Starting phenix.real_space_refine on Tue May 27 02:27:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tas_41141/05_2025/8tas_41141.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tas_41141/05_2025/8tas_41141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tas_41141/05_2025/8tas_41141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tas_41141/05_2025/8tas_41141.map" model { file = "/net/cci-nas-00/data/ceres_data/8tas_41141/05_2025/8tas_41141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tas_41141/05_2025/8tas_41141.cif" } resolution = 4.1 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 386 5.49 5 S 118 5.16 5 C 17318 2.51 5 N 5401 2.21 5 O 6217 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29440 Number of models: 1 Model: "" Number of chains: 16 Chain: "D" Number of atoms: 3633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3633 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 19, 'TRANS': 419} Chain breaks: 7 Chain: "E" Number of atoms: 4580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4580 Classifications: {'peptide': 570} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 538} Chain breaks: 4 Chain: "G" Number of atoms: 2930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2930 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 349} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG%COO:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "H" Number of atoms: 3972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3972 Classifications: {'DNA': 193} Link IDs: {'rna3p': 192} Chain: "J" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "R" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "S" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 742 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 3919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3919 Classifications: {'DNA': 193} Link IDs: {'rna3p': 192} Chain: "U" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "V" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "W" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 817 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "X" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 666 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "O" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3139 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 22, 'TRANS': 372} Chain breaks: 1 Chain: "Y" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1047 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 16.10, per 1000 atoms: 0.55 Number of scatterers: 29440 At special positions: 0 Unit cell: (165.564, 199.29, 168.63, 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 118 16.00 P 386 15.00 O 6217 8.00 N 5401 7.00 C 17318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 565 " - pdb=" SG CYS E 571 " distance=2.03 Simple disulfide: pdb=" SG CYS E 565 " - pdb=" SG CYS E 578 " distance=2.03 Simple disulfide: pdb=" SG CYS E 571 " - pdb=" SG CYS E 590 " distance=2.04 Simple disulfide: pdb=" SG CYS E 590 " - pdb=" SG CYS E 593 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.99 Conformation dependent library (CDL) restraints added in 2.8 seconds 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5102 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 32 sheets defined 37.8% alpha, 15.8% beta 120 base pairs and 281 stacking pairs defined. Time for finding SS restraints: 12.67 Creating SS restraints... Processing helix chain 'D' and resid 82 through 89 Processing helix chain 'D' and resid 90 through 107 removed outlier: 3.507A pdb=" N ILE D 106 " --> pdb=" O THR D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 119 removed outlier: 6.102A pdb=" N THR D 116 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N TYR D 117 " --> pdb=" O THR D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 146 removed outlier: 4.261A pdb=" N MET D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 245 removed outlier: 3.661A pdb=" N MET D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 471 Processing helix chain 'D' and resid 502 through 508 removed outlier: 4.347A pdb=" N ILE D 506 " --> pdb=" O ASN D 502 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N HIS D 507 " --> pdb=" O PRO D 503 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 502 through 508' Processing helix chain 'D' and resid 539 through 543 Processing helix chain 'D' and resid 575 through 579 removed outlier: 3.553A pdb=" N MET D 579 " --> pdb=" O PRO D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 603 removed outlier: 3.962A pdb=" N ARG D 593 " --> pdb=" O PRO D 589 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU D 594 " --> pdb=" O GLU D 590 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE D 603 " --> pdb=" O GLN D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 625 removed outlier: 3.845A pdb=" N VAL D 613 " --> pdb=" O GLY D 609 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N MET D 614 " --> pdb=" O GLU D 610 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS D 615 " --> pdb=" O LYS D 611 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP D 617 " --> pdb=" O VAL D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 651 removed outlier: 3.778A pdb=" N MET D 632 " --> pdb=" O ALA D 628 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN D 633 " --> pdb=" O ASP D 629 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N MET D 637 " --> pdb=" O ASN D 633 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLN D 645 " --> pdb=" O GLU D 641 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LYS D 646 " --> pdb=" O ASN D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 666 Processing helix chain 'D' and resid 670 through 682 removed outlier: 3.952A pdb=" N ILE D 674 " --> pdb=" O SER D 670 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP D 675 " --> pdb=" O ILE D 671 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL D 678 " --> pdb=" O ILE D 674 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 63 removed outlier: 4.409A pdb=" N LYS E 30 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG E 31 " --> pdb=" O ARG E 27 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG E 33 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU E 59 " --> pdb=" O ILE E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 180 removed outlier: 3.996A pdb=" N PHE E 171 " --> pdb=" O ASN E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 231 removed outlier: 4.366A pdb=" N MET E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE E 231 " --> pdb=" O ILE E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 248 removed outlier: 3.582A pdb=" N LYS E 241 " --> pdb=" O ALA E 237 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU E 242 " --> pdb=" O GLU E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 284 removed outlier: 3.918A pdb=" N SER E 280 " --> pdb=" O GLN E 276 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE E 281 " --> pdb=" O SER E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 344 removed outlier: 3.616A pdb=" N ALA E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 453 removed outlier: 3.502A pdb=" N ILE E 449 " --> pdb=" O PHE E 445 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY E 450 " --> pdb=" O ARG E 446 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR E 451 " --> pdb=" O VAL E 447 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR E 452 " --> pdb=" O LEU E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 463 removed outlier: 3.591A pdb=" N ILE E 459 " --> pdb=" O ASN E 455 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA E 460 " --> pdb=" O PHE E 456 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG E 461 " --> pdb=" O CYS E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 482 Processing helix chain 'E' and resid 500 through 515 removed outlier: 3.574A pdb=" N TRP E 504 " --> pdb=" O LYS E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 544 Processing helix chain 'E' and resid 576 through 581 Processing helix chain 'E' and resid 609 through 614 Processing helix chain 'E' and resid 652 through 666 Processing helix chain 'E' and resid 687 through 692 removed outlier: 3.521A pdb=" N ARG E 690 " --> pdb=" O ASN E 687 " (cutoff:3.500A) Processing helix chain 'E' and resid 734 through 742 Processing helix chain 'G' and resid 128 through 130 No H-bonds generated for 'chain 'G' and resid 128 through 130' Processing helix chain 'G' and resid 232 through 234 No H-bonds generated for 'chain 'G' and resid 232 through 234' Processing helix chain 'G' and resid 267 through 280 removed outlier: 3.636A pdb=" N MET G 271 " --> pdb=" O SER G 267 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN G 272 " --> pdb=" O LYS G 268 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP G 279 " --> pdb=" O LYS G 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 56 removed outlier: 3.532A pdb=" N LEU I 48 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG I 49 " --> pdb=" O THR I 45 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG I 53 " --> pdb=" O ARG I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 79 removed outlier: 4.468A pdb=" N PHE I 67 " --> pdb=" O ARG I 63 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLN I 68 " --> pdb=" O LYS I 64 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG I 72 " --> pdb=" O GLN I 68 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU I 73 " --> pdb=" O ARG I 69 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN I 76 " --> pdb=" O ARG I 72 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP I 77 " --> pdb=" O GLU I 73 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE I 78 " --> pdb=" O ILE I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 114 removed outlier: 3.521A pdb=" N VAL I 89 " --> pdb=" O GLN I 85 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET I 90 " --> pdb=" O SER I 86 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU I 97 " --> pdb=" O GLN I 93 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA I 102 " --> pdb=" O ALA I 98 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU I 109 " --> pdb=" O GLU I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 131 removed outlier: 3.548A pdb=" N ILE I 124 " --> pdb=" O MET I 120 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN I 125 " --> pdb=" O PRO I 121 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU I 126 " --> pdb=" O LYS I 122 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG I 131 " --> pdb=" O ALA I 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 29 Processing helix chain 'J' and resid 30 through 41 Processing helix chain 'J' and resid 49 through 76 removed outlier: 3.571A pdb=" N GLU J 53 " --> pdb=" O LEU J 49 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG J 55 " --> pdb=" O TYR J 51 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY J 56 " --> pdb=" O GLU J 52 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR J 71 " --> pdb=" O ARG J 67 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR J 72 " --> pdb=" O ASP J 68 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR J 73 " --> pdb=" O ALA J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 93 removed outlier: 4.506A pdb=" N ALA J 89 " --> pdb=" O ASP J 85 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN J 93 " --> pdb=" O ALA J 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 21 Processing helix chain 'R' and resid 26 through 36 Processing helix chain 'R' and resid 46 through 73 removed outlier: 3.806A pdb=" N TYR R 50 " --> pdb=" O GLY R 46 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ILE R 62 " --> pdb=" O LEU R 58 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN R 68 " --> pdb=" O GLU R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 90 removed outlier: 3.512A pdb=" N ARG R 88 " --> pdb=" O GLN R 84 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN R 89 " --> pdb=" O LEU R 85 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP R 90 " --> pdb=" O ALA R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 95 removed outlier: 3.958A pdb=" N LYS R 95 " --> pdb=" O GLU R 91 " (cutoff:3.500A) Processing helix chain 'S' and resid 34 through 46 removed outlier: 3.527A pdb=" N LYS S 43 " --> pdb=" O TYR S 39 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN S 44 " --> pdb=" O LYS S 40 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL S 45 " --> pdb=" O VAL S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 81 removed outlier: 4.353A pdb=" N MET S 59 " --> pdb=" O ALA S 55 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN S 64 " --> pdb=" O ASN S 60 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU S 73 " --> pdb=" O ARG S 69 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG S 76 " --> pdb=" O GLY S 72 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU S 77 " --> pdb=" O GLU S 73 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS S 79 " --> pdb=" O SER S 75 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 99 removed outlier: 3.534A pdb=" N ILE S 91 " --> pdb=" O THR S 87 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG S 96 " --> pdb=" O GLN S 92 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU S 99 " --> pdb=" O VAL S 95 " (cutoff:3.500A) Processing helix chain 'S' and resid 101 through 121 removed outlier: 4.121A pdb=" N LYS S 105 " --> pdb=" O GLY S 101 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS S 106 " --> pdb=" O GLU S 102 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER S 109 " --> pdb=" O LYS S 105 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 21 Processing helix chain 'U' and resid 26 through 37 removed outlier: 3.787A pdb=" N VAL U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG U 35 " --> pdb=" O HIS U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 72 removed outlier: 3.610A pdb=" N ILE U 62 " --> pdb=" O LEU U 58 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU U 63 " --> pdb=" O THR U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 89 removed outlier: 3.975A pdb=" N LEU U 85 " --> pdb=" O ARG U 81 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA U 86 " --> pdb=" O HIS U 82 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL U 87 " --> pdb=" O LEU U 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 90 through 95 removed outlier: 3.858A pdb=" N LYS U 95 " --> pdb=" O GLU U 91 " (cutoff:3.500A) Processing helix chain 'U' and resid 112 through 116 Processing helix chain 'V' and resid 34 through 44 removed outlier: 3.778A pdb=" N TYR V 39 " --> pdb=" O ALA V 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 81 removed outlier: 4.479A pdb=" N MET V 59 " --> pdb=" O ALA V 55 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN V 64 " --> pdb=" O ASN V 60 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU V 73 " --> pdb=" O ARG V 69 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU V 77 " --> pdb=" O GLU V 73 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA V 78 " --> pdb=" O ALA V 74 " (cutoff:3.500A) Processing helix chain 'V' and resid 88 through 99 removed outlier: 4.119A pdb=" N ALA V 94 " --> pdb=" O GLU V 90 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG V 96 " --> pdb=" O GLN V 92 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU V 97 " --> pdb=" O THR V 93 " (cutoff:3.500A) Processing helix chain 'V' and resid 102 through 121 removed outlier: 3.573A pdb=" N VAL V 108 " --> pdb=" O ALA V 104 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER V 109 " --> pdb=" O LYS V 105 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA V 114 " --> pdb=" O GLU V 110 " (cutoff:3.500A) Processing helix chain 'W' and resid 44 through 55 removed outlier: 3.635A pdb=" N GLN W 55 " --> pdb=" O ILE W 51 " (cutoff:3.500A) Processing helix chain 'W' and resid 63 through 76 removed outlier: 3.614A pdb=" N GLU W 73 " --> pdb=" O ARG W 69 " (cutoff:3.500A) Processing helix chain 'W' and resid 86 through 114 removed outlier: 4.047A pdb=" N MET W 90 " --> pdb=" O SER W 86 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU W 92 " --> pdb=" O ALA W 88 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN W 93 " --> pdb=" O VAL W 89 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA W 95 " --> pdb=" O ALA W 91 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA W 98 " --> pdb=" O GLU W 94 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TYR W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA W 102 " --> pdb=" O ALA W 98 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP W 106 " --> pdb=" O ALA W 102 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU W 109 " --> pdb=" O GLU W 105 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS W 110 " --> pdb=" O ASP W 106 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 132 removed outlier: 3.695A pdb=" N ILE W 124 " --> pdb=" O MET W 120 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN W 125 " --> pdb=" O PRO W 121 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU W 126 " --> pdb=" O LYS W 122 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG W 131 " --> pdb=" O ALA W 127 " (cutoff:3.500A) Processing helix chain 'X' and resid 24 through 29 removed outlier: 3.841A pdb=" N ILE X 29 " --> pdb=" O ILE X 26 " (cutoff:3.500A) Processing helix chain 'X' and resid 30 through 42 removed outlier: 3.818A pdb=" N LEU X 37 " --> pdb=" O ALA X 33 " (cutoff:3.500A) Processing helix chain 'X' and resid 50 through 76 removed outlier: 3.893A pdb=" N GLY X 56 " --> pdb=" O GLU X 52 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS X 59 " --> pdb=" O ARG X 55 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASP X 68 " --> pdb=" O ASN X 64 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR X 71 " --> pdb=" O ARG X 67 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR X 73 " --> pdb=" O ALA X 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 93 removed outlier: 4.214A pdb=" N TYR X 88 " --> pdb=" O MET X 84 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG X 92 " --> pdb=" O TYR X 88 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN X 93 " --> pdb=" O ALA X 89 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 28 removed outlier: 3.560A pdb=" N ARG O 15 " --> pdb=" O ALA O 11 " (cutoff:3.500A) Processing helix chain 'O' and resid 208 through 210 No H-bonds generated for 'chain 'O' and resid 208 through 210' Processing helix chain 'O' and resid 348 through 350 No H-bonds generated for 'chain 'O' and resid 348 through 350' Processing helix chain 'O' and resid 355 through 360 Processing helix chain 'O' and resid 406 through 410 removed outlier: 3.698A pdb=" N ASN O 410 " --> pdb=" O ASN O 407 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 210 removed outlier: 3.674A pdb=" N LEU Y 195 " --> pdb=" O ASP Y 191 " (cutoff:3.500A) Processing helix chain 'Y' and resid 257 through 259 No H-bonds generated for 'chain 'Y' and resid 257 through 259' Processing helix chain 'Y' and resid 270 through 272 No H-bonds generated for 'chain 'Y' and resid 270 through 272' Processing helix chain 'Y' and resid 275 through 281 removed outlier: 3.628A pdb=" N LEU Y 279 " --> pdb=" O ASP Y 275 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP Y 281 " --> pdb=" O ALA Y 277 " (cutoff:3.500A) Processing helix chain 'Y' and resid 282 through 285 Processing sheet with id=AA1, first strand: chain 'D' and resid 162 through 165 removed outlier: 4.688A pdb=" N GLY D 163 " --> pdb=" O GLN D 356 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN D 356 " --> pdb=" O GLY D 163 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ILE Y 227 " --> pdb=" O ALA D 318 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N VAL Y 226 " --> pdb=" O HIS Y 242 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS Y 242 " --> pdb=" O VAL Y 226 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA Y 228 " --> pdb=" O LEU Y 240 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL Y 252 " --> pdb=" O LEU Y 241 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 230 through 232 removed outlier: 3.690A pdb=" N LEU D 159 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR D 358 " --> pdb=" O THR D 160 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ILE Y 227 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 203 through 211 removed outlier: 3.619A pdb=" N THR D 208 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL D 186 " --> pdb=" O THR D 208 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LYS D 210 " --> pdb=" O LEU D 184 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU D 184 " --> pdb=" O LYS D 210 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 438 through 443 removed outlier: 3.641A pdb=" N THR D 438 " --> pdb=" O TYR D 434 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE D 429 " --> pdb=" O ILE D 487 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL D 489 " --> pdb=" O PHE D 429 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLN D 431 " --> pdb=" O VAL D 489 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N ILE D 491 " --> pdb=" O GLN D 431 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N LEU D 433 " --> pdb=" O ILE D 491 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 557 through 560 removed outlier: 4.114A pdb=" N LEU D 529 " --> pdb=" O VAL O 35 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL O 35 " --> pdb=" O LEU D 529 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN O 403 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE O 398 " --> pdb=" O SER O 394 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP O 402 " --> pdb=" O ILE O 390 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET O 404 " --> pdb=" O TRP O 388 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N TRP O 388 " --> pdb=" O MET O 404 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL O 389 " --> pdb=" O ASN O 383 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASN O 383 " --> pdb=" O VAL O 389 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP O 379 " --> pdb=" O VAL O 393 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 566 through 567 removed outlier: 3.566A pdb=" N LEU D 572 " --> pdb=" O HIS D 567 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 94 through 97 removed outlier: 5.395A pdb=" N CYS G 84 " --> pdb=" O ASP G 438 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ASP G 438 " --> pdb=" O CYS G 84 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER G 433 " --> pdb=" O CYS G 429 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN G 415 " --> pdb=" O VAL G 428 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 120 through 121 removed outlier: 6.392A pdb=" N PHE E 120 " --> pdb=" O ILE E 650 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 285 through 286 Processing sheet with id=AB1, first strand: chain 'E' and resid 619 through 623 removed outlier: 4.134A pdb=" N ALA E 622 " --> pdb=" O GLY E 630 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 642 through 643 removed outlier: 4.470A pdb=" N ILE E 715 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 99 through 101 removed outlier: 4.617A pdb=" N GLN G 136 " --> pdb=" O LEU G 123 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU G 125 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU G 134 " --> pdb=" O GLU G 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 147 through 154 removed outlier: 3.968A pdb=" N ILE G 174 " --> pdb=" O LYS G 184 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LYS G 184 " --> pdb=" O ILE G 174 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 193 through 198 removed outlier: 6.111A pdb=" N VAL G 209 " --> pdb=" O ASN G 194 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LEU G 196 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU G 207 " --> pdb=" O LEU G 196 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N PHE G 198 " --> pdb=" O LEU G 205 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU G 205 " --> pdb=" O PHE G 198 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER G 210 " --> pdb=" O ALA G 214 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA G 214 " --> pdb=" O SER G 210 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU G 215 " --> pdb=" O ILE G 228 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE G 228 " --> pdb=" O LEU G 215 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU G 217 " --> pdb=" O VAL G 226 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 239 through 244 Processing sheet with id=AB7, first strand: chain 'G' and resid 309 through 315 Processing sheet with id=AB8, first strand: chain 'G' and resid 369 through 370 removed outlier: 4.219A pdb=" N SER G 369 " --> pdb=" O ALA G 378 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA G 378 " --> pdb=" O SER G 369 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 83 through 84 removed outlier: 7.184A pdb=" N ARG I 83 " --> pdb=" O VAL J 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'I' and resid 118 through 119 Processing sheet with id=AC2, first strand: chain 'J' and resid 96 through 98 removed outlier: 6.530A pdb=" N THR J 96 " --> pdb=" O THR R 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'R' and resid 42 through 43 removed outlier: 7.429A pdb=" N ARG R 42 " --> pdb=" O ILE S 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'R' and resid 77 through 78 Processing sheet with id=AC5, first strand: chain 'U' and resid 42 through 43 removed outlier: 6.918A pdb=" N ARG U 42 " --> pdb=" O ILE V 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'U' and resid 77 through 78 Processing sheet with id=AC7, first strand: chain 'W' and resid 83 through 84 removed outlier: 7.249A pdb=" N ARG W 83 " --> pdb=" O VAL X 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'O' and resid 47 through 49 removed outlier: 3.979A pdb=" N ASN O 77 " --> pdb=" O HIS O 123 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER O 83 " --> pdb=" O ILE O 117 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE O 117 " --> pdb=" O SER O 83 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLN O 85 " --> pdb=" O ILE O 115 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE O 115 " --> pdb=" O GLN O 85 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 129 through 133 removed outlier: 3.737A pdb=" N ARG O 129 " --> pdb=" O LYS O 143 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE O 139 " --> pdb=" O MET O 133 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 172 through 173 removed outlier: 6.397A pdb=" N ARG O 172 " --> pdb=" O VAL O 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'O' and resid 183 through 185 removed outlier: 3.554A pdb=" N LEU O 193 " --> pdb=" O TRP O 205 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP O 205 " --> pdb=" O LEU O 193 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 230 through 235 removed outlier: 4.342A pdb=" N ALA O 247 " --> pdb=" O LYS O 251 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYS O 251 " --> pdb=" O ALA O 247 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 280 through 281 removed outlier: 3.539A pdb=" N SER O 280 " --> pdb=" O ALA O 290 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS O 311 " --> pdb=" O LEU O 300 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 320 through 325 removed outlier: 3.821A pdb=" N GLN O 322 " --> pdb=" O SER O 336 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER O 336 " --> pdb=" O GLN O 322 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN O 324 " --> pdb=" O ALA O 334 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA O 334 " --> pdb=" O GLN O 324 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASP O 346 " --> pdb=" O LEU O 366 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LEU O 366 " --> pdb=" O ASP O 346 " (cutoff:3.500A) 799 hydrogen bonds defined for protein. 2274 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 281 hydrogen bonds 482 hydrogen bond angles 0 basepair planarities 120 basepair parallelities 281 stacking parallelities Total time for adding SS restraints: 14.62 Time building geometry restraints manager: 8.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8435 1.34 - 1.46: 9127 1.46 - 1.59: 12354 1.59 - 1.71: 765 1.71 - 1.84: 171 Bond restraints: 30852 Sorted by residual: bond pdb=" C LEU S 99 " pdb=" N PRO S 100 " ideal model delta sigma weight residual 1.335 1.296 0.039 8.70e-03 1.32e+04 1.96e+01 bond pdb=" C2 SAH E 801 " pdb=" N3 SAH E 801 " ideal model delta sigma weight residual 1.322 1.380 -0.058 2.00e-02 2.50e+03 8.45e+00 bond pdb=" C8 SAH E 801 " pdb=" N7 SAH E 801 " ideal model delta sigma weight residual 1.299 1.353 -0.054 2.00e-02 2.50e+03 7.34e+00 bond pdb=" C2 SAH E 801 " pdb=" N1 SAH E 801 " ideal model delta sigma weight residual 1.330 1.379 -0.049 2.00e-02 2.50e+03 6.11e+00 bond pdb=" CA LEU J 97 " pdb=" CB LEU J 97 " ideal model delta sigma weight residual 1.526 1.484 0.042 1.70e-02 3.46e+03 6.06e+00 ... (remaining 30847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 42609 3.97 - 7.94: 160 7.94 - 11.92: 519 11.92 - 15.89: 38 15.89 - 19.86: 14 Bond angle restraints: 43340 Sorted by residual: angle pdb=" O3' DC T 67 " pdb=" P DC T 68 " pdb=" OP1 DC T 68 " ideal model delta sigma weight residual 108.00 127.86 -19.86 3.00e+00 1.11e-01 4.38e+01 angle pdb=" O3' DG T 46 " pdb=" P DA T 47 " pdb=" OP1 DA T 47 " ideal model delta sigma weight residual 108.00 127.03 -19.03 3.00e+00 1.11e-01 4.02e+01 angle pdb=" O3' DC T 150 " pdb=" P DC T 151 " pdb=" OP1 DC T 151 " ideal model delta sigma weight residual 108.00 126.96 -18.96 3.00e+00 1.11e-01 3.99e+01 angle pdb=" O3' DC H 104 " pdb=" P DG H 105 " pdb=" OP1 DG H 105 " ideal model delta sigma weight residual 108.00 126.69 -18.69 3.00e+00 1.11e-01 3.88e+01 angle pdb=" O3' DC T 120 " pdb=" P DC T 121 " pdb=" OP1 DC T 121 " ideal model delta sigma weight residual 108.00 126.50 -18.50 3.00e+00 1.11e-01 3.80e+01 ... (remaining 43335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 15859 35.89 - 71.78: 1643 71.78 - 107.67: 61 107.67 - 143.56: 3 143.56 - 179.45: 24 Dihedral angle restraints: 17590 sinusoidal: 9746 harmonic: 7844 Sorted by residual: dihedral pdb=" CB CYS E 565 " pdb=" SG CYS E 565 " pdb=" SG CYS E 578 " pdb=" CB CYS E 578 " ideal model delta sinusoidal sigma weight residual -86.00 -174.31 88.31 1 1.00e+01 1.00e-02 9.32e+01 dihedral pdb=" CB CYS E 565 " pdb=" SG CYS E 565 " pdb=" SG CYS E 571 " pdb=" CB CYS E 571 " ideal model delta sinusoidal sigma weight residual -86.00 -165.38 79.38 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS E 590 " pdb=" SG CYS E 590 " pdb=" SG CYS E 593 " pdb=" CB CYS E 593 " ideal model delta sinusoidal sigma weight residual 93.00 150.00 -57.00 1 1.00e+01 1.00e-02 4.37e+01 ... (remaining 17587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 4459 0.124 - 0.247: 37 0.247 - 0.371: 103 0.371 - 0.495: 184 0.495 - 0.618: 21 Chirality restraints: 4804 Sorted by residual: chirality pdb=" P DC T 68 " pdb=" OP1 DC T 68 " pdb=" OP2 DC T 68 " pdb=" O5' DC T 68 " both_signs ideal model delta sigma weight residual True 2.35 -2.96 -0.62 2.00e-01 2.50e+01 9.55e+00 chirality pdb=" P DC T 110 " pdb=" OP1 DC T 110 " pdb=" OP2 DC T 110 " pdb=" O5' DC T 110 " both_signs ideal model delta sigma weight residual True 2.35 -2.95 -0.60 2.00e-01 2.50e+01 9.01e+00 chirality pdb=" P DC T 151 " pdb=" OP1 DC T 151 " pdb=" OP2 DC T 151 " pdb=" O5' DC T 151 " both_signs ideal model delta sigma weight residual True 2.35 -2.94 -0.59 2.00e-01 2.50e+01 8.75e+00 ... (remaining 4801 not shown) Planarity restraints: 4208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 326 " -0.084 5.00e-02 4.00e+02 1.28e-01 2.63e+01 pdb=" N PRO E 327 " 0.222 5.00e-02 4.00e+02 pdb=" CA PRO E 327 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO E 327 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR V 80 " -0.036 2.00e-02 2.50e+03 2.65e-02 1.40e+01 pdb=" CG TYR V 80 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR V 80 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR V 80 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR V 80 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR V 80 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR V 80 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR V 80 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 67 " -0.014 2.00e-02 2.50e+03 1.51e-02 3.99e+00 pdb=" CG PHE I 67 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE I 67 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE I 67 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE I 67 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE I 67 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE I 67 " -0.001 2.00e-02 2.50e+03 ... (remaining 4205 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 713 2.63 - 3.20: 28738 3.20 - 3.77: 53240 3.77 - 4.33: 70130 4.33 - 4.90: 101065 Nonbonded interactions: 253886 Sorted by model distance: nonbonded pdb=" OH TYR J 98 " pdb=" OD2 ASP S 65 " model vdw 2.069 3.040 nonbonded pdb=" O CYS E 567 " pdb=" OG1 THR E 592 " model vdw 2.098 3.040 nonbonded pdb=" OD2 ASP O 318 " pdb=" OG1 THR O 338 " model vdw 2.104 3.040 nonbonded pdb=" OG SER G 210 " pdb=" OD1 ASP G 212 " model vdw 2.110 3.040 nonbonded pdb=" O HIS V 106 " pdb=" OG SER V 109 " model vdw 2.124 3.040 ... (remaining 253881 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'I' and resid 37 through 135) selection = chain 'W' } ncs_group { reference = (chain 'J' and ((resid 20 through 23 and (name N or name CA or name C or name O \ or name CB )) or resid 24 through 102)) selection = (chain 'X' and resid 20 through 102) } ncs_group { reference = (chain 'R' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 119)) selection = chain 'U' } ncs_group { reference = (chain 'S' and resid 28 through 122) selection = chain 'V' } 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 group one per residue 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: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.210 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 73.490 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 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 : 0.006 0.095 30856 Z= 0.258 Angle : 1.417 19.860 43348 Z= 0.567 Chirality : 0.108 0.618 4804 Planarity : 0.005 0.128 4208 Dihedral : 23.568 179.445 12476 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.46 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.16), residues: 2632 helix: -1.00 (0.17), residues: 870 sheet: -0.73 (0.26), residues: 385 loop : -1.10 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 113 HIS 0.008 0.001 HIS X 75 PHE 0.035 0.002 PHE I 67 TYR 0.058 0.002 TYR V 80 ARG 0.005 0.001 ARG U 77 Details of bonding type rmsd hydrogen bonds : bond 0.30886 ( 1071) hydrogen bonds : angle 10.94658 ( 2756) SS BOND : bond 0.00752 ( 4) SS BOND : angle 3.21059 ( 8) covalent geometry : bond 0.00573 (30852) covalent geometry : angle 1.41666 (43340) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 2.629 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: J 84 MET cc_start: 0.7819 (mmm) cc_final: 0.6985 (mpp) REVERT: R 38 ASN cc_start: 0.8261 (m-40) cc_final: 0.7991 (m-40) REVERT: X 49 LEU cc_start: 0.8762 (tp) cc_final: 0.8562 (tp) REVERT: O 36 MET cc_start: 0.0594 (tpt) cc_final: -0.0227 (tpt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.3808 time to fit residues: 69.8920 Evaluate side-chains 87 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 252 optimal weight: 50.0000 chunk 226 optimal weight: 0.5980 chunk 125 optimal weight: 9.9990 chunk 77 optimal weight: 0.0000 chunk 152 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 234 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 174 optimal weight: 0.9990 chunk 271 optimal weight: 9.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 156 HIS D 166 HIS D 356 GLN D 449 HIS D 517 ASN D 624 HIS D 667 ASN E 45 ASN ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 ASN E 273 GLN E 331 GLN E 520 ASN G 146 ASN G 160 HIS ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 272 ASN G 283 ASN G 382 GLN I 108 ASN S 92 GLN ** U 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 104 GLN V 46 HIS V 92 GLN W 39 HIS W 125 GLN ** O 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 329 ASN ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.108816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.093622 restraints weight = 160701.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.092867 restraints weight = 309756.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.092806 restraints weight = 248679.250| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 30856 Z= 0.166 Angle : 0.660 8.515 43348 Z= 0.371 Chirality : 0.043 0.248 4804 Planarity : 0.005 0.124 4208 Dihedral : 28.197 178.294 7122 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.83 % Favored : 95.10 % Rotamer: Outliers : 0.17 % Allowed : 4.13 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.16), residues: 2632 helix: -0.11 (0.17), residues: 907 sheet: -1.10 (0.25), residues: 397 loop : -0.95 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP O 255 HIS 0.005 0.001 HIS X 75 PHE 0.017 0.001 PHE O 243 TYR 0.021 0.002 TYR V 80 ARG 0.008 0.000 ARG J 39 Details of bonding type rmsd hydrogen bonds : bond 0.08967 ( 1071) hydrogen bonds : angle 5.50257 ( 2756) SS BOND : bond 0.01960 ( 4) SS BOND : angle 2.55112 ( 8) covalent geometry : bond 0.00363 (30852) covalent geometry : angle 0.65880 (43340) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 2.580 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: J 84 MET cc_start: 0.7603 (mmm) cc_final: 0.7182 (mpp) REVERT: R 38 ASN cc_start: 0.8067 (m-40) cc_final: 0.7866 (m-40) REVERT: S 92 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.6565 (tp40) REVERT: U 78 ILE cc_start: 0.8134 (mt) cc_final: 0.7932 (mt) REVERT: V 56 MET cc_start: 0.8325 (tpt) cc_final: 0.7626 (tmm) REVERT: V 65 ASP cc_start: 0.8396 (t0) cc_final: 0.8087 (t0) REVERT: V 80 TYR cc_start: 0.8384 (m-10) cc_final: 0.8102 (m-80) REVERT: X 49 LEU cc_start: 0.8511 (tp) cc_final: 0.8282 (tp) outliers start: 4 outliers final: 0 residues processed: 124 average time/residue: 0.3849 time to fit residues: 79.9845 Evaluate side-chains 93 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 60 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 20.0000 chunk 271 optimal weight: 50.0000 chunk 182 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 ASN J 75 HIS R 31 HIS ** R 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN S 106 HIS ** U 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 104 GLN V 81 ASN ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.106781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.092304 restraints weight = 161798.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.092281 restraints weight = 337133.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.092223 restraints weight = 229076.628| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 30856 Z= 0.225 Angle : 0.658 8.193 43348 Z= 0.364 Chirality : 0.043 0.237 4804 Planarity : 0.005 0.120 4208 Dihedral : 28.219 178.270 7122 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.36 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.16), residues: 2632 helix: -0.16 (0.17), residues: 908 sheet: -1.16 (0.24), residues: 401 loop : -0.95 (0.18), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 113 HIS 0.017 0.001 HIS D 659 PHE 0.018 0.001 PHE I 67 TYR 0.016 0.002 TYR V 80 ARG 0.005 0.000 ARG U 81 Details of bonding type rmsd hydrogen bonds : bond 0.07953 ( 1071) hydrogen bonds : angle 5.34696 ( 2756) SS BOND : bond 0.00663 ( 4) SS BOND : angle 2.96648 ( 8) covalent geometry : bond 0.00511 (30852) covalent geometry : angle 0.65725 (43340) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 2.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 49 LEU cc_start: 0.8634 (tp) cc_final: 0.8361 (tp) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.4183 time to fit residues: 76.8721 Evaluate side-chains 86 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 231 optimal weight: 9.9990 chunk 254 optimal weight: 20.0000 chunk 127 optimal weight: 30.0000 chunk 42 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 287 optimal weight: 20.0000 chunk 18 optimal weight: 30.0000 chunk 238 optimal weight: 0.8980 chunk 264 optimal weight: 50.0000 chunk 28 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 overall best weight: 8.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 148 GLN ** D 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 664 HIS ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 HIS ** E 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 286 ASN ** G 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 305 HIS ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 81 ASN ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 ASN W 68 GLN ** X 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 78 HIS ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.099671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.087006 restraints weight = 166546.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.086559 restraints weight = 284491.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.085622 restraints weight = 283232.730| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.184 30856 Z= 0.851 Angle : 1.312 21.091 43348 Z= 0.702 Chirality : 0.073 0.439 4804 Planarity : 0.010 0.120 4208 Dihedral : 29.888 172.796 7122 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 47.91 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.11 % Favored : 89.59 % Rotamer: Outliers : 0.81 % Allowed : 7.91 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.46 (0.16), residues: 2632 helix: -1.77 (0.15), residues: 895 sheet: -1.05 (0.25), residues: 393 loop : -1.66 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP G 373 HIS 0.029 0.003 HIS S 79 PHE 0.081 0.004 PHE I 67 TYR 0.051 0.005 TYR W 54 ARG 0.020 0.002 ARG X 39 Details of bonding type rmsd hydrogen bonds : bond 0.14224 ( 1071) hydrogen bonds : angle 7.45893 ( 2756) SS BOND : bond 0.03005 ( 4) SS BOND : angle 7.02697 ( 8) covalent geometry : bond 0.01945 (30852) covalent geometry : angle 1.30843 (43340) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 271 MET cc_start: 0.8394 (mpp) cc_final: 0.8102 (mpp) REVERT: I 90 MET cc_start: 0.7852 (mmt) cc_final: 0.7604 (mmt) REVERT: S 39 TYR cc_start: 0.7980 (t80) cc_final: 0.7765 (t80) REVERT: S 56 MET cc_start: 0.8615 (tmm) cc_final: 0.8143 (tmm) REVERT: S 80 TYR cc_start: 0.7340 (t80) cc_final: 0.7114 (t80) REVERT: V 56 MET cc_start: 0.9139 (tpp) cc_final: 0.8693 (tpp) outliers start: 19 outliers final: 13 residues processed: 109 average time/residue: 0.4297 time to fit residues: 76.1813 Evaluate side-chains 88 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 213 optimal weight: 0.8980 chunk 168 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 248 optimal weight: 50.0000 chunk 294 optimal weight: 9.9990 chunk 283 optimal weight: 50.0000 chunk 293 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 262 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 GLN D 567 HIS ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 GLN E 273 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 HIS ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 HIS ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 415 GLN I 108 ASN S 92 GLN ** U 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 ASN W 68 GLN O 226 HIS ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.104643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.091172 restraints weight = 163046.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.091269 restraints weight = 352406.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.091041 restraints weight = 246604.617| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 30856 Z= 0.234 Angle : 0.745 10.771 43348 Z= 0.408 Chirality : 0.045 0.245 4804 Planarity : 0.005 0.123 4208 Dihedral : 29.587 177.060 7122 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.74 % Favored : 94.15 % Rotamer: Outliers : 0.13 % Allowed : 3.19 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.16), residues: 2632 helix: -0.98 (0.16), residues: 909 sheet: -1.14 (0.25), residues: 381 loop : -1.43 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 218 HIS 0.012 0.001 HIS D 659 PHE 0.024 0.002 PHE I 67 TYR 0.020 0.002 TYR S 39 ARG 0.009 0.001 ARG E 475 Details of bonding type rmsd hydrogen bonds : bond 0.08237 ( 1071) hydrogen bonds : angle 5.68990 ( 2756) SS BOND : bond 0.01137 ( 4) SS BOND : angle 4.99961 ( 8) covalent geometry : bond 0.00538 (30852) covalent geometry : angle 0.74214 (43340) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 117 time to evaluate : 2.862 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: S 56 MET cc_start: 0.8338 (tmm) cc_final: 0.7809 (tmm) REVERT: S 92 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.7343 (tm-30) REVERT: V 56 MET cc_start: 0.8852 (tpp) cc_final: 0.8451 (tpp) outliers start: 3 outliers final: 0 residues processed: 120 average time/residue: 0.4932 time to fit residues: 91.1985 Evaluate side-chains 90 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 236 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 219 optimal weight: 0.5980 chunk 156 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 258 optimal weight: 9.9990 chunk 14 optimal weight: 30.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 607 ASN ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 GLN E 273 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 ASN S 81 ASN S 92 GLN ** U 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 ASN W 68 GLN ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 400 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.104544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.091477 restraints weight = 163974.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.091568 restraints weight = 350079.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.091148 restraints weight = 235775.341| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 30856 Z= 0.255 Angle : 0.720 9.513 43348 Z= 0.395 Chirality : 0.045 0.234 4804 Planarity : 0.005 0.124 4208 Dihedral : 29.297 176.791 7122 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.57 % Favored : 93.28 % Rotamer: Outliers : 0.04 % Allowed : 2.47 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.16), residues: 2632 helix: -0.75 (0.16), residues: 910 sheet: -1.21 (0.25), residues: 391 loop : -1.32 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 255 HIS 0.023 0.001 HIS G 213 PHE 0.028 0.002 PHE I 84 TYR 0.017 0.002 TYR J 72 ARG 0.007 0.001 ARG U 29 Details of bonding type rmsd hydrogen bonds : bond 0.07844 ( 1071) hydrogen bonds : angle 5.48597 ( 2756) SS BOND : bond 0.00938 ( 4) SS BOND : angle 4.22553 ( 8) covalent geometry : bond 0.00586 (30852) covalent geometry : angle 0.71730 (43340) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 244 MET cc_start: 0.4481 (mmm) cc_final: 0.3971 (tpt) REVERT: J 58 LEU cc_start: 0.8802 (tp) cc_final: 0.8459 (tt) REVERT: S 56 MET cc_start: 0.8352 (tmm) cc_final: 0.7769 (tmm) REVERT: V 56 MET cc_start: 0.8920 (tpp) cc_final: 0.8428 (tpp) REVERT: W 90 MET cc_start: 0.8167 (ptt) cc_final: 0.7900 (ptt) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.4300 time to fit residues: 73.4252 Evaluate side-chains 87 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 244 optimal weight: 0.5980 chunk 24 optimal weight: 8.9990 chunk 112 optimal weight: 8.9990 chunk 200 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 213 optimal weight: 0.5980 chunk 241 optimal weight: 0.1980 chunk 110 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN E 575 GLN G 92 HIS ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 ASN S 92 GLN ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.106466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.093224 restraints weight = 161649.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.092910 restraints weight = 310715.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.092559 restraints weight = 216059.632| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 30856 Z= 0.163 Angle : 0.648 9.576 43348 Z= 0.357 Chirality : 0.042 0.226 4804 Planarity : 0.004 0.123 4208 Dihedral : 28.951 177.435 7122 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.60 % Favored : 95.25 % Rotamer: Outliers : 0.04 % Allowed : 1.74 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.16), residues: 2632 helix: -0.20 (0.17), residues: 911 sheet: -1.10 (0.25), residues: 383 loop : -1.22 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP O 255 HIS 0.014 0.001 HIS D 659 PHE 0.017 0.001 PHE I 67 TYR 0.015 0.001 TYR E 23 ARG 0.005 0.000 ARG S 76 Details of bonding type rmsd hydrogen bonds : bond 0.07387 ( 1071) hydrogen bonds : angle 4.99185 ( 2756) SS BOND : bond 0.00957 ( 4) SS BOND : angle 4.40355 ( 8) covalent geometry : bond 0.00367 (30852) covalent geometry : angle 0.64504 (43340) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 2.567 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: symmetry clash REVERT: D 244 MET cc_start: 0.4588 (mmm) cc_final: 0.4082 (tpt) REVERT: D 299 MET cc_start: 0.6184 (ppp) cc_final: 0.5813 (tpt) REVERT: J 58 LEU cc_start: 0.8657 (tp) cc_final: 0.8381 (tt) REVERT: V 56 MET cc_start: 0.8806 (tpp) cc_final: 0.8460 (tpp) outliers start: 1 outliers final: 1 residues processed: 117 average time/residue: 0.4295 time to fit residues: 79.8757 Evaluate side-chains 92 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 140 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 170 optimal weight: 0.9990 chunk 252 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 297 optimal weight: 0.0570 chunk 232 optimal weight: 0.1980 chunk 45 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 222 optimal weight: 0.9990 overall best weight: 0.8504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 356 GLN ** D 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN E 331 GLN E 575 GLN ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN O 272 HIS ** O 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.106548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.093569 restraints weight = 163413.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.093360 restraints weight = 311628.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.092754 restraints weight = 225811.438| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 30856 Z= 0.162 Angle : 0.633 8.089 43348 Z= 0.348 Chirality : 0.041 0.213 4804 Planarity : 0.004 0.123 4208 Dihedral : 28.736 176.800 7122 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.17 % Favored : 94.72 % Rotamer: Outliers : 0.04 % Allowed : 1.06 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.16), residues: 2632 helix: -0.08 (0.17), residues: 906 sheet: -1.03 (0.25), residues: 383 loop : -1.15 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 255 HIS 0.013 0.001 HIS D 659 PHE 0.015 0.001 PHE E 729 TYR 0.016 0.001 TYR D 117 ARG 0.004 0.000 ARG O 65 Details of bonding type rmsd hydrogen bonds : bond 0.07204 ( 1071) hydrogen bonds : angle 4.84873 ( 2756) SS BOND : bond 0.00496 ( 4) SS BOND : angle 3.51298 ( 8) covalent geometry : bond 0.00363 (30852) covalent geometry : angle 0.63108 (43340) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 2.718 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: D 244 MET cc_start: 0.4670 (mmm) cc_final: 0.4204 (tpt) REVERT: D 540 MET cc_start: 0.0329 (tpt) cc_final: 0.0091 (tpt) REVERT: D 657 MET cc_start: 0.8116 (mmm) cc_final: 0.7733 (mmp) REVERT: J 58 LEU cc_start: 0.8629 (tp) cc_final: 0.8334 (tt) REVERT: R 38 ASN cc_start: 0.8104 (m-40) cc_final: 0.7725 (m-40) REVERT: V 56 MET cc_start: 0.8793 (tpp) cc_final: 0.8394 (tpp) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.4393 time to fit residues: 76.8585 Evaluate side-chains 91 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 179 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 290 optimal weight: 50.0000 chunk 191 optimal weight: 2.9990 chunk 22 optimal weight: 50.0000 chunk 271 optimal weight: 0.0070 chunk 203 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 242 optimal weight: 0.7980 chunk 291 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN ** U 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.106009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.092965 restraints weight = 163023.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.092796 restraints weight = 325732.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.092394 restraints weight = 246879.826| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6253 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 30856 Z= 0.188 Angle : 0.642 8.208 43348 Z= 0.353 Chirality : 0.042 0.270 4804 Planarity : 0.005 0.122 4208 Dihedral : 28.700 179.754 7122 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.24 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.16), residues: 2632 helix: -0.03 (0.17), residues: 908 sheet: -1.06 (0.25), residues: 393 loop : -1.09 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP O 255 HIS 0.013 0.001 HIS D 659 PHE 0.023 0.001 PHE I 84 TYR 0.015 0.001 TYR J 72 ARG 0.020 0.000 ARG O 65 Details of bonding type rmsd hydrogen bonds : bond 0.07161 ( 1071) hydrogen bonds : angle 4.90828 ( 2756) SS BOND : bond 0.00567 ( 4) SS BOND : angle 3.28792 ( 8) covalent geometry : bond 0.00428 (30852) covalent geometry : angle 0.64016 (43340) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 3.069 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: D 244 MET cc_start: 0.4706 (mmm) cc_final: 0.4267 (tpt) REVERT: D 540 MET cc_start: 0.0538 (tpt) cc_final: 0.0313 (tpt) REVERT: J 58 LEU cc_start: 0.8679 (tp) cc_final: 0.8385 (tt) REVERT: V 39 TYR cc_start: 0.8728 (t80) cc_final: 0.8498 (t80) REVERT: V 56 MET cc_start: 0.8882 (tpp) cc_final: 0.8348 (tpp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.4396 time to fit residues: 73.8857 Evaluate side-chains 88 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 19 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 175 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 285 optimal weight: 7.9990 chunk 89 optimal weight: 0.4980 chunk 168 optimal weight: 0.9980 chunk 93 optimal weight: 0.1980 chunk 7 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 137 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 471 HIS ** D 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN O 373 HIS ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 410 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.107454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.094678 restraints weight = 163524.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.094177 restraints weight = 297626.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.093296 restraints weight = 212864.779| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6213 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 30856 Z= 0.142 Angle : 0.615 11.016 43348 Z= 0.338 Chirality : 0.040 0.216 4804 Planarity : 0.005 0.123 4208 Dihedral : 28.554 176.948 7122 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.94 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.16), residues: 2632 helix: 0.23 (0.17), residues: 899 sheet: -0.93 (0.25), residues: 383 loop : -1.03 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP O 255 HIS 0.012 0.001 HIS D 659 PHE 0.023 0.001 PHE R 25 TYR 0.017 0.001 TYR S 37 ARG 0.006 0.000 ARG J 92 Details of bonding type rmsd hydrogen bonds : bond 0.07353 ( 1071) hydrogen bonds : angle 4.62452 ( 2756) SS BOND : bond 0.00608 ( 4) SS BOND : angle 3.07670 ( 8) covalent geometry : bond 0.00317 (30852) covalent geometry : angle 0.61319 (43340) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 2.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 244 MET cc_start: 0.4690 (mmm) cc_final: 0.4014 (tpt) REVERT: D 299 MET cc_start: 0.5423 (ppp) cc_final: 0.5007 (tpt) REVERT: D 319 MET cc_start: -0.2447 (mmt) cc_final: -0.3135 (mmt) REVERT: D 540 MET cc_start: 0.0466 (tpt) cc_final: 0.0234 (tpt) REVERT: D 632 MET cc_start: 0.6496 (ptt) cc_final: 0.6290 (ptt) REVERT: E 121 MET cc_start: 0.3716 (ptt) cc_final: 0.3424 (ptp) REVERT: E 667 MET cc_start: 0.7098 (tmm) cc_final: 0.6822 (tpp) REVERT: J 58 LEU cc_start: 0.8564 (tp) cc_final: 0.8265 (tt) REVERT: R 38 ASN cc_start: 0.8162 (m-40) cc_final: 0.7745 (m-40) REVERT: U 78 ILE cc_start: 0.8269 (mt) cc_final: 0.8026 (mt) REVERT: V 56 MET cc_start: 0.8690 (tpp) cc_final: 0.8426 (tpp) REVERT: V 65 ASP cc_start: 0.8481 (t0) cc_final: 0.8195 (t0) REVERT: V 108 VAL cc_start: 0.8666 (m) cc_final: 0.8408 (t) REVERT: O 404 MET cc_start: 0.3595 (mpp) cc_final: 0.3243 (mpp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.4328 time to fit residues: 80.9071 Evaluate side-chains 93 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 0.2980 chunk 226 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 231 optimal weight: 1.9990 chunk 121 optimal weight: 0.0970 chunk 178 optimal weight: 0.5980 chunk 241 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN ** E 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.107386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.094671 restraints weight = 163491.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.094259 restraints weight = 305175.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.093591 restraints weight = 230760.043| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6194 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 30856 Z= 0.144 Angle : 0.610 10.060 43348 Z= 0.334 Chirality : 0.040 0.229 4804 Planarity : 0.004 0.121 4208 Dihedral : 28.439 178.850 7122 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.67 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2632 helix: 0.33 (0.17), residues: 898 sheet: -0.82 (0.25), residues: 383 loop : -0.98 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP O 255 HIS 0.012 0.001 HIS D 659 PHE 0.013 0.001 PHE E 729 TYR 0.014 0.001 TYR S 37 ARG 0.010 0.000 ARG O 340 Details of bonding type rmsd hydrogen bonds : bond 0.07149 ( 1071) hydrogen bonds : angle 4.58596 ( 2756) SS BOND : bond 0.00513 ( 4) SS BOND : angle 2.69733 ( 8) covalent geometry : bond 0.00322 (30852) covalent geometry : angle 0.60866 (43340) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6332.40 seconds wall clock time: 114 minutes 0.63 seconds (6840.63 seconds total)