Starting phenix.real_space_refine on Sat Aug 8 15:29:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tas_41141/08_2026/8tas_41141.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tas_41141/08_2026/8tas_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_41141/08_2026/8tas_41141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tas_41141/08_2026/8tas_41141.map" model { file = "/net/cci-nas-00/data/ceres_data/8tas_41141/08_2026/8tas_41141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tas_41141/08_2026/8tas_41141.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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: 5.29, per 1000 atoms: 0.18 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: 2.19 Conformation dependent library (CDL) restraints added in 792.7 milliseconds 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: 2.85 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: 5.84 Time building geometry restraints manager: 2.88 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=" C3' DG H 140 " pdb=" O3' DG H 140 " ideal model delta sigma weight residual 1.435 1.387 0.048 1.30e-02 5.92e+03 1.39e+01 bond pdb=" C3' DG H 136 " pdb=" C2' DG H 136 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.33e+01 bond pdb=" C3' DG T 172 " pdb=" O3' DG T 172 " ideal model delta sigma weight residual 1.435 1.390 0.045 1.30e-02 5.92e+03 1.20e+01 bond pdb=" C3' DC H 111 " pdb=" C2' DC H 111 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 ... (remaining 30847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 42608 3.97 - 7.94: 161 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 - 0.126: 4426 0.126 - 0.251: 69 0.251 - 0.377: 93 0.377 - 0.503: 194 0.503 - 0.628: 22 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 2.34 -2.96 -0.63 2.00e-01 2.50e+01 9.87e+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 2.34 -2.95 -0.61 2.00e-01 2.50e+01 9.32e+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 2.34 -2.94 -0.60 2.00e-01 2.50e+01 9.05e+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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 25.240 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 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= 0.475 Angle : 1.457 19.860 43348 Z= 0.691 Chirality : 0.113 0.628 4804 Planarity : 0.005 0.128 4208 Dihedral : 23.568 179.445 12476 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 19.77 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.001 ARG U 77 TYR 0.058 0.002 TYR V 80 PHE 0.035 0.002 PHE I 67 TRP 0.019 0.002 TRP E 113 HIS 0.008 0.001 HIS X 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.48 (30852) covalent geometry : angle 1.45643 / 0.69 (43340) SS BOND : bond 0.00752 / 0.32 ( 4) SS BOND : angle 3.21059 / 1.64 ( 8) hydrogen bonds : bond 0.30886 / 20.45 ( 1071) hydrogen bonds : angle 10.94658 / 7.50 ( 2756) *********************** 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 : 0.620 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: 0.6986 (mpp) REVERT: R 38 ASN cc_start: 0.8261 (m-40) cc_final: 0.7992 (m-40) REVERT: X 49 LEU cc_start: 0.8762 (tp) cc_final: 0.8561 (tp) REVERT: O 36 MET cc_start: 0.0594 (tpt) cc_final: -0.0229 (tpt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1538 time to fit residues: 28.2947 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 : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 6.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 156 HIS ** D 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN ** D 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 HIS D 517 ASN ** D 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 667 ASN E 45 ASN ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 ASN E 180 GLN E 273 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 520 ASN G 146 ASN G 160 HIS ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 272 ASN G 283 ASN G 382 GLN I 68 GLN I 108 ASN 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** ** V 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 GLN W 39 HIS W 125 GLN O 48 GLN 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 = 0.4264 r_free = 0.4264 target = 0.105659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.091337 restraints weight = 162168.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.091705 restraints weight = 350129.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.091481 restraints weight = 207938.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.091347 restraints weight = 176263.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.091518 restraints weight = 149039.822| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 30856 Z= 0.306 Angle : 0.839 11.652 43348 Z= 0.460 Chirality : 0.054 0.300 4804 Planarity : 0.006 0.125 4208 Dihedral : 28.261 179.994 7122 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.12 % Favored : 93.77 % Rotamer: Outliers : 0.21 % Allowed : 5.06 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.16), residues: 2632 helix: -0.85 (0.16), residues: 902 sheet: -1.21 (0.24), residues: 405 loop : -1.11 (0.18), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 39 TYR 0.026 0.002 TYR V 80 PHE 0.026 0.002 PHE I 67 TRP 0.019 0.002 TRP E 113 HIS 0.012 0.001 HIS X 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.31 (30852) covalent geometry : angle 0.83707 / 0.46 (43340) SS BOND : bond 0.01353 / 0.66 ( 4) SS BOND : angle 3.84958 / 1.84 ( 8) hydrogen bonds : bond 0.10228 / 6.40 ( 1071) hydrogen bonds : angle 6.54237 / 4.38 ( 2756) *********************** 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 105 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.970 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: E 748 MET cc_start: 0.5238 (pmm) cc_final: 0.4986 (pmm) REVERT: S 92 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7631 (tm-30) REVERT: V 39 TYR cc_start: 0.8957 (t80) cc_final: 0.8726 (t80) REVERT: X 49 LEU cc_start: 0.8641 (tp) cc_final: 0.8414 (tp) outliers start: 5 outliers final: 2 residues processed: 105 average time/residue: 0.1747 time to fit residues: 31.2826 Evaluate side-chains 84 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 78 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 282 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 261 optimal weight: 50.0000 chunk 291 optimal weight: 9.9990 chunk 166 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 126 optimal weight: 0.0060 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 166 HIS ** D 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN E 331 GLN ** 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 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN U 84 GLN V 46 HIS V 81 ASN O 157 HIS ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.107324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.092791 restraints weight = 161756.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.092869 restraints weight = 334290.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.092460 restraints weight = 216176.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.092350 restraints weight = 171189.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.092471 restraints weight = 150656.529| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.1840 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= 0.180 Angle : 0.715 8.487 43348 Z= 0.395 Chirality : 0.049 0.317 4804 Planarity : 0.005 0.123 4208 Dihedral : 28.399 176.606 7122 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.09 % Favored : 94.83 % Rotamer: Outliers : 0.04 % Allowed : 4.60 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.16), residues: 2632 helix: -0.37 (0.16), residues: 907 sheet: -1.29 (0.24), residues: 389 loop : -1.06 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 76 TYR 0.022 0.002 TYR X 88 PHE 0.023 0.001 PHE I 67 TRP 0.014 0.001 TRP O 255 HIS 0.019 0.001 HIS E 711 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 (30852) covalent geometry : angle 0.71328 / 0.39 (43340) SS BOND : bond 0.00827 / 0.36 ( 4) SS BOND : angle 3.44564 / 1.76 ( 8) hydrogen bonds : bond 0.08675 / 5.61 ( 1071) hydrogen bonds : angle 5.65888 / 3.77 ( 2756) *********************** 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 115 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 73 THR cc_start: 0.9295 (p) cc_final: 0.9071 (t) REVERT: J 84 MET cc_start: 0.7624 (mmm) cc_final: 0.7138 (mpp) outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.1912 time to fit residues: 36.2117 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 : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 168 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 196 optimal weight: 10.0000 chunk 224 optimal weight: 0.0770 chunk 247 optimal weight: 0.9980 chunk 195 optimal weight: 20.0000 chunk 297 optimal weight: 0.3980 chunk 1 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 241 optimal weight: 0.6980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 624 HIS ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN E 711 HIS ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN ** O 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 157 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.108064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.093272 restraints weight = 160839.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.093110 restraints weight = 309214.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.092869 restraints weight = 222263.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.092790 restraints weight = 170359.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.092972 restraints weight = 150698.573| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.2180 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= 0.150 Angle : 0.682 8.385 43348 Z= 0.378 Chirality : 0.048 0.349 4804 Planarity : 0.005 0.123 4208 Dihedral : 28.325 179.898 7122 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.09 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.16), residues: 2632 helix: -0.05 (0.17), residues: 911 sheet: -1.33 (0.24), residues: 396 loop : -0.98 (0.18), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 288 TYR 0.012 0.001 TYR W 41 PHE 0.025 0.001 PHE U 25 TRP 0.032 0.001 TRP O 402 HIS 0.009 0.001 HIS G 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (30852) covalent geometry : angle 0.68107 / 0.38 (43340) SS BOND : bond 0.02365 / 1.03 ( 4) SS BOND : angle 3.21787 / 1.50 ( 8) hydrogen bonds : bond 0.08068 / 5.26 ( 1071) hydrogen bonds : angle 5.21884 / 3.47 ( 2756) *********************** 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 122 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 667 MET cc_start: 0.7152 (tmm) cc_final: 0.6903 (tmm) REVERT: U 78 ILE cc_start: 0.8088 (mt) cc_final: 0.7861 (mt) REVERT: V 65 ASP cc_start: 0.8321 (t0) cc_final: 0.7920 (t0) REVERT: V 80 TYR cc_start: 0.8237 (m-10) cc_final: 0.7979 (m-10) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1966 time to fit residues: 39.4077 Evaluate side-chains 92 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 288 optimal weight: 8.9990 chunk 279 optimal weight: 50.0000 chunk 172 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 171 optimal weight: 0.7980 chunk 48 optimal weight: 30.0000 chunk 269 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 295 optimal weight: 4.9990 chunk 267 optimal weight: 0.0770 chunk 143 optimal weight: 0.6980 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN E 331 GLN ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN ** O 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 410 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.107812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.093247 restraints weight = 161493.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.093058 restraints weight = 314115.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.093090 restraints weight = 221213.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.092988 restraints weight = 171436.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.093030 restraints weight = 159295.840| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 30856 Z= 0.153 Angle : 0.665 8.316 43348 Z= 0.368 Chirality : 0.047 0.358 4804 Planarity : 0.004 0.121 4208 Dihedral : 28.297 179.991 7122 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.13 % Favored : 94.79 % Rotamer: Outliers : 0.04 % Allowed : 2.51 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.16), residues: 2632 helix: 0.05 (0.17), residues: 915 sheet: -1.24 (0.24), residues: 387 loop : -1.00 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 461 TYR 0.013 0.001 TYR G 186 PHE 0.019 0.001 PHE U 25 TRP 0.016 0.001 TRP O 255 HIS 0.006 0.001 HIS G 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (30852) covalent geometry : angle 0.66377 / 0.37 (43340) SS BOND : bond 0.00824 / 0.32 ( 4) SS BOND : angle 2.70251 / 1.30 ( 8) hydrogen bonds : bond 0.07883 / 5.10 ( 1071) hydrogen bonds : angle 5.07356 / 3.38 ( 2756) *********************** 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 122 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 253 ARG cc_start: 0.6421 (tpt90) cc_final: 0.6174 (mmm-85) REVERT: E 667 MET cc_start: 0.7125 (tmm) cc_final: 0.6872 (tmm) REVERT: J 84 MET cc_start: 0.7516 (mmm) cc_final: 0.7125 (mpp) REVERT: V 65 ASP cc_start: 0.8326 (t0) cc_final: 0.7950 (t0) REVERT: V 80 TYR cc_start: 0.8343 (m-10) cc_final: 0.7805 (m-10) outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 0.1987 time to fit residues: 39.2188 Evaluate side-chains 94 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 1 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 217 optimal weight: 0.9990 chunk 282 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 298 optimal weight: 9.9990 chunk 215 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 201 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 567 HIS D 659 HIS E 273 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN ** U 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 226 HIS ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.105489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.091124 restraints weight = 161116.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.091579 restraints weight = 341838.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.091264 restraints weight = 206092.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.091096 restraints weight = 177027.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.091214 restraints weight = 151828.965| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 30856 Z= 0.294 Angle : 0.779 9.873 43348 Z= 0.423 Chirality : 0.051 0.313 4804 Planarity : 0.005 0.121 4208 Dihedral : 28.480 177.305 7122 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.81 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.16), residues: 2632 helix: -0.36 (0.17), residues: 903 sheet: -1.34 (0.24), residues: 404 loop : -1.03 (0.18), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 76 TYR 0.019 0.002 TYR W 54 PHE 0.022 0.002 PHE O 243 TRP 0.023 0.002 TRP E 113 HIS 0.013 0.001 HIS X 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.29 (30852) covalent geometry : angle 0.77785 / 0.42 (43340) SS BOND : bond 0.00828 / 0.40 ( 4) SS BOND : angle 3.18050 / 1.68 ( 8) hydrogen bonds : bond 0.08527 / 5.40 ( 1071) hydrogen bonds : angle 5.53000 / 3.69 ( 2756) *********************** 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 104 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 253 ARG cc_start: 0.6414 (tpt90) cc_final: 0.6141 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1872 time to fit residues: 31.8544 Evaluate side-chains 82 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 222 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 188 optimal weight: 0.4980 chunk 7 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 152 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 133 optimal weight: 30.0000 chunk 256 optimal weight: 40.0000 chunk 229 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 189 HIS ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.107017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.092160 restraints weight = 160985.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.092125 restraints weight = 316901.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.092040 restraints weight = 223827.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.091943 restraints weight = 173388.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.092000 restraints weight = 159228.902| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6358 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 30856 Z= 0.168 Angle : 0.682 8.587 43348 Z= 0.376 Chirality : 0.047 0.344 4804 Planarity : 0.004 0.119 4208 Dihedral : 28.472 179.675 7122 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.09 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.16), residues: 2632 helix: -0.10 (0.17), residues: 906 sheet: -1.18 (0.24), residues: 385 loop : -1.00 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 360 TYR 0.019 0.001 TYR G 278 PHE 0.019 0.001 PHE U 25 TRP 0.025 0.001 TRP D 361 HIS 0.006 0.001 HIS E 711 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 (30852) covalent geometry : angle 0.68072 / 0.38 (43340) SS BOND : bond 0.00779 / 0.30 ( 4) SS BOND : angle 3.58705 / 1.63 ( 8) hydrogen bonds : bond 0.07669 / 4.94 ( 1071) hydrogen bonds : angle 5.11739 / 3.41 ( 2756) *********************** 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 108 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 253 ARG cc_start: 0.6367 (tpt90) cc_final: 0.6104 (mmm-85) REVERT: E 667 MET cc_start: 0.6898 (tmm) cc_final: 0.6656 (tmm) REVERT: J 84 MET cc_start: 0.7221 (mmm) cc_final: 0.6772 (mpp) REVERT: V 65 ASP cc_start: 0.8470 (t0) cc_final: 0.8030 (t0) REVERT: O 253 MET cc_start: -0.2362 (tpp) cc_final: -0.3760 (tpp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1908 time to fit residues: 33.6722 Evaluate side-chains 83 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 113 optimal weight: 0.7980 chunk 228 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 142 optimal weight: 0.4980 chunk 61 optimal weight: 5.9990 chunk 176 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 266 optimal weight: 50.0000 chunk 184 optimal weight: 0.0980 chunk 185 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 273 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN G 213 HIS ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.107952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.093220 restraints weight = 161191.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.093235 restraints weight = 306709.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.093120 restraints weight = 213638.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.092976 restraints weight = 172045.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.093060 restraints weight = 155172.184| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 30856 Z= 0.140 Angle : 0.654 8.513 43348 Z= 0.362 Chirality : 0.047 0.365 4804 Planarity : 0.004 0.119 4208 Dihedral : 28.370 179.652 7122 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.24 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.16), residues: 2632 helix: 0.06 (0.17), residues: 908 sheet: -1.25 (0.24), residues: 391 loop : -0.96 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 288 TYR 0.013 0.001 TYR S 37 PHE 0.013 0.001 PHE O 243 TRP 0.018 0.001 TRP O 255 HIS 0.011 0.001 HIS O 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (30852) covalent geometry : angle 0.65301 / 0.36 (43340) SS BOND : bond 0.00840 / 0.36 ( 4) SS BOND : angle 3.03744 / 1.39 ( 8) hydrogen bonds : bond 0.07671 / 4.96 ( 1071) hydrogen bonds : angle 4.86428 / 3.24 ( 2756) *********************** 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 108 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 253 ARG cc_start: 0.6331 (tpt90) cc_final: 0.6060 (mmm-85) REVERT: I 79 LYS cc_start: 0.8683 (tmmt) cc_final: 0.8377 (ptmm) REVERT: J 84 MET cc_start: 0.7407 (mmm) cc_final: 0.6970 (mpp) REVERT: U 78 ILE cc_start: 0.8338 (mt) cc_final: 0.8133 (mt) REVERT: V 65 ASP cc_start: 0.8362 (t0) cc_final: 0.7930 (t0) REVERT: V 80 TYR cc_start: 0.8300 (m-10) cc_final: 0.7644 (m-10) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1922 time to fit residues: 34.1781 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 : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 19 optimal weight: 9.9990 chunk 186 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 204 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 205 optimal weight: 9.9990 chunk 245 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 273 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN G 213 HIS ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN ** U 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.106444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.093438 restraints weight = 162967.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.093340 restraints weight = 320366.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.092452 restraints weight = 205575.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.092191 restraints weight = 196749.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.092044 restraints weight = 169732.580| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 30856 Z= 0.211 Angle : 0.705 9.546 43348 Z= 0.385 Chirality : 0.048 0.337 4804 Planarity : 0.005 0.119 4208 Dihedral : 28.471 176.439 7122 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.43 % Favored : 94.45 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.16), residues: 2632 helix: -0.07 (0.17), residues: 908 sheet: -1.07 (0.25), residues: 379 loop : -1.03 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 236 TYR 0.015 0.002 TYR J 72 PHE 0.022 0.002 PHE I 104 TRP 0.018 0.001 TRP E 113 HIS 0.010 0.001 HIS G 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.21 (30852) covalent geometry : angle 0.70386 / 0.38 (43340) SS BOND : bond 0.00565 / 0.26 ( 4) SS BOND : angle 2.84187 / 1.36 ( 8) hydrogen bonds : bond 0.07761 / 4.94 ( 1071) hydrogen bonds : angle 5.08629 / 3.39 ( 2756) *********************** 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 102 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 253 MET cc_start: -0.1892 (tpp) cc_final: -0.2339 (tpp) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2113 time to fit residues: 34.6622 Evaluate side-chains 84 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 227 optimal weight: 0.7980 chunk 268 optimal weight: 8.9990 chunk 172 optimal weight: 0.6980 chunk 271 optimal weight: 50.0000 chunk 16 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 263 optimal weight: 4.9990 chunk 238 optimal weight: 0.5980 chunk 277 optimal weight: 9.9990 chunk 256 optimal weight: 40.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 273 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN ** I 93 GLN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.106747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.093870 restraints weight = 161328.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.093672 restraints weight = 338148.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.093382 restraints weight = 248970.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.093161 restraints weight = 200919.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.093101 restraints weight = 183659.141| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 30856 Z= 0.173 Angle : 0.684 10.405 43348 Z= 0.375 Chirality : 0.047 0.342 4804 Planarity : 0.004 0.119 4208 Dihedral : 28.493 176.813 7122 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.17 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.16), residues: 2632 helix: -0.03 (0.17), residues: 910 sheet: -1.07 (0.25), residues: 383 loop : -1.01 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 76 TYR 0.014 0.001 TYR J 72 PHE 0.022 0.001 PHE U 25 TRP 0.014 0.001 TRP O 255 HIS 0.006 0.001 HIS X 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (30852) covalent geometry : angle 0.68302 / 0.37 (43340) SS BOND : bond 0.00577 / 0.24 ( 4) SS BOND : angle 2.85846 / 1.35 ( 8) hydrogen bonds : bond 0.07556 / 4.85 ( 1071) hydrogen bonds : angle 4.99368 / 3.32 ( 2756) ********************** 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 105 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 84 MET cc_start: 0.7459 (mmm) cc_final: 0.7104 (mpp) REVERT: V 39 TYR cc_start: 0.8624 (t80) cc_final: 0.8236 (t80) REVERT: V 80 TYR cc_start: 0.8450 (m-10) cc_final: 0.7734 (m-10) REVERT: O 253 MET cc_start: -0.1823 (tpp) cc_final: -0.2292 (tpp) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1987 time to fit residues: 33.6229 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 : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 32 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 20 optimal weight: 0.0470 chunk 49 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 269 optimal weight: 30.0000 chunk 117 optimal weight: 3.9990 chunk 215 optimal weight: 0.6980 chunk 185 optimal weight: 0.9980 chunk 211 optimal weight: 30.0000 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 273 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN ** I 93 GLN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.106542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.093332 restraints weight = 162539.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.093270 restraints weight = 326323.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.092900 restraints weight = 287068.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.092862 restraints weight = 207057.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.092888 restraints weight = 185545.898| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 30856 Z= 0.182 Angle : 0.692 10.319 43348 Z= 0.378 Chirality : 0.048 0.343 4804 Planarity : 0.005 0.119 4208 Dihedral : 28.518 176.103 7122 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.32 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.16), residues: 2632 helix: -0.03 (0.17), residues: 916 sheet: -1.02 (0.25), residues: 381 loop : -1.02 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG U 29 TYR 0.014 0.001 TYR J 72 PHE 0.019 0.001 PHE I 67 TRP 0.016 0.001 TRP E 113 HIS 0.007 0.001 HIS X 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (30852) covalent geometry : angle 0.69050 / 0.38 (43340) SS BOND : bond 0.00579 / 0.25 ( 4) SS BOND : angle 2.82846 / 1.36 ( 8) hydrogen bonds : bond 0.07585 / 4.85 ( 1071) hydrogen bonds : angle 5.00136 / 3.33 ( 2756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3407.46 seconds wall clock time: 60 minutes 52.77 seconds (3652.77 seconds total)