE cc_start: 0.6266 (t80) cc_final: 0.6063 (t80) REVERT: F 210 ARG cc_start: 0.6356 (tpp-160) cc_final: 0.5977 (ttp80) REVERT: F 230 PHE cc_start: 0.6614 (t80) cc_final: 0.6382 (t80) REVERT: F 236 LYS cc_start: 0.7619 (mmtt) cc_final: 0.6760 (mttp) REVERT: F 268 LEU cc_start: 0.8150 (tp) cc_final: 0.7873 (tp) REVERT: F 288 LYS cc_start: 0.7710 (mtmm) cc_final: 0.7413 (mttm) REVERT: F 291 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7111 (mt-10) REVERT: F 327 GLN cc_start: 0.5373 (tp40) cc_final: 0.4728 (tp-100) REVERT: F 365 ARG cc_start: 0.5882 (mtm180) cc_final: 0.5044 (mtt180) REVERT: F 378 LEU cc_start: 0.7542 (tt) cc_final: 0.7132 (mt) REVERT: F 392 ASP cc_start: 0.6719 (p0) cc_final: 0.6210 (t0) REVERT: F 395 ASP cc_start: 0.5450 (p0) cc_final: 0.5194 (p0) REVERT: F 487 ARG cc_start: 0.7371 (ttp80) cc_final: 0.7052 (ptp90) REVERT: F 502 LYS cc_start: 0.7093 (mmtp) cc_final: 0.6805 (ttmm) REVERT: F 560 ARG cc_start: 0.6185 (tpt170) cc_final: 0.5391 (ttp80) REVERT: F 561 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6437 (mp0) REVERT: F 567 ARG cc_start: 0.6139 (ttp80) cc_final: 0.5406 (ttm-80) REVERT: F 578 GLU cc_start: 0.6648 (tp30) cc_final: 0.6237 (tt0) REVERT: F 624 ASN cc_start: 0.6566 (m-40) cc_final: 0.5632 (p0) REVERT: F 669 ASP cc_start: 0.6599 (OUTLIER) cc_final: 0.5990 (m-30) outliers start: 65 outliers final: 51 residues processed: 475 average time/residue: 0.4866 time to fit residues: 355.5838 Evaluate side-chains 484 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 425 time to evaluate : 3.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 491 GLU 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 640 ASP Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 319 GLU 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 538 ASN Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 360 PHE Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 649 ASP Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 410 ASP Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 353 ILE 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 561 GLU Chi-restraints excluded: chain F residue 598 ASP Chi-restraints excluded: chain F residue 651 LYS Chi-restraints excluded: chain F residue 669 ASP 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 261 optimal weight: 0.6980 chunk 421 optimal weight: 0.7980 chunk 257 optimal weight: 0.9990 chunk 200 optimal weight: 0.9990 chunk 293 optimal weight: 2.9990 chunk 442 optimal weight: 0.2980 chunk 407 optimal weight: 6.9990 chunk 352 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 272 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5321 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 32488 Z= 0.201 Angle : 0.588 9.800 44167 Z= 0.284 Chirality : 0.044 0.220 5130 Planarity : 0.004 0.064 5916 Dihedral : 9.180 164.457 4901 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.14 % Allowed : 18.13 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.13), residues: 4464 helix: 0.91 (0.12), residues: 1872 sheet: -1.35 (0.19), residues: 622 loop : -1.00 (0.15), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 454 HIS 0.017 0.001 HIS E 340 PHE 0.016 0.001 PHE F 267 TYR 0.025 0.002 TYR F 244 ARG 0.007 0.000 ARG A 560 ********************** 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 502 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 442 time to evaluate : 3.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8053 (mmtt) cc_final: 0.6878 (mmtm) REVERT: A 281 GLU cc_start: 0.5903 (tp30) cc_final: 0.5297 (mm-30) REVERT: A 304 ASP cc_start: 0.6252 (p0) cc_final: 0.5930 (t0) REVERT: A 307 ASP cc_start: 0.7264 (p0) cc_final: 0.5844 (t70) REVERT: A 364 ASP cc_start: 0.5566 (m-30) cc_final: 0.4741 (t0) REVERT: A 401 ASN cc_start: 0.7464 (m-40) cc_final: 0.6517 (t0) REVERT: A 410 ASP cc_start: 0.7590 (t0) cc_final: 0.6610 (m-30) REVERT: A 450 ASP cc_start: 0.7103 (m-30) cc_final: 0.6546 (p0) REVERT: A 534 GLU cc_start: 0.6413 (tt0) cc_final: 0.5893 (tt0) REVERT: A 554 GLU cc_start: 0.6121 (mm-30) cc_final: 0.5801 (mm-30) REVERT: A 635 ARG cc_start: 0.6072 (mmm-85) cc_final: 0.5356 (mmt90) REVERT: A 651 LYS cc_start: 0.7592 (mppt) cc_final: 0.7206 (mmtp) REVERT: A 720 MET cc_start: -0.0037 (tpt) cc_final: -0.0594 (mmt) REVERT: A 730 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6274 (pm20) REVERT: A 757 MET cc_start: 0.6925 (ppp) cc_final: 0.5972 (mtm) REVERT: B 239 ARG cc_start: 0.5651 (mtt180) cc_final: 0.4699 (mtt-85) REVERT: B 252 THR cc_start: 0.8042 (t) cc_final: 0.7322 (m) REVERT: B 256 ARG cc_start: 0.6430 (ttm-80) cc_final: 0.5926 (mtt-85) REVERT: B 265 PHE cc_start: 0.7165 (t80) cc_final: 0.6605 (t80) REVERT: B 275 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6613 (mmm) REVERT: B 288 LYS cc_start: 0.7774 (mtmm) cc_final: 0.7156 (ttpt) REVERT: B 304 ASP cc_start: 0.6916 (p0) cc_final: 0.6527 (t0) REVERT: B 478 ASP cc_start: 0.7366 (t0) cc_final: 0.6773 (m-30) REVERT: B 504 LEU cc_start: 0.8047 (tp) cc_final: 0.7595 (mt) REVERT: B 560 ARG cc_start: 0.6193 (tpt170) cc_final: 0.5685 (ttt90) REVERT: B 561 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6664 (pm20) REVERT: C 230 PHE cc_start: 0.6742 (OUTLIER) cc_final: 0.5930 (m-80) REVERT: C 265 PHE cc_start: 0.7006 (t80) cc_final: 0.6741 (t80) REVERT: C 267 PHE cc_start: 0.7516 (t80) cc_final: 0.7290 (t80) REVERT: C 273 GLU cc_start: 0.6788 (tp30) cc_final: 0.5609 (pt0) REVERT: C 304 ASP cc_start: 0.6681 (p0) cc_final: 0.6445 (t0) REVERT: C 305 GLU cc_start: 0.6558 (mm-30) cc_final: 0.5690 (mt-10) REVERT: C 323 ARG cc_start: 0.6115 (ttp-170) cc_final: 0.5336 (ttm-80) REVERT: C 401 ASN cc_start: 0.6249 (m-40) cc_final: 0.5927 (m110) REVERT: C 427 MET cc_start: 0.6008 (OUTLIER) cc_final: 0.5703 (tmm) REVERT: C 450 ASP cc_start: 0.7991 (m-30) cc_final: 0.7668 (m-30) REVERT: C 536 GLN cc_start: 0.6857 (mm110) cc_final: 0.6113 (mm-40) REVERT: C 558 ASN cc_start: 0.6952 (m110) cc_final: 0.6069 (t0) REVERT: C 586 ARG cc_start: 0.6789 (ttp80) cc_final: 0.6424 (ptm-80) REVERT: C 662 ARG cc_start: 0.7626 (ptp90) cc_final: 0.7421 (ttp-170) REVERT: C 686 ASP cc_start: 0.6865 (t70) cc_final: 0.6558 (t0) REVERT: C 720 MET cc_start: -0.0681 (tpt) cc_final: -0.0960 (tpt) REVERT: D 236 LYS cc_start: 0.6268 (mmtt) cc_final: 0.5577 (mmtm) REVERT: D 317 HIS cc_start: 0.4586 (t-90) cc_final: 0.3940 (m-70) REVERT: D 358 ARG cc_start: 0.6774 (mtp180) cc_final: 0.6324 (mtm180) REVERT: D 397 GLU cc_start: 0.6885 (mp0) cc_final: 0.6361 (pm20) REVERT: D 398 GLN cc_start: 0.7422 (tt0) cc_final: 0.6288 (tt0) REVERT: D 410 ASP cc_start: 0.6846 (m-30) cc_final: 0.6585 (m-30) REVERT: D 543 LYS cc_start: 0.6871 (mttp) cc_final: 0.6250 (mtmt) REVERT: D 554 GLU cc_start: 0.6198 (mm-30) cc_final: 0.4697 (tt0) REVERT: D 556 GLU cc_start: 0.5828 (pt0) cc_final: 0.5346 (mp0) REVERT: D 560 ARG cc_start: 0.6002 (tpt170) cc_final: 0.5099 (tpp80) REVERT: D 578 GLU cc_start: 0.6973 (tp30) cc_final: 0.6320 (mp0) REVERT: D 668 LYS cc_start: 0.7480 (mmtm) cc_final: 0.6485 (tttm) REVERT: D 708 ARG cc_start: 0.5397 (ttp80) cc_final: 0.4977 (tmm160) REVERT: D 734 ASP cc_start: 0.7142 (t0) cc_final: 0.6802 (t0) REVERT: E 265 PHE cc_start: 0.7748 (t80) cc_final: 0.7302 (t80) REVERT: E 273 GLU cc_start: 0.6592 (tp30) cc_final: 0.6200 (tt0) REVERT: E 291 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6358 (mm-30) REVERT: E 373 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6932 (p0) REVERT: E 402 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.5987 (mt-10) REVERT: E 483 GLU cc_start: 0.7508 (tp30) cc_final: 0.6987 (mp0) REVERT: E 505 LYS cc_start: 0.7135 (tptp) cc_final: 0.6767 (ptmt) REVERT: E 543 LYS cc_start: 0.7287 (mttp) cc_final: 0.7018 (mttm) REVERT: E 554 GLU cc_start: 0.6566 (mm-30) cc_final: 0.5811 (tt0) REVERT: E 560 ARG cc_start: 0.5900 (tpt170) cc_final: 0.5420 (tpt-90) REVERT: E 561 GLU cc_start: 0.7205 (pt0) cc_final: 0.6401 (mp0) REVERT: E 578 GLU cc_start: 0.6744 (tp30) cc_final: 0.5942 (mt-10) REVERT: E 607 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6043 (mm-30) REVERT: E 677 LYS cc_start: 0.7523 (ttmm) cc_final: 0.7098 (tttm) REVERT: E 757 MET cc_start: 0.6857 (ppp) cc_final: 0.5562 (mtp) REVERT: E 758 PHE cc_start: 0.6253 (t80) cc_final: 0.6038 (t80) REVERT: F 210 ARG cc_start: 0.6354 (tpp-160) cc_final: 0.5978 (ttp80) REVERT: F 230 PHE cc_start: 0.6591 (t80) cc_final: 0.6339 (t80) REVERT: F 236 LYS cc_start: 0.7628 (mmtt) cc_final: 0.6754 (mtmt) REVERT: F 268 LEU cc_start: 0.8071 (tp) cc_final: 0.7801 (tp) REVERT: F 288 LYS cc_start: 0.7738 (mtmm) cc_final: 0.7448 (mttm) REVERT: F 291 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7113 (mt-10) REVERT: F 327 GLN cc_start: 0.5336 (tp40) cc_final: 0.4706 (tp-100) REVERT: F 365 ARG cc_start: 0.5909 (mtm180) cc_final: 0.5189 (mtt180) REVERT: F 378 LEU cc_start: 0.7388 (tt) cc_final: 0.6974 (mt) REVERT: F 392 ASP cc_start: 0.6735 (p0) cc_final: 0.6209 (t0) REVERT: F 395 ASP cc_start: 0.5469 (p0) cc_final: 0.5208 (p0) REVERT: F 487 ARG cc_start: 0.7361 (ttp80) cc_final: 0.7045 (ptp90) REVERT: F 502 LYS cc_start: 0.7046 (mmtp) cc_final: 0.6756 (ttmm) REVERT: F 560 ARG cc_start: 0.6164 (tpt170) cc_final: 0.5371 (ttp80) REVERT: F 561 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6476 (mp0) REVERT: F 567 ARG cc_start: 0.6113 (ttp80) cc_final: 0.5397 (ttm-80) REVERT: F 578 GLU cc_start: 0.6642 (tp30) cc_final: 0.5931 (tt0) REVERT: F 624 ASN cc_start: 0.6546 (m-40) cc_final: 0.6201 (m110) REVERT: F 669 ASP cc_start: 0.6556 (t70) cc_final: 0.5992 (m-30) outliers start: 60 outliers final: 50 residues processed: 474 average time/residue: 0.4815 time to fit residues: 354.1925 Evaluate side-chains 483 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 426 time to evaluate : 3.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 491 GLU 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 640 ASP Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 319 GLU 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 538 ASN Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 360 PHE Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 649 ASP Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 410 ASP Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 353 ILE 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 561 GLU Chi-restraints excluded: chain F residue 598 ASP Chi-restraints excluded: chain F residue 651 LYS Chi-restraints excluded: chain F residue 752 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 9.9990 chunk 375 optimal weight: 20.0000 chunk 107 optimal weight: 0.7980 chunk 324 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 352 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 362 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.197437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.167490 restraints weight = 42161.193| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 1.57 r_work: 0.3804 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 32488 Z= 0.216 Angle : 0.596 10.817 44167 Z= 0.287 Chirality : 0.044 0.284 5130 Planarity : 0.004 0.060 5916 Dihedral : 9.130 165.827 4901 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.21 % Allowed : 18.17 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.13), residues: 4464 helix: 0.90 (0.12), residues: 1873 sheet: -1.34 (0.19), residues: 622 loop : -0.98 (0.15), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 454 HIS 0.017 0.001 HIS E 340 PHE 0.014 0.001 PHE D 302 TYR 0.026 0.002 TYR F 244 ARG 0.008 0.000 ARG A 560 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8412.57 seconds wall clock time: 149 minutes 7.69 seconds (8947.69 seconds total)