Starting phenix.real_space_refine on Mon Aug 25 15:21:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tas_41141/08_2025/8tas_41141.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tas_41141/08_2025/8tas_41141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tas_41141/08_2025/8tas_41141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tas_41141/08_2025/8tas_41141.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tas_41141/08_2025/8tas_41141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tas_41141/08_2025/8tas_41141.map" } 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-2.0-5787/lib/python3.9/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: 5.57, per 1000 atoms: 0.19 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: 2.04 Conformation dependent library (CDL) restraints added in 850.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 4.19 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: 6.13 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8435 1.34 - 1.46: 9127 1.46 - 1.59: 12354 1.59 - 1.71: 765 1.71 - 1.84: 171 Bond restraints: 30852 Sorted by residual: bond pdb=" C LEU S 99 " pdb=" N PRO S 100 " ideal model delta sigma weight residual 1.335 1.296 0.039 8.70e-03 1.32e+04 1.96e+01 bond pdb=" C2 SAH E 801 " pdb=" N3 SAH E 801 " ideal model delta sigma weight residual 1.322 1.380 -0.058 2.00e-02 2.50e+03 8.45e+00 bond pdb=" C8 SAH E 801 " pdb=" N7 SAH E 801 " ideal model delta sigma weight residual 1.299 1.353 -0.054 2.00e-02 2.50e+03 7.34e+00 bond pdb=" C2 SAH E 801 " pdb=" N1 SAH E 801 " ideal model delta sigma weight residual 1.330 1.379 -0.049 2.00e-02 2.50e+03 6.11e+00 bond pdb=" CA LEU J 97 " pdb=" CB LEU J 97 " ideal model delta sigma weight residual 1.526 1.484 0.042 1.70e-02 3.46e+03 6.06e+00 ... (remaining 30847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 42609 3.97 - 7.94: 160 7.94 - 11.92: 519 11.92 - 15.89: 38 15.89 - 19.86: 14 Bond angle restraints: 43340 Sorted by residual: angle pdb=" O3' DC T 67 " pdb=" P DC T 68 " pdb=" OP1 DC T 68 " ideal model delta sigma weight residual 108.00 127.86 -19.86 3.00e+00 1.11e-01 4.38e+01 angle pdb=" O3' DG T 46 " pdb=" P DA T 47 " pdb=" OP1 DA T 47 " ideal model delta sigma weight residual 108.00 127.03 -19.03 3.00e+00 1.11e-01 4.02e+01 angle pdb=" O3' DC T 150 " pdb=" P DC T 151 " pdb=" OP1 DC T 151 " ideal model delta sigma weight residual 108.00 126.96 -18.96 3.00e+00 1.11e-01 3.99e+01 angle pdb=" O3' DC H 104 " pdb=" P DG H 105 " pdb=" OP1 DG H 105 " ideal model delta sigma weight residual 108.00 126.69 -18.69 3.00e+00 1.11e-01 3.88e+01 angle pdb=" O3' DC T 120 " pdb=" P DC T 121 " pdb=" OP1 DC T 121 " ideal model delta sigma weight residual 108.00 126.50 -18.50 3.00e+00 1.11e-01 3.80e+01 ... (remaining 43335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 15859 35.89 - 71.78: 1643 71.78 - 107.67: 61 107.67 - 143.56: 3 143.56 - 179.45: 24 Dihedral angle restraints: 17590 sinusoidal: 9746 harmonic: 7844 Sorted by residual: dihedral pdb=" CB CYS E 565 " pdb=" SG CYS E 565 " pdb=" SG CYS E 578 " pdb=" CB CYS E 578 " ideal model delta sinusoidal sigma weight residual -86.00 -174.31 88.31 1 1.00e+01 1.00e-02 9.32e+01 dihedral pdb=" CB CYS E 565 " pdb=" SG CYS E 565 " pdb=" SG CYS E 571 " pdb=" CB CYS E 571 " ideal model delta sinusoidal sigma weight residual -86.00 -165.38 79.38 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS E 590 " pdb=" SG CYS E 590 " pdb=" SG CYS E 593 " pdb=" CB CYS E 593 " ideal model delta sinusoidal sigma weight residual 93.00 150.00 -57.00 1 1.00e+01 1.00e-02 4.37e+01 ... (remaining 17587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 4459 0.124 - 0.247: 37 0.247 - 0.371: 103 0.371 - 0.495: 184 0.495 - 0.618: 21 Chirality restraints: 4804 Sorted by residual: chirality pdb=" P DC T 68 " pdb=" OP1 DC T 68 " pdb=" OP2 DC T 68 " pdb=" O5' DC T 68 " both_signs ideal model delta sigma weight residual True 2.35 -2.96 -0.62 2.00e-01 2.50e+01 9.55e+00 chirality pdb=" P DC T 110 " pdb=" OP1 DC T 110 " pdb=" OP2 DC T 110 " pdb=" O5' DC T 110 " both_signs ideal model delta sigma weight residual True 2.35 -2.95 -0.60 2.00e-01 2.50e+01 9.01e+00 chirality pdb=" P DC T 151 " pdb=" OP1 DC T 151 " pdb=" OP2 DC T 151 " pdb=" O5' DC T 151 " both_signs ideal model delta sigma weight residual True 2.35 -2.94 -0.59 2.00e-01 2.50e+01 8.75e+00 ... (remaining 4801 not shown) Planarity restraints: 4208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 326 " -0.084 5.00e-02 4.00e+02 1.28e-01 2.63e+01 pdb=" N PRO E 327 " 0.222 5.00e-02 4.00e+02 pdb=" CA PRO E 327 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO E 327 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR V 80 " -0.036 2.00e-02 2.50e+03 2.65e-02 1.40e+01 pdb=" CG TYR V 80 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR V 80 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR V 80 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR V 80 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR V 80 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR V 80 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR V 80 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 67 " -0.014 2.00e-02 2.50e+03 1.51e-02 3.99e+00 pdb=" CG PHE I 67 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE I 67 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE I 67 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE I 67 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE I 67 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE I 67 " -0.001 2.00e-02 2.50e+03 ... (remaining 4205 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 713 2.63 - 3.20: 28738 3.20 - 3.77: 53240 3.77 - 4.33: 70130 4.33 - 4.90: 101065 Nonbonded interactions: 253886 Sorted by model distance: nonbonded pdb=" OH TYR J 98 " pdb=" OD2 ASP S 65 " model vdw 2.069 3.040 nonbonded pdb=" O CYS E 567 " pdb=" OG1 THR E 592 " model vdw 2.098 3.040 nonbonded pdb=" OD2 ASP O 318 " pdb=" OG1 THR O 338 " model vdw 2.104 3.040 nonbonded pdb=" OG SER G 210 " pdb=" OD1 ASP G 212 " model vdw 2.110 3.040 nonbonded pdb=" O HIS V 106 " pdb=" OG SER V 109 " model vdw 2.124 3.040 ... (remaining 253881 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'I' and resid 37 through 135) selection = chain 'W' } ncs_group { reference = (chain 'J' and ((resid 20 through 23 and (name N or name CA or name C or name O \ or name CB )) or resid 24 through 102)) selection = (chain 'X' and resid 20 through 102) } ncs_group { reference = (chain 'R' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 119)) selection = chain 'U' } ncs_group { reference = (chain 'S' and resid 28 through 122) selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.210 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: 0.040 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 27.120 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 30856 Z= 0.258 Angle : 1.417 19.860 43348 Z= 0.567 Chirality : 0.108 0.618 4804 Planarity : 0.005 0.128 4208 Dihedral : 23.568 179.445 12476 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 19.77 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 aren 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 covalent geometry : bond 0.00573 (30852) covalent geometry : angle 1.41666 (43340) SS BOND : bond 0.00752 ( 4) SS BOND : angle 3.21059 ( 8) hydrogen bonds : bond 0.30886 ( 1071) hydrogen bonds : angle 10.94658 ( 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 : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 84 MET cc_start: 0.7819 (mmm) cc_final: 0.6985 (mpp) REVERT: R 38 ASN cc_start: 0.8261 (m-40) cc_final: 0.7992 (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: 0.1416 time to fit residues: 26.2821 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 : 0.860 ------------------------------------------------------------------------------- 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: 2.9990 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: 3.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 156 HIS D 166 HIS D 356 GLN D 449 HIS D 517 ASN ** D 624 HIS ** 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 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 108 ASN R 31 HIS ** 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** V 46 HIS V 92 GLN W 39 HIS W 125 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 = 0.4278 r_free = 0.4278 target = 0.106584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.092229 restraints weight = 162241.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.092519 restraints weight = 338026.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.092122 restraints weight = 214345.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.092014 restraints weight = 176266.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.092218 restraints weight = 150542.914| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6320 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 30856 Z= 0.257 Angle : 0.712 10.442 43348 Z= 0.397 Chirality : 0.045 0.243 4804 Planarity : 0.005 0.125 4208 Dihedral : 28.359 178.997 7122 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.62 % Favored : 94.26 % Rotamer: Outliers : 0.21 % Allowed : 5.02 % Favored : 94.77 % 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 aren not related in a simple way. whole: -1.30 (0.16), residues: 2632 helix: -0.40 (0.17), residues: 909 sheet: -1.07 (0.25), residues: 392 loop : -1.04 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 39 TYR 0.022 0.002 TYR V 80 PHE 0.024 0.002 PHE I 67 TRP 0.016 0.001 TRP O 255 HIS 0.011 0.001 HIS X 75 Details of bonding type rmsd covalent geometry : bond 0.00580 (30852) covalent geometry : angle 0.71066 (43340) SS BOND : bond 0.01306 ( 4) SS BOND : angle 3.34388 ( 8) hydrogen bonds : bond 0.08496 ( 1071) hydrogen bonds : angle 5.93883 ( 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 112 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 748 MET cc_start: 0.5226 (pmm) cc_final: 0.4993 (pmm) REVERT: S 56 MET cc_start: 0.8155 (tmm) cc_final: 0.7953 (tmm) REVERT: S 92 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: V 39 TYR cc_start: 0.8891 (t80) cc_final: 0.8623 (t80) REVERT: X 49 LEU cc_start: 0.8600 (tp) cc_final: 0.8380 (tp) outliers start: 5 outliers final: 1 residues processed: 112 average time/residue: 0.1592 time to fit residues: 29.7449 Evaluate side-chains 84 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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: 2.9990 chunk 63 optimal weight: 10.0000 chunk 282 optimal weight: 0.0980 chunk 248 optimal weight: 8.9990 chunk 261 optimal weight: 50.0000 chunk 291 optimal weight: 9.9990 chunk 166 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 S 106 HIS ** U 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 ASN ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.106281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.091896 restraints weight = 162100.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.092097 restraints weight = 336619.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.091581 restraints weight = 206062.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.091546 restraints weight = 160849.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.091564 restraints weight = 146312.340| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 30856 Z= 0.234 Angle : 0.677 8.134 43348 Z= 0.374 Chirality : 0.043 0.238 4804 Planarity : 0.005 0.121 4208 Dihedral : 28.428 179.609 7122 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.66 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % 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 aren not related in a simple way. whole: -1.28 (0.16), residues: 2632 helix: -0.35 (0.17), residues: 912 sheet: -1.22 (0.24), residues: 400 loop : -1.00 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 76 TYR 0.018 0.002 TYR J 72 PHE 0.030 0.002 PHE I 67 TRP 0.014 0.001 TRP O 402 HIS 0.012 0.001 HIS X 75 Details of bonding type rmsd covalent geometry : bond 0.00531 (30852) covalent geometry : angle 0.67597 (43340) SS BOND : bond 0.00831 ( 4) SS BOND : angle 3.39689 ( 8) hydrogen bonds : bond 0.07969 ( 1071) hydrogen bonds : angle 5.44967 ( 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 103 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 56 MET cc_start: 0.8304 (tmm) cc_final: 0.7749 (tmm) REVERT: V 39 TYR cc_start: 0.8458 (t80) cc_final: 0.8253 (t80) REVERT: V 56 MET cc_start: 0.8960 (tpp) cc_final: 0.8750 (tpp) REVERT: X 49 LEU cc_start: 0.8685 (tp) cc_final: 0.8389 (tp) REVERT: O 404 MET cc_start: 0.4807 (mpp) cc_final: 0.4509 (mpp) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1645 time to fit residues: 27.6552 Evaluate side-chains 86 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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: 2.9990 chunk 129 optimal weight: 8.9990 chunk 24 optimal weight: 50.0000 chunk 196 optimal weight: 4.9990 chunk 224 optimal weight: 0.0470 chunk 247 optimal weight: 0.5980 chunk 195 optimal weight: 5.9990 chunk 297 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 172 optimal weight: 0.8980 chunk 241 optimal weight: 0.7980 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 624 HIS E 273 GLN E 331 GLN ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 81 ASN S 92 GLN U 84 GLN ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 410 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.107415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.092707 restraints weight = 160370.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.092584 restraints weight = 313689.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.092587 restraints weight = 221089.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.092526 restraints weight = 168157.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.092604 restraints weight = 154036.568| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 30856 Z= 0.170 Angle : 0.624 7.984 43348 Z= 0.347 Chirality : 0.041 0.224 4804 Planarity : 0.004 0.122 4208 Dihedral : 28.331 179.827 7122 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.09 % Favored : 94.83 % Rotamer: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.26 % 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 aren not related in a simple way. whole: -1.05 (0.16), residues: 2632 helix: -0.06 (0.17), residues: 915 sheet: -1.08 (0.25), residues: 396 loop : -0.95 (0.18), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 76 TYR 0.012 0.001 TYR G 186 PHE 0.014 0.001 PHE I 67 TRP 0.020 0.001 TRP O 255 HIS 0.009 0.001 HIS D 659 Details of bonding type rmsd covalent geometry : bond 0.00382 (30852) covalent geometry : angle 0.62295 (43340) SS BOND : bond 0.01163 ( 4) SS BOND : angle 2.99743 ( 8) hydrogen bonds : bond 0.07456 ( 1071) hydrogen bonds : angle 5.02783 ( 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 117 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 667 MET cc_start: 0.6889 (tmm) cc_final: 0.6616 (tmm) REVERT: J 84 MET cc_start: 0.7771 (mmm) cc_final: 0.7274 (mpp) REVERT: S 39 TYR cc_start: 0.7962 (t80) cc_final: 0.7729 (t80) REVERT: S 56 MET cc_start: 0.8067 (tmm) cc_final: 0.7742 (tmm) REVERT: V 39 TYR cc_start: 0.8444 (t80) cc_final: 0.8189 (t80) REVERT: V 56 MET cc_start: 0.8987 (tpp) cc_final: 0.8660 (tpp) REVERT: V 65 ASP cc_start: 0.8455 (t0) cc_final: 0.8039 (t0) REVERT: V 80 TYR cc_start: 0.8224 (m-10) cc_final: 0.7681 (m-10) outliers start: 1 outliers final: 0 residues processed: 117 average time/residue: 0.1786 time to fit residues: 32.5942 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 : 0.887 ------------------------------------------------------------------------------- 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: 5.9990 chunk 279 optimal weight: 7.9990 chunk 172 optimal weight: 0.9980 chunk 74 optimal weight: 0.0020 chunk 171 optimal weight: 0.6980 chunk 48 optimal weight: 20.0000 chunk 269 optimal weight: 50.0000 chunk 176 optimal weight: 1.9990 chunk 295 optimal weight: 9.9990 chunk 267 optimal weight: 10.0000 chunk 143 optimal weight: 0.6980 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 58 GLN E 273 GLN E 575 GLN ** G 213 HIS ** 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 = 0.4302 r_free = 0.4302 target = 0.107923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.093530 restraints weight = 161244.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.093304 restraints weight = 308554.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.092828 restraints weight = 230584.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.092728 restraints weight = 173775.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.092728 restraints weight = 159344.987| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 30856 Z= 0.158 Angle : 0.607 7.588 43348 Z= 0.336 Chirality : 0.041 0.219 4804 Planarity : 0.004 0.119 4208 Dihedral : 28.196 179.796 7122 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.02 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.16), residues: 2632 helix: 0.17 (0.17), residues: 907 sheet: -1.02 (0.25), residues: 403 loop : -0.90 (0.18), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 52 TYR 0.013 0.001 TYR J 72 PHE 0.012 0.001 PHE O 243 TRP 0.019 0.001 TRP O 255 HIS 0.012 0.001 HIS D 659 Details of bonding type rmsd covalent geometry : bond 0.00352 (30852) covalent geometry : angle 0.60641 (43340) SS BOND : bond 0.00649 ( 4) SS BOND : angle 2.59500 ( 8) hydrogen bonds : bond 0.07330 ( 1071) hydrogen bonds : angle 4.80453 ( 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 117 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 253 ARG cc_start: 0.6439 (tpt90) cc_final: 0.6181 (mmm-85) REVERT: E 667 MET cc_start: 0.7177 (tmm) cc_final: 0.6896 (tmm) REVERT: S 56 MET cc_start: 0.8004 (tmm) cc_final: 0.7760 (tmm) REVERT: U 78 ILE cc_start: 0.8158 (mt) cc_final: 0.7950 (mt) REVERT: V 39 TYR cc_start: 0.8324 (t80) cc_final: 0.8052 (t80) REVERT: V 56 MET cc_start: 0.8954 (tpp) cc_final: 0.8647 (tpp) REVERT: V 65 ASP cc_start: 0.8469 (t0) cc_final: 0.8060 (t0) REVERT: V 80 TYR cc_start: 0.8245 (m-10) cc_final: 0.7678 (m-10) REVERT: X 49 LEU cc_start: 0.8496 (tp) cc_final: 0.8286 (tp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1749 time to fit residues: 32.3058 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 : 0.798 ------------------------------------------------------------------------------- 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: 40.0000 chunk 88 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 chunk 282 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 273 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN G 189 HIS ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN ** U 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 226 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 = 0.4276 r_free = 0.4276 target = 0.106355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.093525 restraints weight = 161484.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.093268 restraints weight = 334835.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.092991 restraints weight = 245282.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.092821 restraints weight = 201802.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.092819 restraints weight = 179560.114| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 30856 Z= 0.204 Angle : 0.637 7.548 43348 Z= 0.351 Chirality : 0.042 0.209 4804 Planarity : 0.005 0.119 4208 Dihedral : 28.292 179.232 7122 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.66 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.16), residues: 2632 helix: 0.05 (0.17), residues: 909 sheet: -0.92 (0.25), residues: 400 loop : -0.96 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 461 TYR 0.016 0.001 TYR J 72 PHE 0.019 0.001 PHE E 670 TRP 0.019 0.001 TRP O 255 HIS 0.011 0.001 HIS D 659 Details of bonding type rmsd covalent geometry : bond 0.00467 (30852) covalent geometry : angle 0.63610 (43340) SS BOND : bond 0.01095 ( 4) SS BOND : angle 3.11505 ( 8) hydrogen bonds : bond 0.07345 ( 1071) hydrogen bonds : angle 4.93040 ( 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 : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 667 MET cc_start: 0.7168 (tmm) cc_final: 0.6881 (tmm) REVERT: J 84 MET cc_start: 0.7554 (mmm) cc_final: 0.7018 (mpp) REVERT: S 56 MET cc_start: 0.8160 (tmm) cc_final: 0.7723 (tmm) REVERT: V 56 MET cc_start: 0.8935 (tpp) cc_final: 0.8587 (tpp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1565 time to fit residues: 26.0235 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 : 0.589 ------------------------------------------------------------------------------- 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: 2.9990 chunk 5 optimal weight: 5.9990 chunk 86 optimal weight: 0.2980 chunk 188 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 256 optimal weight: 40.0000 chunk 229 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 273 GLN E 331 GLN E 575 GLN G 213 HIS S 92 GLN ** 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 = 0.4289 r_free = 0.4289 target = 0.107078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.093991 restraints weight = 162739.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.093751 restraints weight = 332862.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.093560 restraints weight = 233392.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.093352 restraints weight = 191743.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.093426 restraints weight = 168263.548| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 30856 Z= 0.169 Angle : 0.610 7.581 43348 Z= 0.337 Chirality : 0.040 0.210 4804 Planarity : 0.004 0.118 4208 Dihedral : 28.246 179.568 7122 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.05 % Favored : 94.83 % Rotamer: Outliers : 0.04 % Allowed : 2.04 % Favored : 97.91 % 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 aren not related in a simple way. whole: -0.86 (0.16), residues: 2632 helix: 0.17 (0.17), residues: 911 sheet: -0.93 (0.25), residues: 384 loop : -0.91 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 52 TYR 0.011 0.001 TYR J 72 PHE 0.013 0.001 PHE E 729 TRP 0.010 0.001 TRP O 255 HIS 0.013 0.001 HIS D 659 Details of bonding type rmsd covalent geometry : bond 0.00384 (30852) covalent geometry : angle 0.60881 (43340) SS BOND : bond 0.00522 ( 4) SS BOND : angle 2.72537 ( 8) hydrogen bonds : bond 0.07221 ( 1071) hydrogen bonds : angle 4.76290 ( 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 109 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 667 MET cc_start: 0.7097 (tmm) cc_final: 0.6838 (tmm) REVERT: J 84 MET cc_start: 0.7727 (mmm) cc_final: 0.7290 (mpp) REVERT: S 56 MET cc_start: 0.7967 (tmm) cc_final: 0.7729 (tmm) REVERT: V 56 MET cc_start: 0.8931 (tpp) cc_final: 0.8506 (tpp) REVERT: V 80 TYR cc_start: 0.8185 (m-10) cc_final: 0.7554 (m-10) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.1793 time to fit residues: 31.1338 Evaluate side-chains 89 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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: 8.9990 chunk 228 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 53 optimal weight: 0.3980 chunk 142 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 chunk 176 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 266 optimal weight: 5.9990 chunk 184 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 273 GLN E 575 GLN G 92 HIS S 92 GLN ** U 84 GLN ** 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 = 0.4298 r_free = 0.4298 target = 0.107573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.094135 restraints weight = 162555.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.093900 restraints weight = 313386.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.093647 restraints weight = 260338.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.093569 restraints weight = 192867.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.093581 restraints weight = 178463.372| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 30856 Z= 0.150 Angle : 0.597 9.351 43348 Z= 0.330 Chirality : 0.040 0.218 4804 Planarity : 0.004 0.118 4208 Dihedral : 28.192 178.979 7122 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.86 % Favored : 95.02 % Rotamer: Outliers : 0.04 % Allowed : 1.45 % Favored : 98.51 % 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 aren not related in a simple way. whole: -0.77 (0.16), residues: 2632 helix: 0.29 (0.17), residues: 921 sheet: -0.87 (0.25), residues: 390 loop : -0.91 (0.18), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 340 TYR 0.011 0.001 TYR E 23 PHE 0.012 0.001 PHE E 729 TRP 0.009 0.001 TRP O 255 HIS 0.013 0.001 HIS D 659 Details of bonding type rmsd covalent geometry : bond 0.00336 (30852) covalent geometry : angle 0.59619 (43340) SS BOND : bond 0.00576 ( 4) SS BOND : angle 2.35532 ( 8) hydrogen bonds : bond 0.07201 ( 1071) hydrogen bonds : angle 4.63228 ( 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 112 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.774 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 667 MET cc_start: 0.7133 (tmm) cc_final: 0.6884 (tmm) REVERT: J 84 MET cc_start: 0.7896 (mmm) cc_final: 0.7455 (mpp) REVERT: R 84 GLN cc_start: 0.8619 (tp40) cc_final: 0.8108 (tp-100) REVERT: V 56 MET cc_start: 0.8817 (tpp) cc_final: 0.8489 (tpp) REVERT: V 65 ASP cc_start: 0.8414 (t0) cc_final: 0.8118 (t0) REVERT: V 80 TYR cc_start: 0.8353 (m-10) cc_final: 0.7643 (m-10) outliers start: 1 outliers final: 1 residues processed: 112 average time/residue: 0.1760 time to fit residues: 31.8920 Evaluate side-chains 94 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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: 30.0000 chunk 186 optimal weight: 0.2980 chunk 16 optimal weight: 10.0000 chunk 204 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 115 optimal weight: 0.4980 chunk 139 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 205 optimal weight: 4.9990 chunk 245 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 HIS D 471 HIS E 273 GLN E 575 GLN S 92 GLN ** U 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 84 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.106985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.094027 restraints weight = 163085.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.093723 restraints weight = 318344.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.093411 restraints weight = 256067.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.093335 restraints weight = 196029.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.093276 restraints weight = 182619.700| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.3608 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= 0.177 Angle : 0.613 8.753 43348 Z= 0.338 Chirality : 0.041 0.220 4804 Planarity : 0.004 0.118 4208 Dihedral : 28.224 179.548 7122 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.90 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.16), residues: 2632 helix: 0.24 (0.17), residues: 908 sheet: -0.76 (0.25), residues: 389 loop : -0.92 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 52 TYR 0.013 0.001 TYR J 72 PHE 0.017 0.001 PHE E 32 TRP 0.013 0.001 TRP E 113 HIS 0.013 0.001 HIS D 659 Details of bonding type rmsd covalent geometry : bond 0.00405 (30852) covalent geometry : angle 0.61236 (43340) SS BOND : bond 0.00526 ( 4) SS BOND : angle 2.40374 ( 8) hydrogen bonds : bond 0.07138 ( 1071) hydrogen bonds : angle 4.73788 ( 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 106 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 121 MET cc_start: 0.4070 (ptt) cc_final: 0.3750 (ptp) REVERT: E 667 MET cc_start: 0.7020 (tmm) cc_final: 0.6798 (tmm) REVERT: R 84 GLN cc_start: 0.8839 (tp40) cc_final: 0.8169 (tp-100) REVERT: V 56 MET cc_start: 0.8865 (tpp) cc_final: 0.8466 (tpp) REVERT: V 80 TYR cc_start: 0.8364 (m-10) cc_final: 0.7602 (m-10) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1625 time to fit residues: 28.3177 Evaluate side-chains 90 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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: 0.0370 chunk 268 optimal weight: 50.0000 chunk 172 optimal weight: 0.5980 chunk 271 optimal weight: 40.0000 chunk 16 optimal weight: 0.0870 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 263 optimal weight: 9.9990 chunk 238 optimal weight: 0.0270 chunk 277 optimal weight: 0.9990 chunk 256 optimal weight: 30.0000 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN E 273 GLN E 332 HIS E 575 GLN ** G 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN ** 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 = 0.4318 r_free = 0.4318 target = 0.108732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.095981 restraints weight = 161552.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.096578 restraints weight = 333137.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.096204 restraints weight = 232102.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.095962 restraints weight = 216859.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.096161 restraints weight = 171862.635| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6092 moved from start: 0.4007 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= 0.136 Angle : 0.591 9.239 43348 Z= 0.325 Chirality : 0.040 0.231 4804 Planarity : 0.004 0.118 4208 Dihedral : 28.075 178.722 7122 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.33 % Favored : 95.55 % Rotamer: Outliers : 0.04 % Allowed : 0.34 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.16), residues: 2632 helix: 0.49 (0.17), residues: 912 sheet: -0.67 (0.25), residues: 381 loop : -0.90 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 52 TYR 0.012 0.001 TYR S 37 PHE 0.017 0.001 PHE O 243 TRP 0.025 0.001 TRP O 255 HIS 0.013 0.001 HIS D 659 Details of bonding type rmsd covalent geometry : bond 0.00301 (30852) covalent geometry : angle 0.59046 (43340) SS BOND : bond 0.00699 ( 4) SS BOND : angle 2.20064 ( 8) hydrogen bonds : bond 0.07554 ( 1071) hydrogen bonds : angle 4.46004 ( 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 117 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 632 MET cc_start: 0.6732 (ptt) cc_final: 0.6501 (ptt) REVERT: J 84 MET cc_start: 0.7794 (mmm) cc_final: 0.7137 (mpp) REVERT: R 84 GLN cc_start: 0.8826 (tp40) cc_final: 0.8354 (tp-100) REVERT: V 56 MET cc_start: 0.8615 (tpp) cc_final: 0.8389 (tpp) REVERT: V 65 ASP cc_start: 0.8233 (t0) cc_final: 0.7863 (t0) REVERT: V 80 TYR cc_start: 0.8143 (m-10) cc_final: 0.7560 (m-10) REVERT: O 404 MET cc_start: 0.3713 (mpp) cc_final: 0.3394 (mpp) outliers start: 1 outliers final: 0 residues processed: 117 average time/residue: 0.1732 time to fit residues: 32.7013 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 : 0.663 ------------------------------------------------------------------------------- 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: 0.9980 chunk 20 optimal weight: 20.0000 chunk 49 optimal weight: 30.0000 chunk 184 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 269 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 215 optimal weight: 0.6980 chunk 185 optimal weight: 0.8980 chunk 211 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN D 624 HIS E 273 GLN E 575 GLN ** G 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN ** U 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 84 GLN W 68 GLN ** O 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.106952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.093690 restraints weight = 163106.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.093506 restraints weight = 310124.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.093111 restraints weight = 246546.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.093004 restraints weight = 191604.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.092878 restraints weight = 183285.474| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.3952 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= 0.185 Angle : 0.623 10.993 43348 Z= 0.341 Chirality : 0.041 0.239 4804 Planarity : 0.004 0.117 4208 Dihedral : 28.226 179.786 7122 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.75 % Favored : 95.14 % Rotamer: Outliers : 0.04 % Allowed : 0.38 % Favored : 99.57 % 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 aren not related in a simple way. whole: -0.70 (0.16), residues: 2632 helix: 0.33 (0.17), residues: 909 sheet: -0.61 (0.25), residues: 390 loop : -0.92 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 76 TYR 0.015 0.001 TYR J 72 PHE 0.018 0.001 PHE I 67 TRP 0.023 0.001 TRP O 255 HIS 0.011 0.001 HIS D 659 Details of bonding type rmsd covalent geometry : bond 0.00423 (30852) covalent geometry : angle 0.62072 (43340) SS BOND : bond 0.00973 ( 4) SS BOND : angle 3.67315 ( 8) hydrogen bonds : bond 0.07024 ( 1071) hydrogen bonds : angle 4.67789 ( 2756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2895.64 seconds wall clock time: 51 minutes 39.84 seconds (3099.84 seconds total)