Starting phenix.real_space_refine (version: 1.21rc1) on Mon Aug 14 18:36:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu7_32823/08_2023/7wu7_32823_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu7_32823/08_2023/7wu7_32823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu7_32823/08_2023/7wu7_32823.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu7_32823/08_2023/7wu7_32823.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu7_32823/08_2023/7wu7_32823_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu7_32823/08_2023/7wu7_32823_updated.pdb" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.019 sd= 0.246 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 8 5.49 5 S 416 5.16 5 C 42020 2.51 5 N 11626 2.21 5 O 12961 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 115": "OE1" <-> "OE2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A GLU 505": "OE1" <-> "OE2" Residue "B ASP 92": "OD1" <-> "OD2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C ASP 145": "OD1" <-> "OD2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 365": "OD1" <-> "OD2" Residue "C GLU 497": "OE1" <-> "OE2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 456": "OD1" <-> "OD2" Residue "D GLU 524": "OE1" <-> "OE2" Residue "E ASP 100": "OD1" <-> "OD2" Residue "E GLU 207": "OE1" <-> "OE2" Residue "E TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 86": "OD1" <-> "OD2" Residue "F TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 112": "OE1" <-> "OE2" Residue "F ASP 144": "OD1" <-> "OD2" Residue "F GLU 195": "OE1" <-> "OE2" Residue "F GLU 201": "OE1" <-> "OE2" Residue "F GLU 520": "OE1" <-> "OE2" Residue "G PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H GLU 117": "OE1" <-> "OE2" Residue "H TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 99": "OE1" <-> "OE2" Residue "I GLU 142": "OE1" <-> "OE2" Residue "I TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 132": "OE1" <-> "OE2" Residue "J TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 110": "OE1" <-> "OE2" Residue "K PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 327": "OD1" <-> "OD2" Residue "L PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 158": "OD1" <-> "OD2" Residue "M ASP 233": "OD1" <-> "OD2" Residue "N GLU 101": "OE1" <-> "OE2" Residue "N GLU 121": "OE1" <-> "OE2" Residue "N GLU 124": "OE1" <-> "OE2" Residue "N GLU 135": "OE1" <-> "OE2" Residue "N GLU 146": "OE1" <-> "OE2" Residue "N GLU 163": "OE1" <-> "OE2" Residue "N ASP 187": "OD1" <-> "OD2" Residue "O PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 494": "OE1" <-> "OE2" Residue "P GLU 127": "OE1" <-> "OE2" Residue "P GLU 130": "OE1" <-> "OE2" Residue "P GLU 159": "OE1" <-> "OE2" Residue "P GLU 176": "OE1" <-> "OE2" Residue "P GLU 462": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 67031 Number of models: 1 Model: "" Number of chains: 26 Chain: "1" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 873 Classifications: {'peptide': 107} Link IDs: {'TRANS': 106} Chain: "2" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 667 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "3" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 956 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "4" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 711 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "5" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1017 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "6" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 825 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "A" Number of atoms: 3919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3919 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 12, 'TRANS': 503} Chain: "B" Number of atoms: 3736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3736 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 8, 'TRANS': 488} Chain: "C" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3924 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 16, 'TRANS': 488} Chain: "D" Number of atoms: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3847 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 496} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3883 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 16, 'TRANS': 489} Chain: "F" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3903 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 13, 'TRANS': 494} Chain: "G" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3910 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 14, 'TRANS': 494} Chain: "H" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3816 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 12, 'TRANS': 487} Chain: "I" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3903 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 12, 'TRANS': 501} Chain: "J" Number of atoms: 3736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3736 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 8, 'TRANS': 488} Chain: "K" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3924 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 16, 'TRANS': 488} Chain: "L" Number of atoms: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3847 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 496} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3883 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 16, 'TRANS': 489} Chain: "N" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3903 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 13, 'TRANS': 494} Chain: "O" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3910 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 14, 'TRANS': 494} Chain: "P" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3830 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 12, 'TRANS': 489} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 24.55, per 1000 atoms: 0.37 Number of scatterers: 67031 At special positions: 0 Unit cell: (230.52, 176.46, 185.64, 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 416 16.00 P 8 15.00 O 12961 8.00 N 11626 7.00 C 42020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 22.46 Conformation dependent library (CDL) restraints added in 7.6 seconds 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16330 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 301 helices and 87 sheets defined 52.4% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.08 Creating SS restraints... Processing helix chain '1' and resid 14 through 56 removed outlier: 3.929A pdb=" N ILE 1 32 " --> pdb=" O LYS 1 28 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU 1 37 " --> pdb=" O GLN 1 33 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ASP 1 56 " --> pdb=" O MET 1 52 " (cutoff:3.500A) Processing helix chain '1' and resid 73 through 116 removed outlier: 3.618A pdb=" N LEU 1 81 " --> pdb=" O HIS 1 77 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS 1 83 " --> pdb=" O GLN 1 79 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLN 1 84 " --> pdb=" O LEU 1 80 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE 1 86 " --> pdb=" O GLU 1 82 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR 1 100 " --> pdb=" O GLN 1 96 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA 1 108 " --> pdb=" O SER 1 104 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU 1 114 " --> pdb=" O ASP 1 110 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N MET 1 115 " --> pdb=" O ASN 1 111 " (cutoff:3.500A) Processing helix chain '2' and resid 31 through 62 removed outlier: 4.261A pdb=" N GLU 2 36 " --> pdb=" O ARG 2 32 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA 2 44 " --> pdb=" O LEU 2 40 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU 2 47 " --> pdb=" O LYS 2 43 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE 2 58 " --> pdb=" O HIS 2 54 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASP 2 59 " --> pdb=" O SER 2 55 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N THR 2 60 " --> pdb=" O LEU 2 56 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU 2 61 " --> pdb=" O VAL 2 57 " (cutoff:3.500A) Processing helix chain '2' and resid 86 through 109 removed outlier: 3.649A pdb=" N ASN 2 93 " --> pdb=" O ALA 2 89 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS 2 94 " --> pdb=" O LEU 2 90 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN 2 96 " --> pdb=" O ASN 2 92 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS 2 99 " --> pdb=" O GLU 2 95 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN 2 109 " --> pdb=" O THR 2 105 " (cutoff:3.500A) Processing helix chain '3' and resid 55 through 98 removed outlier: 3.998A pdb=" N LYS 3 70 " --> pdb=" O ASN 3 66 " (cutoff:3.500A) Proline residue: 3 79 - end of helix removed outlier: 3.940A pdb=" N LEU 3 88 " --> pdb=" O THR 3 84 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS 3 93 " --> pdb=" O LYS 3 89 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LYS 3 94 " --> pdb=" O TYR 3 90 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER 3 97 " --> pdb=" O LYS 3 93 " (cutoff:3.500A) Processing helix chain '3' and resid 139 through 166 removed outlier: 3.975A pdb=" N LYS 3 146 " --> pdb=" O ALA 3 142 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN 3 147 " --> pdb=" O LEU 3 143 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU 3 148 " --> pdb=" O LEU 3 144 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA 3 151 " --> pdb=" O ASN 3 147 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS 3 153 " --> pdb=" O SER 3 149 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN 3 154 " --> pdb=" O THR 3 150 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU 3 162 " --> pdb=" O LEU 3 158 " (cutoff:3.500A) Processing helix chain '4' and resid 29 through 59 removed outlier: 5.182A pdb=" N GLU 4 35 " --> pdb=" O SER 4 31 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU 4 36 " --> pdb=" O ARG 4 32 " (cutoff:3.500A) Processing helix chain '4' and resid 82 through 112 removed outlier: 4.967A pdb=" N GLU 4 88 " --> pdb=" O GLU 4 85 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU 4 96 " --> pdb=" O ASN 4 93 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP 4 99 " --> pdb=" O GLU 4 96 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL 4 111 " --> pdb=" O ILE 4 108 " (cutoff:3.500A) Processing helix chain '5' and resid 12 through 56 removed outlier: 3.755A pdb=" N ASN 5 20 " --> pdb=" O GLU 5 16 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN 5 21 " --> pdb=" O MET 5 17 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN 5 40 " --> pdb=" O LEU 5 36 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N THR 5 41 " --> pdb=" O LYS 5 37 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LYS 5 42 " --> pdb=" O VAL 5 38 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYR 5 43 " --> pdb=" O VAL 5 39 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASN 5 51 " --> pdb=" O LYS 5 47 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N VAL 5 52 " --> pdb=" O ASP 5 48 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU 5 53 " --> pdb=" O CYS 5 49 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN 5 54 " --> pdb=" O LEU 5 50 " (cutoff:3.500A) Processing helix chain '5' and resid 79 through 81 No H-bonds generated for 'chain '5' and resid 79 through 81' Processing helix chain '5' and resid 96 through 101 Processing helix chain '5' and resid 103 through 136 Proline residue: 5 119 - end of helix removed outlier: 4.414A pdb=" N LYS 5 124 " --> pdb=" O ALA 5 120 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N MET 5 127 " --> pdb=" O GLU 5 123 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS 5 128 " --> pdb=" O LYS 5 124 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER 5 136 " --> pdb=" O MET 5 132 " (cutoff:3.500A) Processing helix chain '6' and resid 14 through 47 removed outlier: 3.829A pdb=" N GLY 6 29 " --> pdb=" O LYS 6 25 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU 6 39 " --> pdb=" O ALA 6 35 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE 6 42 " --> pdb=" O THR 6 38 " (cutoff:3.500A) Processing helix chain '6' and resid 69 through 113 removed outlier: 4.030A pdb=" N GLU 6 102 " --> pdb=" O GLU 6 98 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLN 6 103 " --> pdb=" O ARG 6 99 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG 6 105 " --> pdb=" O SER 6 101 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LEU 6 108 " --> pdb=" O GLN 6 104 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA 6 109 " --> pdb=" O ARG 6 105 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU 6 111 " --> pdb=" O THR 6 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 35 removed outlier: 3.748A pdb=" N ALA A 24 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N SER A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 70 through 85 Processing helix chain 'A' and resid 90 through 109 Processing helix chain 'A' and resid 114 through 135 Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.993A pdb=" N SER A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 178 Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 259 through 281 removed outlier: 5.415A pdb=" N ARG A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN A 265 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 removed outlier: 3.532A pdb=" N TYR A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A 300 " --> pdb=" O CYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 382 through 404 Processing helix chain 'A' and resid 414 through 427 Processing helix chain 'A' and resid 433 through 454 removed outlier: 3.568A pdb=" N LEU A 436 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 448 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Proline residue: A 449 - end of helix Processing helix chain 'A' and resid 460 through 476 Processing helix chain 'A' and resid 481 through 485 removed outlier: 4.088A pdb=" N TRP A 485 " --> pdb=" O ASN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 523 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.622A pdb=" N GLY B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N THR B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 99 through 118 removed outlier: 3.510A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 144 Processing helix chain 'B' and resid 153 through 169 Processing helix chain 'B' and resid 176 through 190 Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 266 through 285 removed outlier: 4.244A pdb=" N LYS B 272 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU B 273 " --> pdb=" O HIS B 269 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS B 276 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL B 279 " --> pdb=" O MET B 275 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE B 282 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 317 through 327 removed outlier: 4.460A pdb=" N GLU B 321 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 326 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR B 327 " --> pdb=" O ALA B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 380 through 401 Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 431 through 454 Proline residue: B 447 - end of helix Processing helix chain 'B' and resid 458 through 471 Processing helix chain 'B' and resid 488 through 491 No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 497 through 515 Processing helix chain 'C' and resid 21 through 40 removed outlier: 4.586A pdb=" N THR C 39 " --> pdb=" O ASP C 35 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N CYS C 40 " --> pdb=" O ILE C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 67 Processing helix chain 'C' and resid 75 through 90 removed outlier: 3.734A pdb=" N GLU C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 113 removed outlier: 3.620A pdb=" N HIS C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 140 Processing helix chain 'C' and resid 149 through 163 removed outlier: 4.711A pdb=" N THR C 162 " --> pdb=" O SER C 158 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LYS C 163 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 180 removed outlier: 4.475A pdb=" N ASN C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing helix chain 'C' and resid 209 through 211 No H-bonds generated for 'chain 'C' and resid 209 through 211' Processing helix chain 'C' and resid 261 through 284 removed outlier: 3.704A pdb=" N PHE C 264 " --> pdb=" O GLU C 261 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU C 268 " --> pdb=" O THR C 265 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP C 281 " --> pdb=" O LEU C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.516A pdb=" N TYR C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 326 removed outlier: 3.876A pdb=" N ASN C 321 " --> pdb=" O LYS C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 403 removed outlier: 3.615A pdb=" N SER C 385 " --> pdb=" O LYS C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 427 Processing helix chain 'C' and resid 432 through 454 removed outlier: 3.522A pdb=" N TRP C 435 " --> pdb=" O VAL C 432 " (cutoff:3.500A) Proline residue: C 436 - end of helix Proline residue: C 448 - end of helix removed outlier: 3.688A pdb=" N GLN C 453 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 470 Processing helix chain 'C' and resid 490 through 493 No H-bonds generated for 'chain 'C' and resid 490 through 493' Processing helix chain 'C' and resid 499 through 517 Processing helix chain 'D' and resid 29 through 51 removed outlier: 4.573A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N SER D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 80 Processing helix chain 'D' and resid 86 through 101 Processing helix chain 'D' and resid 106 through 126 removed outlier: 3.659A pdb=" N ILE D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 151 Processing helix chain 'D' and resid 160 through 172 Processing helix chain 'D' and resid 180 through 194 Proline residue: D 185 - end of helix Processing helix chain 'D' and resid 269 through 293 removed outlier: 4.361A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLU D 278 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA D 281 " --> pdb=" O ARG D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 319 removed outlier: 3.597A pdb=" N LYS D 319 " --> pdb=" O HIS D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 338 Processing helix chain 'D' and resid 353 through 355 No H-bonds generated for 'chain 'D' and resid 353 through 355' Processing helix chain 'D' and resid 395 through 417 Processing helix chain 'D' and resid 427 through 442 Processing helix chain 'D' and resid 445 through 467 removed outlier: 3.963A pdb=" N TYR D 449 " --> pdb=" O GLY D 445 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ILE D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) Proline residue: D 462 - end of helix Processing helix chain 'D' and resid 473 through 486 Processing helix chain 'D' and resid 512 through 530 Processing helix chain 'E' and resid 30 through 51 removed outlier: 3.539A pdb=" N THR E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N SER E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 79 Processing helix chain 'E' and resid 86 through 97 Processing helix chain 'E' and resid 104 through 125 removed outlier: 3.634A pdb=" N THR E 107 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N VAL E 109 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 150 removed outlier: 3.835A pdb=" N LYS E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 175 removed outlier: 4.054A pdb=" N GLU E 163 " --> pdb=" O LYS E 160 " (cutoff:3.500A) Proline residue: E 164 - end of helix removed outlier: 3.869A pdb=" N GLY E 174 " --> pdb=" O THR E 171 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER E 175 " --> pdb=" O THR E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 196 Processing helix chain 'E' and resid 271 through 294 removed outlier: 4.019A pdb=" N MET E 288 " --> pdb=" O LYS E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 316 removed outlier: 3.945A pdb=" N LEU E 313 " --> pdb=" O GLU E 309 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU E 314 " --> pdb=" O ALA E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 337 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 392 through 414 Processing helix chain 'E' and resid 424 through 439 removed outlier: 4.359A pdb=" N ASP E 438 " --> pdb=" O SER E 434 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LYS E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 464 removed outlier: 3.529A pdb=" N ASP E 453 " --> pdb=" O ALA E 450 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU E 456 " --> pdb=" O ASP E 453 " (cutoff:3.500A) Proline residue: E 459 - end of helix Processing helix chain 'E' and resid 470 through 483 removed outlier: 3.709A pdb=" N VAL E 482 " --> pdb=" O ARG E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 504 No H-bonds generated for 'chain 'E' and resid 501 through 504' Processing helix chain 'E' and resid 510 through 528 removed outlier: 3.911A pdb=" N ILE E 527 " --> pdb=" O MET E 523 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 37 removed outlier: 4.476A pdb=" N THR F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ASN F 37 " --> pdb=" O VAL F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 66 Processing helix chain 'F' and resid 73 through 88 removed outlier: 4.132A pdb=" N ILE F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR F 88 " --> pdb=" O GLN F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 112 removed outlier: 3.774A pdb=" N TYR F 109 " --> pdb=" O GLN F 105 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLU F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 137 removed outlier: 3.608A pdb=" N GLN F 132 " --> pdb=" O GLU F 128 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU F 136 " --> pdb=" O GLN F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 158 removed outlier: 4.414A pdb=" N THR F 158 " --> pdb=" O THR F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 182 removed outlier: 4.268A pdb=" N GLU F 170 " --> pdb=" O ASP F 166 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA F 171 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE F 176 " --> pdb=" O VAL F 172 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS F 181 " --> pdb=" O LEU F 177 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N GLN F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 259 removed outlier: 3.797A pdb=" N GLU F 254 " --> pdb=" O LYS F 251 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU F 257 " --> pdb=" O GLU F 254 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU F 259 " --> pdb=" O ARG F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 282 removed outlier: 3.844A pdb=" N GLU F 268 " --> pdb=" O ARG F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 307 removed outlier: 3.770A pdb=" N ALA F 304 " --> pdb=" O PHE F 300 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 328 removed outlier: 4.101A pdb=" N GLU F 322 " --> pdb=" O ARG F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 403 removed outlier: 3.712A pdb=" N GLN F 386 " --> pdb=" O HIS F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 425 Processing helix chain 'F' and resid 431 through 455 removed outlier: 3.643A pdb=" N LEU F 435 " --> pdb=" O ARG F 432 " (cutoff:3.500A) Proline residue: F 448 - end of helix Processing helix chain 'F' and resid 459 through 473 Processing helix chain 'F' and resid 489 through 492 No H-bonds generated for 'chain 'F' and resid 489 through 492' Processing helix chain 'F' and resid 498 through 517 Processing helix chain 'G' and resid 18 through 34 removed outlier: 4.076A pdb=" N VAL G 23 " --> pdb=" O PRO G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 62 through 68 Processing helix chain 'G' and resid 74 through 89 Processing helix chain 'G' and resid 93 through 114 Proline residue: G 110 - end of helix Processing helix chain 'G' and resid 118 through 139 Processing helix chain 'G' and resid 149 through 163 Processing helix chain 'G' and resid 171 through 184 Processing helix chain 'G' and resid 223 through 226 No H-bonds generated for 'chain 'G' and resid 223 through 226' Processing helix chain 'G' and resid 263 through 283 removed outlier: 3.658A pdb=" N VAL G 267 " --> pdb=" O GLN G 264 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASN G 272 " --> pdb=" O ALA G 269 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ILE G 273 " --> pdb=" O GLU G 270 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS G 282 " --> pdb=" O GLU G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 305 Processing helix chain 'G' and resid 316 through 324 Processing helix chain 'G' and resid 380 through 401 removed outlier: 4.223A pdb=" N GLU G 384 " --> pdb=" O GLN G 380 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG G 397 " --> pdb=" O ILE G 393 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS G 401 " --> pdb=" O ARG G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 411 through 426 removed outlier: 3.548A pdb=" N THR G 426 " --> pdb=" O ASP G 422 " (cutoff:3.500A) Processing helix chain 'G' and resid 431 through 454 removed outlier: 3.515A pdb=" N GLU G 443 " --> pdb=" O ALA G 439 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE G 444 " --> pdb=" O LYS G 440 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ILE G 445 " --> pdb=" O ALA G 441 " (cutoff:3.500A) Proline residue: G 446 - end of helix Processing helix chain 'G' and resid 457 through 470 removed outlier: 3.966A pdb=" N LYS G 463 " --> pdb=" O ASN G 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 514 Processing helix chain 'H' and resid 28 through 46 removed outlier: 3.803A pdb=" N ALA H 35 " --> pdb=" O ARG H 31 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N CYS H 36 " --> pdb=" O ASN H 32 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR H 45 " --> pdb=" O GLN H 41 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ALA H 46 " --> pdb=" O THR H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 75 Processing helix chain 'H' and resid 81 through 96 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.665A pdb=" N LEU H 105 " --> pdb=" O THR H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 146 Proline residue: H 144 - end of helix Processing helix chain 'H' and resid 157 through 171 removed outlier: 3.826A pdb=" N SER H 162 " --> pdb=" O ASP H 158 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR H 166 " --> pdb=" O SER H 162 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER H 167 " --> pdb=" O LEU H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 190 removed outlier: 3.533A pdb=" N ALA H 180 " --> pdb=" O GLU H 176 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER H 189 " --> pdb=" O GLN H 185 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE H 190 " --> pdb=" O ALA H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 201 No H-bonds generated for 'chain 'H' and resid 199 through 201' Processing helix chain 'H' and resid 212 through 214 No H-bonds generated for 'chain 'H' and resid 212 through 214' Processing helix chain 'H' and resid 263 through 282 removed outlier: 3.578A pdb=" N PHE H 268 " --> pdb=" O GLU H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 299 through 308 Processing helix chain 'H' and resid 318 through 328 Processing helix chain 'H' and resid 341 through 343 No H-bonds generated for 'chain 'H' and resid 341 through 343' Processing helix chain 'H' and resid 382 through 404 removed outlier: 3.802A pdb=" N ASP H 387 " --> pdb=" O ASN H 383 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 429 Processing helix chain 'H' and resid 433 through 456 removed outlier: 3.941A pdb=" N TYR H 436 " --> pdb=" O LEU H 433 " (cutoff:3.500A) Proline residue: H 449 - end of helix Processing helix chain 'H' and resid 460 through 472 Processing helix chain 'H' and resid 501 through 520 Processing helix chain 'I' and resid 17 through 35 removed outlier: 3.570A pdb=" N VAL I 32 " --> pdb=" O ILE I 28 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER I 34 " --> pdb=" O ASN I 30 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N SER I 35 " --> pdb=" O ILE I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 64 Processing helix chain 'I' and resid 70 through 86 Processing helix chain 'I' and resid 90 through 109 Processing helix chain 'I' and resid 114 through 134 Processing helix chain 'I' and resid 142 through 144 No H-bonds generated for 'chain 'I' and resid 142 through 144' Processing helix chain 'I' and resid 146 through 157 removed outlier: 4.369A pdb=" N ALA I 151 " --> pdb=" O CYS I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 177 removed outlier: 4.277A pdb=" N VAL I 173 " --> pdb=" O ASN I 170 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL I 176 " --> pdb=" O VAL I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 186 No H-bonds generated for 'chain 'I' and resid 184 through 186' Processing helix chain 'I' and resid 192 through 194 No H-bonds generated for 'chain 'I' and resid 192 through 194' Processing helix chain 'I' and resid 226 through 228 No H-bonds generated for 'chain 'I' and resid 226 through 228' Processing helix chain 'I' and resid 262 through 281 removed outlier: 4.113A pdb=" N THR I 281 " --> pdb=" O LYS I 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 303 removed outlier: 3.636A pdb=" N VAL I 301 " --> pdb=" O LEU I 297 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU I 302 " --> pdb=" O LYS I 298 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 323 Processing helix chain 'I' and resid 327 through 329 No H-bonds generated for 'chain 'I' and resid 327 through 329' Processing helix chain 'I' and resid 342 through 344 No H-bonds generated for 'chain 'I' and resid 342 through 344' Processing helix chain 'I' and resid 356 through 358 No H-bonds generated for 'chain 'I' and resid 356 through 358' Processing helix chain 'I' and resid 382 through 404 Processing helix chain 'I' and resid 414 through 429 Processing helix chain 'I' and resid 435 through 455 removed outlier: 3.668A pdb=" N ALA I 439 " --> pdb=" O GLN I 435 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU I 446 " --> pdb=" O ALA I 442 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL I 447 " --> pdb=" O ARG I 443 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ILE I 448 " --> pdb=" O SER I 444 " (cutoff:3.500A) Proline residue: I 449 - end of helix Processing helix chain 'I' and resid 460 through 476 removed outlier: 3.787A pdb=" N ALA I 465 " --> pdb=" O THR I 461 " (cutoff:3.500A) Processing helix chain 'I' and resid 478 through 485 removed outlier: 3.612A pdb=" N LYS I 481 " --> pdb=" O PRO I 478 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ASN I 482 " --> pdb=" O GLU I 479 " (cutoff:3.500A) Processing helix chain 'I' and resid 507 through 525 Processing helix chain 'J' and resid 30 through 42 removed outlier: 3.655A pdb=" N GLY J 36 " --> pdb=" O ALA J 32 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER J 41 " --> pdb=" O ASP J 37 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N THR J 42 " --> pdb=" O LEU J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 57 No H-bonds generated for 'chain 'J' and resid 55 through 57' Processing helix chain 'J' and resid 67 through 73 Processing helix chain 'J' and resid 79 through 89 Processing helix chain 'J' and resid 99 through 118 removed outlier: 3.996A pdb=" N VAL J 104 " --> pdb=" O THR J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 144 Processing helix chain 'J' and resid 152 through 166 Processing helix chain 'J' and resid 173 through 190 removed outlier: 3.805A pdb=" N ARG J 189 " --> pdb=" O GLU J 185 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU J 190 " --> pdb=" O ALA J 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 261 through 285 removed outlier: 3.612A pdb=" N VAL J 264 " --> pdb=" O THR J 261 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ALA J 265 " --> pdb=" O ALA J 262 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE J 267 " --> pdb=" O VAL J 264 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLU J 268 " --> pdb=" O ALA J 265 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA J 270 " --> pdb=" O ILE J 267 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS J 272 " --> pdb=" O HIS J 269 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU J 277 " --> pdb=" O LYS J 274 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLU J 280 " --> pdb=" O GLU J 277 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 307 Processing helix chain 'J' and resid 317 through 327 Processing helix chain 'J' and resid 338 through 340 No H-bonds generated for 'chain 'J' and resid 338 through 340' Processing helix chain 'J' and resid 380 through 402 removed outlier: 3.636A pdb=" N GLU J 385 " --> pdb=" O GLN J 381 " (cutoff:3.500A) Processing helix chain 'J' and resid 412 through 427 removed outlier: 3.714A pdb=" N ARG J 427 " --> pdb=" O GLN J 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 454 Proline residue: J 447 - end of helix removed outlier: 3.691A pdb=" N ASN J 453 " --> pdb=" O ILE J 450 " (cutoff:3.500A) Processing helix chain 'J' and resid 458 through 470 Processing helix chain 'J' and resid 488 through 491 No H-bonds generated for 'chain 'J' and resid 488 through 491' Processing helix chain 'J' and resid 497 through 516 Processing helix chain 'K' and resid 21 through 37 Processing helix chain 'K' and resid 63 through 69 Processing helix chain 'K' and resid 76 through 90 removed outlier: 3.665A pdb=" N GLU K 90 " --> pdb=" O GLN K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 113 Processing helix chain 'K' and resid 121 through 140 Processing helix chain 'K' and resid 149 through 161 removed outlier: 4.835A pdb=" N ASN K 154 " --> pdb=" O ASP K 150 " (cutoff:3.500A) Processing helix chain 'K' and resid 169 through 183 removed outlier: 3.971A pdb=" N ASN K 174 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE K 175 " --> pdb=" O LEU K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 209 through 211 No H-bonds generated for 'chain 'K' and resid 209 through 211' Processing helix chain 'K' and resid 247 through 249 No H-bonds generated for 'chain 'K' and resid 247 through 249' Processing helix chain 'K' and resid 261 through 285 removed outlier: 3.806A pdb=" N GLU K 271 " --> pdb=" O ILE K 267 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN K 284 " --> pdb=" O GLU K 280 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU K 285 " --> pdb=" O ASP K 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 303 removed outlier: 4.160A pdb=" N TYR K 303 " --> pdb=" O LEU K 299 " (cutoff:3.500A) Processing helix chain 'K' and resid 317 through 327 removed outlier: 4.143A pdb=" N ALA K 324 " --> pdb=" O ASN K 320 " (cutoff:3.500A) Processing helix chain 'K' and resid 381 through 403 removed outlier: 3.743A pdb=" N VAL K 387 " --> pdb=" O ILE K 383 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLU K 388 " --> pdb=" O LEU K 384 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARG K 389 " --> pdb=" O SER K 385 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP K 393 " --> pdb=" O ARG K 389 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU K 403 " --> pdb=" O ARG K 399 " (cutoff:3.500A) Processing helix chain 'K' and resid 413 through 428 removed outlier: 3.899A pdb=" N ALA K 417 " --> pdb=" O ALA K 413 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA K 428 " --> pdb=" O GLU K 424 " (cutoff:3.500A) Processing helix chain 'K' and resid 432 through 455 removed outlier: 3.585A pdb=" N TRP K 435 " --> pdb=" O VAL K 432 " (cutoff:3.500A) Proline residue: K 436 - end of helix removed outlier: 3.661A pdb=" N ILE K 447 " --> pdb=" O LEU K 444 " (cutoff:3.500A) Proline residue: K 448 - end of helix removed outlier: 3.535A pdb=" N GLN K 453 " --> pdb=" O THR K 450 " (cutoff:3.500A) Processing helix chain 'K' and resid 459 through 471 Processing helix chain 'K' and resid 499 through 517 Processing helix chain 'L' and resid 29 through 49 Processing helix chain 'L' and resid 75 through 80 removed outlier: 4.502A pdb=" N GLN L 80 " --> pdb=" O THR L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 102 Processing helix chain 'L' and resid 106 through 126 removed outlier: 4.062A pdb=" N VAL L 110 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 151 Processing helix chain 'L' and resid 160 through 171 Processing helix chain 'L' and resid 177 through 194 removed outlier: 5.419A pdb=" N LEU L 182 " --> pdb=" O GLN L 178 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU L 183 " --> pdb=" O TYR L 179 " (cutoff:3.500A) Proline residue: L 185 - end of helix Processing helix chain 'L' and resid 272 through 291 removed outlier: 4.179A pdb=" N LEU L 284 " --> pdb=" O ARG L 280 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 319 removed outlier: 4.778A pdb=" N PHE L 316 " --> pdb=" O LEU L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 330 through 340 Processing helix chain 'L' and resid 348 through 350 No H-bonds generated for 'chain 'L' and resid 348 through 350' Processing helix chain 'L' and resid 353 through 355 No H-bonds generated for 'chain 'L' and resid 353 through 355' Processing helix chain 'L' and resid 395 through 416 Processing helix chain 'L' and resid 427 through 442 Processing helix chain 'L' and resid 446 through 469 removed outlier: 3.704A pdb=" N TYR L 449 " --> pdb=" O MET L 446 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA L 457 " --> pdb=" O PHE L 454 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLU L 459 " --> pdb=" O ASP L 456 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL L 460 " --> pdb=" O ALA L 457 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE L 461 " --> pdb=" O MET L 458 " (cutoff:3.500A) Proline residue: L 462 - end of helix Processing helix chain 'L' and resid 473 through 484 Processing helix chain 'L' and resid 512 through 531 Processing helix chain 'M' and resid 30 through 48 removed outlier: 3.735A pdb=" N THR M 47 " --> pdb=" O ALA M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 80 removed outlier: 4.114A pdb=" N MET M 80 " --> pdb=" O THR M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 102 removed outlier: 4.204A pdb=" N GLN M 98 " --> pdb=" O LEU M 94 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP M 99 " --> pdb=" O SER M 95 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASP M 100 " --> pdb=" O LYS M 96 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU M 101 " --> pdb=" O SER M 97 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 125 removed outlier: 3.617A pdb=" N GLN M 122 " --> pdb=" O GLU M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 150 removed outlier: 3.842A pdb=" N LYS M 150 " --> pdb=" O GLU M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 173 Processing helix chain 'M' and resid 183 through 194 Processing helix chain 'M' and resid 271 through 295 removed outlier: 3.656A pdb=" N THR M 295 " --> pdb=" O GLN M 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 317 Processing helix chain 'M' and resid 327 through 336 removed outlier: 4.136A pdb=" N GLU M 331 " --> pdb=" O GLY M 327 " (cutoff:3.500A) Processing helix chain 'M' and resid 345 through 347 No H-bonds generated for 'chain 'M' and resid 345 through 347' Processing helix chain 'M' and resid 350 through 352 No H-bonds generated for 'chain 'M' and resid 350 through 352' Processing helix chain 'M' and resid 392 through 414 Processing helix chain 'M' and resid 424 through 437 Processing helix chain 'M' and resid 443 through 465 Proline residue: M 459 - end of helix removed outlier: 4.470A pdb=" N ASN M 465 " --> pdb=" O LEU M 462 " (cutoff:3.500A) Processing helix chain 'M' and resid 470 through 483 Processing helix chain 'M' and resid 501 through 504 No H-bonds generated for 'chain 'M' and resid 501 through 504' Processing helix chain 'M' and resid 510 through 529 Processing helix chain 'N' and resid 19 through 34 Processing helix chain 'N' and resid 60 through 65 removed outlier: 3.732A pdb=" N HIS N 65 " --> pdb=" O ASN N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 85 Processing helix chain 'N' and resid 92 through 112 removed outlier: 3.808A pdb=" N VAL N 96 " --> pdb=" O THR N 92 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLU N 112 " --> pdb=" O LEU N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 116 through 137 removed outlier: 3.659A pdb=" N GLN N 132 " --> pdb=" O GLU N 128 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU N 136 " --> pdb=" O GLN N 132 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 156 Processing helix chain 'N' and resid 162 through 179 removed outlier: 4.466A pdb=" N ASP N 166 " --> pdb=" O ALA N 162 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL N 167 " --> pdb=" O GLU N 163 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU N 168 " --> pdb=" O LEU N 164 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA N 171 " --> pdb=" O VAL N 167 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE N 179 " --> pdb=" O SER N 175 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 255 No H-bonds generated for 'chain 'N' and resid 253 through 255' Processing helix chain 'N' and resid 257 through 282 removed outlier: 4.507A pdb=" N GLU N 263 " --> pdb=" O LEU N 259 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG N 264 " --> pdb=" O VAL N 260 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL N 271 " --> pdb=" O ILE N 267 " (cutoff:3.500A) Processing helix chain 'N' and resid 299 through 305 Processing helix chain 'N' and resid 318 through 328 Processing helix chain 'N' and resid 382 through 403 Processing helix chain 'N' and resid 413 through 428 Proline residue: N 427 - end of helix Processing helix chain 'N' and resid 431 through 454 removed outlier: 3.608A pdb=" N ILE N 447 " --> pdb=" O LEU N 444 " (cutoff:3.500A) Proline residue: N 448 - end of helix Processing helix chain 'N' and resid 460 through 472 removed outlier: 3.639A pdb=" N VAL N 464 " --> pdb=" O GLN N 460 " (cutoff:3.500A) Processing helix chain 'N' and resid 489 through 492 No H-bonds generated for 'chain 'N' and resid 489 through 492' Processing helix chain 'N' and resid 498 through 516 Processing helix chain 'O' and resid 19 through 39 removed outlier: 3.627A pdb=" N ALA O 35 " --> pdb=" O VAL O 31 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL O 36 " --> pdb=" O ILE O 32 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR O 38 " --> pdb=" O GLU O 34 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N THR O 39 " --> pdb=" O ALA O 35 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 68 Processing helix chain 'O' and resid 74 through 86 removed outlier: 3.744A pdb=" N GLN O 86 " --> pdb=" O ILE O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 93 through 113 Proline residue: O 110 - end of helix Processing helix chain 'O' and resid 120 through 139 Processing helix chain 'O' and resid 149 through 162 removed outlier: 3.813A pdb=" N ARG O 152 " --> pdb=" O VAL O 149 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLU O 156 " --> pdb=" O LYS O 153 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 185 Processing helix chain 'O' and resid 193 through 195 No H-bonds generated for 'chain 'O' and resid 193 through 195' Processing helix chain 'O' and resid 257 through 283 removed outlier: 3.982A pdb=" N VAL O 260 " --> pdb=" O VAL O 257 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLU O 261 " --> pdb=" O HIS O 258 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ILE O 266 " --> pdb=" O TYR O 263 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA O 269 " --> pdb=" O ILE O 266 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS O 283 " --> pdb=" O LYS O 280 " (cutoff:3.500A) Processing helix chain 'O' and resid 297 through 305 Processing helix chain 'O' and resid 316 through 326 Processing helix chain 'O' and resid 380 through 401 removed outlier: 4.344A pdb=" N ARG O 387 " --> pdb=" O GLU O 383 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N HIS O 390 " --> pdb=" O GLU O 386 " (cutoff:3.500A) Processing helix chain 'O' and resid 411 through 426 removed outlier: 3.904A pdb=" N ARG O 421 " --> pdb=" O SER O 417 " (cutoff:3.500A) Processing helix chain 'O' and resid 430 through 452 removed outlier: 3.599A pdb=" N LEU O 433 " --> pdb=" O LYS O 430 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE O 445 " --> pdb=" O LEU O 442 " (cutoff:3.500A) Proline residue: O 446 - end of helix removed outlier: 3.521A pdb=" N ASN O 452 " --> pdb=" O LEU O 449 " (cutoff:3.500A) Processing helix chain 'O' and resid 457 through 467 Processing helix chain 'O' and resid 496 through 514 Processing helix chain 'P' and resid 28 through 46 removed outlier: 3.827A pdb=" N THR P 45 " --> pdb=" O GLN P 41 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ALA P 46 " --> pdb=" O THR P 42 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 75 Processing helix chain 'P' and resid 81 through 96 Processing helix chain 'P' and resid 101 through 121 removed outlier: 3.812A pdb=" N LEU P 105 " --> pdb=" O THR P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 146 Proline residue: P 144 - end of helix Processing helix chain 'P' and resid 157 through 171 removed outlier: 4.821A pdb=" N THR P 166 " --> pdb=" O SER P 162 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N SER P 167 " --> pdb=" O LEU P 163 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS P 171 " --> pdb=" O SER P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 177 through 190 removed outlier: 3.647A pdb=" N ILE P 190 " --> pdb=" O ALA P 186 " (cutoff:3.500A) Processing helix chain 'P' and resid 212 through 214 No H-bonds generated for 'chain 'P' and resid 212 through 214' Processing helix chain 'P' and resid 262 through 281 Processing helix chain 'P' and resid 283 through 286 No H-bonds generated for 'chain 'P' and resid 283 through 286' Processing helix chain 'P' and resid 299 through 308 Processing helix chain 'P' and resid 318 through 328 Processing helix chain 'P' and resid 341 through 343 No H-bonds generated for 'chain 'P' and resid 341 through 343' Processing helix chain 'P' and resid 355 through 357 No H-bonds generated for 'chain 'P' and resid 355 through 357' Processing helix chain 'P' and resid 382 through 404 Processing helix chain 'P' and resid 414 through 429 Processing helix chain 'P' and resid 435 through 456 removed outlier: 3.858A pdb=" N ILE P 448 " --> pdb=" O ALA P 444 " (cutoff:3.500A) Proline residue: P 449 - end of helix Processing helix chain 'P' and resid 460 through 471 Processing helix chain 'P' and resid 492 through 495 No H-bonds generated for 'chain 'P' and resid 492 through 495' Processing helix chain 'P' and resid 501 through 519 Processing sheet with id= A, first strand: chain '1' and resid 60 through 62 removed outlier: 4.889A pdb=" N MET 1 60 " --> pdb=" O GLN 1 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN 1 71 " --> pdb=" O MET 1 60 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '2' and resid 69 through 73 Processing sheet with id= C, first strand: chain '3' and resid 101 through 106 Processing sheet with id= D, first strand: chain '3' and resid 123 through 126 removed outlier: 3.582A pdb=" N LEU 3 133 " --> pdb=" O LEU 3 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '5' and resid 60 through 65 removed outlier: 3.785A pdb=" N VAL 5 64 " --> pdb=" O VAL 5 72 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL 5 72 " --> pdb=" O VAL 5 64 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '5' and resid 82 through 86 removed outlier: 3.544A pdb=" N VAL 5 86 " --> pdb=" O TYR 5 90 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 43 through 45 Processing sheet with id= H, first strand: chain 'A' and resid 196 through 200 Processing sheet with id= I, first strand: chain 'A' and resid 306 through 308 removed outlier: 7.558A pdb=" N LYS A 233 " --> pdb=" O ASN A 284 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE A 286 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ALA A 235 " --> pdb=" O ILE A 286 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 350 through 352 removed outlier: 3.919A pdb=" N GLU A 350 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 408 through 410 Processing sheet with id= L, first strand: chain 'A' and resid 486 through 488 Processing sheet with id= M, first strand: chain 'B' and resid 50 through 52 Processing sheet with id= N, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.349A pdb=" N CYS B 371 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ILE B 202 " --> pdb=" O CYS B 371 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ILE B 373 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LYS B 204 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N LEU B 375 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 218 through 220 Processing sheet with id= P, first strand: chain 'B' and resid 476 through 479 removed outlier: 3.947A pdb=" N THR B 484 " --> pdb=" O ASP B 479 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.848A pdb=" N THR C 60 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 213 through 215 removed outlier: 3.903A pdb=" N CYS C 213 " --> pdb=" O LEU C 375 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C 373 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 239 through 241 removed outlier: 3.778A pdb=" N VAL C 239 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR C 310 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N THR C 292 " --> pdb=" O THR C 310 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE C 312 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 351 through 354 Processing sheet with id= U, first strand: chain 'C' and resid 478 through 481 removed outlier: 3.703A pdb=" N THR C 486 " --> pdb=" O ASN C 481 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 59 through 62 Processing sheet with id= W, first strand: chain 'D' and resid 210 through 213 removed outlier: 8.277A pdb=" N VAL D 211 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE D 388 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LYS D 213 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL D 390 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 227 through 230 removed outlier: 3.573A pdb=" N LEU D 373 " --> pdb=" O VAL D 365 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL D 365 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 246 through 249 removed outlier: 6.986A pdb=" N VAL D 297 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ILE D 249 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU D 299 " --> pdb=" O ILE D 249 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'E' and resid 59 through 62 Processing sheet with id= AA, first strand: chain 'E' and resid 210 through 215 removed outlier: 3.567A pdb=" N LYS E 214 " --> pdb=" O ILE E 387 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 227 through 229 removed outlier: 3.563A pdb=" N GLU E 375 " --> pdb=" O LEU E 358 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU E 358 " --> pdb=" O GLU E 375 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 300 through 302 Processing sheet with id= AD, first strand: chain 'E' and resid 418 through 420 Processing sheet with id= AE, first strand: chain 'F' and resid 45 through 48 removed outlier: 3.854A pdb=" N LYS F 45 " --> pdb=" O THR F 57 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 192 through 195 removed outlier: 3.712A pdb=" N GLU F 192 " --> pdb=" O VAL F 372 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 210 through 212 removed outlier: 4.003A pdb=" N GLU F 358 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU F 355 " --> pdb=" O GLU F 358 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 228 through 230 Processing sheet with id= AI, first strand: chain 'F' and resid 289 through 292 Processing sheet with id= AJ, first strand: chain 'F' and resid 407 through 409 Processing sheet with id= AK, first strand: chain 'F' and resid 477 through 479 Processing sheet with id= AL, first strand: chain 'G' and resid 47 through 50 removed outlier: 3.823A pdb=" N LYS G 47 " --> pdb=" O SER G 59 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'G' and resid 197 through 200 removed outlier: 6.771A pdb=" N PHE G 372 " --> pdb=" O LYS G 198 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL G 200 " --> pdb=" O PHE G 372 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU G 374 " --> pdb=" O VAL G 200 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'G' and resid 237 through 240 removed outlier: 6.789A pdb=" N VAL G 288 " --> pdb=" O ALA G 238 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU G 240 " --> pdb=" O VAL G 288 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LEU G 290 " --> pdb=" O LEU G 240 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain 'G' and resid 347 through 353 removed outlier: 3.808A pdb=" N TYR G 358 " --> pdb=" O THR G 351 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'G' and resid 405 through 407 Processing sheet with id= AQ, first strand: chain 'G' and resid 476 through 478 removed outlier: 3.795A pdb=" N ASP G 483 " --> pdb=" O ASP G 478 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'H' and resid 54 through 57 removed outlier: 3.525A pdb=" N PHE H 64 " --> pdb=" O VAL H 56 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'H' and resid 202 through 208 removed outlier: 6.996A pdb=" N SER H 373 " --> pdb=" O ARG H 203 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N CYS H 205 " --> pdb=" O SER H 373 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE H 375 " --> pdb=" O CYS H 205 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE H 207 " --> pdb=" O ILE H 375 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU H 377 " --> pdb=" O ILE H 207 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'H' and resid 221 through 223 Processing sheet with id= AU, first strand: chain 'H' and resid 290 through 292 removed outlier: 6.142A pdb=" N MET H 311 " --> pdb=" O VAL H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain 'H' and resid 147 through 150 removed outlier: 3.609A pdb=" N CYS H 148 " --> pdb=" O LEU H 408 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU H 408 " --> pdb=" O CYS H 148 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV Processing sheet with id= AW, first strand: chain 'I' and resid 43 through 45 removed outlier: 3.804A pdb=" N THR I 55 " --> pdb=" O LYS I 43 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU I 45 " --> pdb=" O THR I 53 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR I 53 " --> pdb=" O LEU I 45 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'I' and resid 195 through 198 removed outlier: 7.499A pdb=" N ALA I 373 " --> pdb=" O ASN I 196 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N LEU I 198 " --> pdb=" O ALA I 373 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE I 375 " --> pdb=" O LEU I 198 " (cutoff:3.500A) No H-bonds generated for sheet with id= AX Processing sheet with id= AY, first strand: chain 'I' and resid 214 through 217 removed outlier: 3.758A pdb=" N LEU I 361 " --> pdb=" O GLU I 354 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU I 354 " --> pdb=" O LEU I 361 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'I' and resid 237 through 239 Processing sheet with id= BA, first strand: chain 'I' and resid 408 through 410 Processing sheet with id= BB, first strand: chain 'J' and resid 50 through 53 Processing sheet with id= BC, first strand: chain 'J' and resid 200 through 202 removed outlier: 4.119A pdb=" N LEU J 375 " --> pdb=" O ILE J 202 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR J 372 " --> pdb=" O ASP J 215 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'J' and resid 289 through 291 removed outlier: 6.682A pdb=" N MET J 310 " --> pdb=" O PHE J 290 " (cutoff:3.500A) No H-bonds generated for sheet with id= BD Processing sheet with id= BE, first strand: chain 'J' and resid 350 through 352 removed outlier: 3.627A pdb=" N LEU J 359 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'J' and resid 406 through 408 Processing sheet with id= BG, first strand: chain 'J' and resid 476 through 479 Processing sheet with id= BH, first strand: chain 'K' and resid 48 through 51 removed outlier: 3.578A pdb=" N VAL K 58 " --> pdb=" O LEU K 50 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'K' and resid 217 through 220 removed outlier: 4.289A pdb=" N THR K 361 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE K 360 " --> pdb=" O LYS K 353 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'K' and resid 289 through 291 removed outlier: 6.772A pdb=" N THR K 310 " --> pdb=" O VAL K 290 " (cutoff:3.500A) No H-bonds generated for sheet with id= BJ Processing sheet with id= BK, first strand: chain 'L' and resid 210 through 212 removed outlier: 8.203A pdb=" N VAL L 211 " --> pdb=" O VAL L 386 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE L 388 " --> pdb=" O VAL L 211 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'L' and resid 240 through 242 Processing sheet with id= BM, first strand: chain 'L' and resid 245 through 247 Processing sheet with id= BN, first strand: chain 'L' and resid 297 through 299 removed outlier: 6.499A pdb=" N MET L 323 " --> pdb=" O LEU L 298 " (cutoff:3.500A) No H-bonds generated for sheet with id= BN Processing sheet with id= BO, first strand: chain 'L' and resid 492 through 494 removed outlier: 3.514A pdb=" N GLY L 499 " --> pdb=" O ASN L 494 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'M' and resid 59 through 62 Processing sheet with id= BQ, first strand: chain 'M' and resid 211 through 213 removed outlier: 6.937A pdb=" N ILE M 385 " --> pdb=" O GLU M 212 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'M' and resid 227 through 230 removed outlier: 4.112A pdb=" N PHE M 364 " --> pdb=" O THR M 366 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N LYS M 368 " --> pdb=" O ILE M 362 " (cutoff:3.500A) removed outlier: 11.568A pdb=" N ILE M 362 " --> pdb=" O LYS M 368 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N LYS M 370 " --> pdb=" O GLN M 360 " (cutoff:3.500A) removed outlier: 10.042A pdb=" N GLN M 360 " --> pdb=" O LYS M 370 " (cutoff:3.500A) removed outlier: 10.038A pdb=" N LEU M 372 " --> pdb=" O LEU M 358 " (cutoff:3.500A) removed outlier: 11.476A pdb=" N LEU M 358 " --> pdb=" O LEU M 372 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'M' and resid 248 through 250 removed outlier: 7.044A pdb=" N LEU M 299 " --> pdb=" O ALA M 249 " (cutoff:3.500A) No H-bonds generated for sheet with id= BS Processing sheet with id= BT, first strand: chain 'N' and resid 191 through 197 removed outlier: 7.105A pdb=" N VAL N 372 " --> pdb=" O GLU N 192 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N MET N 194 " --> pdb=" O VAL N 372 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LEU N 374 " --> pdb=" O MET N 194 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N MET N 196 " --> pdb=" O LEU N 374 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE N 376 " --> pdb=" O MET N 196 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'N' and resid 224 through 226 Processing sheet with id= BV, first strand: chain 'N' and resid 230 through 233 removed outlier: 7.102A pdb=" N VAL N 290 " --> pdb=" O LEU N 231 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N CYS N 233 " --> pdb=" O VAL N 290 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE N 292 " --> pdb=" O CYS N 233 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL N 311 " --> pdb=" O VAL N 291 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN N 293 " --> pdb=" O VAL N 311 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LEU N 313 " --> pdb=" O ASN N 293 " (cutoff:3.500A) No H-bonds generated for sheet with id= BV Processing sheet with id= BW, first strand: chain 'N' and resid 407 through 409 Processing sheet with id= BX, first strand: chain 'N' and resid 477 through 479 Processing sheet with id= BY, first strand: chain 'O' and resid 47 through 49 Processing sheet with id= BZ, first strand: chain 'O' and resid 210 through 212 Processing sheet with id= CA, first strand: chain 'O' and resid 214 through 216 removed outlier: 3.916A pdb=" N ASN O 359 " --> pdb=" O PHE O 216 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL O 347 " --> pdb=" O THR O 362 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'O' and resid 309 through 311 removed outlier: 3.864A pdb=" N SER O 291 " --> pdb=" O ALA O 311 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LYS O 236 " --> pdb=" O LYS O 287 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL O 289 " --> pdb=" O LYS O 236 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA O 238 " --> pdb=" O VAL O 289 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N SER O 291 " --> pdb=" O ALA O 238 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU O 240 " --> pdb=" O SER O 291 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'O' and resid 405 through 407 Processing sheet with id= CD, first strand: chain 'O' and resid 475 through 477 Processing sheet with id= CE, first strand: chain 'P' and resid 54 through 57 removed outlier: 3.582A pdb=" N PHE P 64 " --> pdb=" O VAL P 56 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'P' and resid 202 through 205 removed outlier: 7.256A pdb=" N SER P 373 " --> pdb=" O ARG P 203 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N CYS P 205 " --> pdb=" O SER P 373 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE P 375 " --> pdb=" O CYS P 205 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER P 216 " --> pdb=" O VAL P 376 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'P' and resid 239 through 242 removed outlier: 5.918A pdb=" N VAL P 290 " --> pdb=" O ALA P 240 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N TYR P 242 " --> pdb=" O VAL P 290 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL P 292 " --> pdb=" O TYR P 242 " (cutoff:3.500A) No H-bonds generated for sheet with id= CG Processing sheet with id= CH, first strand: chain 'P' and resid 349 through 353 Processing sheet with id= CI, first strand: chain 'P' and resid 478 through 480 3348 hydrogen bonds defined for protein. 8739 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 24.54 Time building geometry restraints manager: 24.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 17799 1.33 - 1.45: 10055 1.45 - 1.58: 39214 1.58 - 1.70: 21 1.70 - 1.82: 690 Bond restraints: 67779 Sorted by residual: bond pdb=" C4' ADP N 601 " pdb=" O4' ADP N 601 " ideal model delta sigma weight residual 1.426 1.619 -0.193 2.00e-02 2.50e+03 9.26e+01 bond pdb=" C4' ADP P 601 " pdb=" O4' ADP P 601 " ideal model delta sigma weight residual 1.426 1.615 -0.189 2.00e-02 2.50e+03 8.90e+01 bond pdb=" C4' ADP F 601 " pdb=" O4' ADP F 601 " ideal model delta sigma weight residual 1.426 1.614 -0.188 2.00e-02 2.50e+03 8.82e+01 bond pdb=" C3' ADP P 601 " pdb=" C4' ADP P 601 " ideal model delta sigma weight residual 1.524 1.338 0.186 2.00e-02 2.50e+03 8.60e+01 bond pdb=" C3' ADP H5000 " pdb=" C4' ADP H5000 " ideal model delta sigma weight residual 1.524 1.339 0.185 2.00e-02 2.50e+03 8.60e+01 ... (remaining 67774 not shown) Histogram of bond angle deviations from ideal: 97.27 - 104.64: 918 104.64 - 112.01: 33780 112.01 - 119.37: 24684 119.37 - 126.74: 31600 126.74 - 134.11: 459 Bond angle restraints: 91441 Sorted by residual: angle pdb=" N THR N 92 " pdb=" CA THR N 92 " pdb=" C THR N 92 " ideal model delta sigma weight residual 111.28 123.21 -11.93 1.09e+00 8.42e-01 1.20e+02 angle pdb=" N VAL I 39 " pdb=" CA VAL I 39 " pdb=" C VAL I 39 " ideal model delta sigma weight residual 112.29 107.51 4.78 9.40e-01 1.13e+00 2.59e+01 angle pdb=" N GLU 1 95 " pdb=" CA GLU 1 95 " pdb=" CB GLU 1 95 " ideal model delta sigma weight residual 110.12 116.96 -6.84 1.47e+00 4.63e-01 2.16e+01 angle pdb=" N ASP 4 62 " pdb=" CA ASP 4 62 " pdb=" C ASP 4 62 " ideal model delta sigma weight residual 113.21 108.25 4.96 1.15e+00 7.56e-01 1.86e+01 angle pdb=" N LEU O 186 " pdb=" CA LEU O 186 " pdb=" C LEU O 186 " ideal model delta sigma weight residual 110.80 101.73 9.07 2.13e+00 2.20e-01 1.81e+01 ... (remaining 91436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.63: 41164 32.63 - 65.27: 824 65.27 - 97.90: 117 97.90 - 130.53: 3 130.53 - 163.17: 3 Dihedral angle restraints: 42111 sinusoidal: 16932 harmonic: 25179 Sorted by residual: dihedral pdb=" O1B ADP H5000 " pdb=" O3A ADP H5000 " pdb=" PB ADP H5000 " pdb=" PA ADP H5000 " ideal model delta sinusoidal sigma weight residual -60.00 103.16 -163.17 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" C5' ADP H5000 " pdb=" O5' ADP H5000 " pdb=" PA ADP H5000 " pdb=" O2A ADP H5000 " ideal model delta sinusoidal sigma weight residual -60.00 103.01 -163.01 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" O1B ADP F 601 " pdb=" O3A ADP F 601 " pdb=" PB ADP F 601 " pdb=" PA ADP F 601 " ideal model delta sinusoidal sigma weight residual -60.00 76.80 -136.80 1 2.00e+01 2.50e-03 4.15e+01 ... (remaining 42108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 10108 0.086 - 0.172: 820 0.172 - 0.258: 23 0.258 - 0.344: 2 0.344 - 0.429: 2 Chirality restraints: 10955 Sorted by residual: chirality pdb=" CA THR N 92 " pdb=" N THR N 92 " pdb=" C THR N 92 " pdb=" CB THR N 92 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" CB ILE G 195 " pdb=" CA ILE G 195 " pdb=" CG1 ILE G 195 " pdb=" CG2 ILE G 195 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CB ILE D 461 " pdb=" CA ILE D 461 " pdb=" CG1 ILE D 461 " pdb=" CG2 ILE D 461 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 10952 not shown) Planarity restraints: 11721 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY N 89 " -0.020 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C GLY N 89 " 0.072 2.00e-02 2.50e+03 pdb=" O GLY N 89 " -0.027 2.00e-02 2.50e+03 pdb=" N ASP N 90 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG O 397 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.04e+00 pdb=" C ARG O 397 " 0.049 2.00e-02 2.50e+03 pdb=" O ARG O 397 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG O 398 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG P 165 " 0.241 9.50e-02 1.11e+02 1.08e-01 7.52e+00 pdb=" NE ARG P 165 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG P 165 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG P 165 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG P 165 " 0.012 2.00e-02 2.50e+03 ... (remaining 11718 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1913 2.70 - 3.25: 75485 3.25 - 3.80: 109568 3.80 - 4.35: 143665 4.35 - 4.90: 226529 Nonbonded interactions: 557160 Sorted by model distance: nonbonded pdb=" O ASP M 198 " pdb=" OD1 ASP M 198 " model vdw 2.146 3.040 nonbonded pdb=" OG SER D 501 " pdb=" OE2 GLU D 506 " model vdw 2.199 2.440 nonbonded pdb=" O THR I 154 " pdb=" OG SER I 158 " model vdw 2.199 2.440 nonbonded pdb=" OG SER H 170 " pdb=" O1A ADP H5000 " model vdw 2.200 2.440 nonbonded pdb=" OG1 THR 3 152 " pdb=" OD2 ASP 3 156 " model vdw 2.201 2.440 ... (remaining 557155 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 16 through 529) selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = (chain 'D' and (resid 28 through 502 or (resid 503 and (name N or name CA or nam \ e C or name O or name CB )) or resid 504 through 538)) selection = (chain 'L' and (resid 28 through 501 or (resid 502 through 503 and (name N or na \ me CA or name C or name O or name CB )) or resid 504 through 538)) } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'O' } ncs_group { reference = chain 'H' selection = (chain 'P' and (resid 27 through 526 or resid 601)) } 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=0.00 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 11.370 Check model and map are aligned: 0.760 Set scattering table: 0.480 Process input model: 136.020 Find NCS groups from input model: 5.640 Set up NCS constraints: 0.420 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: 0.020 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 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 : 0.005 0.193 67779 Z= 0.297 Angle : 0.808 12.049 91441 Z= 0.411 Chirality : 0.047 0.429 10955 Planarity : 0.005 0.108 11721 Dihedral : 14.101 163.166 25781 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.25 % Favored : 94.66 % Rotamer Outliers : 0.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.09), residues: 8683 helix: 0.18 (0.08), residues: 4470 sheet: -1.78 (0.21), residues: 556 loop : -1.74 (0.10), residues: 3657 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1631 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1630 time to evaluate : 6.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 1630 average time/residue: 0.5902 time to fit residues: 1676.5467 Evaluate side-chains 1282 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1282 time to evaluate : 5.850 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.1483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 861 random chunks: chunk 727 optimal weight: 10.0000 chunk 652 optimal weight: 0.2980 chunk 362 optimal weight: 5.9990 chunk 222 optimal weight: 3.9990 chunk 440 optimal weight: 20.0000 chunk 348 optimal weight: 5.9990 chunk 674 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 410 optimal weight: 9.9990 chunk 502 optimal weight: 1.9990 chunk 781 optimal weight: 8.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 HIS ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS B 200 HIS ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN D 468 ASN E 236 HIS ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 HIS F 84 GLN F 95 ASN ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 HIS ** H 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 383 ASN ** I 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 477 ASN K 481 ASN L 98 GLN ** L 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 GLN M 184 GLN M 290 GLN M 376 GLN M 403 HIS M 481 GLN N 71 HIS N 460 GLN O 117 HIS ** O 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 452 ASN ** O 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN P 303 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 67779 Z= 0.323 Angle : 0.762 12.020 91441 Z= 0.390 Chirality : 0.047 0.351 10955 Planarity : 0.005 0.060 11721 Dihedral : 6.909 172.195 9295 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.01 % Favored : 93.95 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.09), residues: 8683 helix: -0.00 (0.07), residues: 4501 sheet: -1.88 (0.19), residues: 640 loop : -1.81 (0.10), residues: 3542 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1562 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1402 time to evaluate : 5.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 160 outliers final: 105 residues processed: 1478 average time/residue: 0.5993 time to fit residues: 1550.0564 Evaluate side-chains 1362 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1257 time to evaluate : 5.889 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 0 residues processed: 105 average time/residue: 0.4780 time to fit residues: 104.2381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 861 random chunks: chunk 434 optimal weight: 20.0000 chunk 242 optimal weight: 40.0000 chunk 650 optimal weight: 0.6980 chunk 532 optimal weight: 7.9990 chunk 215 optimal weight: 0.8980 chunk 783 optimal weight: 30.0000 chunk 846 optimal weight: 20.0000 chunk 697 optimal weight: 9.9990 chunk 776 optimal weight: 0.2980 chunk 267 optimal weight: 4.9990 chunk 628 optimal weight: 0.4980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 113 GLN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 GLN ** E 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 HIS ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 GLN ** G 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 477 ASN K 74 HIS ** K 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 406 GLN K 474 ASN ** L 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 122 GLN ** M 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS ** O 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 380 GLN P 53 ASN P 303 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 67779 Z= 0.218 Angle : 0.694 11.983 91441 Z= 0.349 Chirality : 0.044 0.284 10955 Planarity : 0.004 0.064 11721 Dihedral : 6.689 179.405 9295 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.55 % Favored : 94.41 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.09), residues: 8683 helix: 0.07 (0.07), residues: 4488 sheet: -1.88 (0.20), residues: 609 loop : -1.82 (0.10), residues: 3586 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1523 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1410 time to evaluate : 5.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 113 outliers final: 56 residues processed: 1475 average time/residue: 0.6028 time to fit residues: 1557.1088 Evaluate side-chains 1339 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1283 time to evaluate : 5.887 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.4975 time to fit residues: 60.7357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 861 random chunks: chunk 773 optimal weight: 0.8980 chunk 588 optimal weight: 20.0000 chunk 406 optimal weight: 8.9990 chunk 86 optimal weight: 0.2980 chunk 373 optimal weight: 0.0070 chunk 525 optimal weight: 2.9990 chunk 786 optimal weight: 1.9990 chunk 832 optimal weight: 20.0000 chunk 410 optimal weight: 0.3980 chunk 745 optimal weight: 8.9990 chunk 224 optimal weight: 10.0000 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 109 GLN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN ** E 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 475 GLN I 477 ASN K 74 HIS ** K 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 406 GLN ** L 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 122 GLN ** M 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 GLN M 481 GLN O 117 HIS ** O 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 390 HIS O 452 ASN ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN P 303 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 67779 Z= 0.193 Angle : 0.671 11.590 91441 Z= 0.336 Chirality : 0.044 0.368 10955 Planarity : 0.004 0.064 11721 Dihedral : 6.476 172.296 9295 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.68 % Favored : 94.29 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.09), residues: 8683 helix: 0.15 (0.08), residues: 4489 sheet: -1.84 (0.20), residues: 614 loop : -1.79 (0.10), residues: 3580 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1550 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1408 time to evaluate : 6.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 142 outliers final: 69 residues processed: 1482 average time/residue: 0.6016 time to fit residues: 1564.2669 Evaluate side-chains 1334 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1265 time to evaluate : 6.000 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 69 outliers final: 1 residues processed: 69 average time/residue: 0.5479 time to fit residues: 79.0378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 861 random chunks: chunk 693 optimal weight: 20.0000 chunk 472 optimal weight: 5.9990 chunk 12 optimal weight: 0.2980 chunk 619 optimal weight: 1.9990 chunk 343 optimal weight: 20.0000 chunk 710 optimal weight: 0.9980 chunk 575 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 424 optimal weight: 9.9990 chunk 747 optimal weight: 0.7980 chunk 210 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 HIS ** E 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 487 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 477 ASN K 74 HIS ** K 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 122 GLN ** M 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS ** O 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 303 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 67779 Z= 0.195 Angle : 0.670 11.523 91441 Z= 0.335 Chirality : 0.044 0.323 10955 Planarity : 0.004 0.065 11721 Dihedral : 6.320 179.082 9295 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.86 % Favored : 94.11 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.09), residues: 8683 helix: 0.16 (0.08), residues: 4498 sheet: -1.76 (0.20), residues: 638 loop : -1.79 (0.10), residues: 3547 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1496 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1382 time to evaluate : 5.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 58 residues processed: 1443 average time/residue: 0.6042 time to fit residues: 1532.7240 Evaluate side-chains 1337 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1279 time to evaluate : 5.924 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.4862 time to fit residues: 62.0366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 861 random chunks: chunk 280 optimal weight: 9.9990 chunk 749 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 488 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 833 optimal weight: 8.9990 chunk 691 optimal weight: 2.9990 chunk 385 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 275 optimal weight: 7.9990 chunk 437 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 93 GLN A 135 ASN C 470 HIS ** E 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 GLN H 201 ASN ** H 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 HIS ** K 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 122 GLN ** M 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 316 GLN O 117 HIS O 191 GLN O 452 ASN ** O 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 487 ASN ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN P 80 HIS P 279 GLN P 303 HIS P 359 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 67779 Z= 0.295 Angle : 0.723 12.195 91441 Z= 0.365 Chirality : 0.045 0.305 10955 Planarity : 0.005 0.066 11721 Dihedral : 6.259 156.411 9295 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.50 % Favored : 93.48 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.09), residues: 8683 helix: 0.10 (0.08), residues: 4472 sheet: -1.72 (0.19), residues: 668 loop : -1.85 (0.10), residues: 3543 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1525 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1362 time to evaluate : 6.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 163 outliers final: 105 residues processed: 1445 average time/residue: 0.6110 time to fit residues: 1547.6520 Evaluate side-chains 1364 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1259 time to evaluate : 6.010 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 0 residues processed: 105 average time/residue: 0.4872 time to fit residues: 105.7978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 861 random chunks: chunk 803 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 474 optimal weight: 7.9990 chunk 608 optimal weight: 0.7980 chunk 471 optimal weight: 0.8980 chunk 701 optimal weight: 0.9990 chunk 465 optimal weight: 3.9990 chunk 829 optimal weight: 30.0000 chunk 519 optimal weight: 0.9980 chunk 505 optimal weight: 0.7980 chunk 383 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 35 GLN 5 113 GLN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 HIS ** C 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 GLN F 95 ASN ** F 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 487 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN ** H 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 353 GLN K 74 HIS K 277 GLN ** K 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 122 GLN ** M 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 279 GLN P 303 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 67779 Z= 0.197 Angle : 0.705 14.071 91441 Z= 0.350 Chirality : 0.044 0.351 10955 Planarity : 0.004 0.081 11721 Dihedral : 6.049 147.638 9295 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.68 % Favored : 94.30 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.09), residues: 8683 helix: 0.16 (0.08), residues: 4453 sheet: -1.62 (0.20), residues: 638 loop : -1.79 (0.10), residues: 3592 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1463 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1370 time to evaluate : 6.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 43 residues processed: 1420 average time/residue: 0.6142 time to fit residues: 1529.0724 Evaluate side-chains 1324 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1281 time to evaluate : 5.870 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.5279 time to fit residues: 51.3265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 861 random chunks: chunk 513 optimal weight: 5.9990 chunk 331 optimal weight: 8.9990 chunk 495 optimal weight: 8.9990 chunk 249 optimal weight: 0.6980 chunk 163 optimal weight: 0.0980 chunk 160 optimal weight: 0.9990 chunk 527 optimal weight: 0.0970 chunk 565 optimal weight: 0.0010 chunk 410 optimal weight: 0.3980 chunk 77 optimal weight: 10.0000 chunk 652 optimal weight: 3.9990 overall best weight: 0.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 95 GLN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 ASN F 95 ASN ** F 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN ** H 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 353 GLN K 74 HIS ** K 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 396 GLN ** K 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 122 GLN ** M 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 GLN ** O 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 279 GLN P 303 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 67779 Z= 0.187 Angle : 0.719 20.634 91441 Z= 0.353 Chirality : 0.044 0.306 10955 Planarity : 0.004 0.080 11721 Dihedral : 5.863 138.855 9295 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.51 % Favored : 94.47 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.09), residues: 8683 helix: 0.19 (0.08), residues: 4468 sheet: -1.66 (0.20), residues: 651 loop : -1.75 (0.10), residues: 3564 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1461 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1387 time to evaluate : 5.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 42 residues processed: 1416 average time/residue: 0.5944 time to fit residues: 1473.5567 Evaluate side-chains 1336 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1294 time to evaluate : 5.854 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.4851 time to fit residues: 46.8529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 861 random chunks: chunk 754 optimal weight: 0.9990 chunk 795 optimal weight: 2.9990 chunk 725 optimal weight: 3.9990 chunk 773 optimal weight: 6.9990 chunk 794 optimal weight: 9.9990 chunk 465 optimal weight: 5.9990 chunk 336 optimal weight: 2.9990 chunk 607 optimal weight: 0.9980 chunk 237 optimal weight: 2.9990 chunk 698 optimal weight: 2.9990 chunk 731 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 113 GLN A 135 ASN ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 353 GLN J 241 ASN ** K 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 481 ASN ** L 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 122 GLN ** M 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 GLN O 117 HIS O 452 ASN ** O 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 303 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.092 67779 Z= 0.263 Angle : 0.754 18.749 91441 Z= 0.373 Chirality : 0.046 0.338 10955 Planarity : 0.005 0.116 11721 Dihedral : 5.877 134.511 9295 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.10 % Favored : 93.87 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.09), residues: 8683 helix: 0.14 (0.08), residues: 4488 sheet: -1.53 (0.21), residues: 634 loop : -1.80 (0.10), residues: 3561 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1411 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1343 time to evaluate : 5.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 40 residues processed: 1379 average time/residue: 0.6271 time to fit residues: 1523.9030 Evaluate side-chains 1336 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1296 time to evaluate : 5.938 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.5092 time to fit residues: 47.0878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 861 random chunks: chunk 770 optimal weight: 0.8980 chunk 507 optimal weight: 0.0670 chunk 817 optimal weight: 6.9990 chunk 499 optimal weight: 0.8980 chunk 387 optimal weight: 5.9990 chunk 568 optimal weight: 0.7980 chunk 857 optimal weight: 7.9990 chunk 789 optimal weight: 6.9990 chunk 683 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 527 optimal weight: 5.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 49 ASN 4 95 GLN A 135 ASN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN C 221 ASN ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 241 ASN J 292 ASN ** K 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 481 ASN ** L 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 GLN O 117 HIS ** O 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 303 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 67779 Z= 0.210 Angle : 0.772 18.148 91441 Z= 0.377 Chirality : 0.045 0.335 10955 Planarity : 0.004 0.107 11721 Dihedral : 5.783 129.156 9295 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.79 % Favored : 94.17 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.09), residues: 8683 helix: 0.15 (0.08), residues: 4486 sheet: -1.55 (0.21), residues: 623 loop : -1.78 (0.10), residues: 3574 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1370 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1335 time to evaluate : 5.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 18 residues processed: 1352 average time/residue: 0.6250 time to fit residues: 1487.7336 Evaluate side-chains 1297 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1279 time to evaluate : 5.955 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.5063 time to fit residues: 25.8327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 861 random chunks: chunk 418 optimal weight: 0.7980 chunk 542 optimal weight: 2.9990 chunk 727 optimal weight: 9.9990 chunk 209 optimal weight: 0.9990 chunk 629 optimal weight: 9.9990 chunk 100 optimal weight: 0.0970 chunk 189 optimal weight: 3.9990 chunk 684 optimal weight: 20.0000 chunk 286 optimal weight: 0.8980 chunk 702 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 54 ASN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 504 GLN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 487 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 241 ASN ** K 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS ** O 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 303 HIS P 435 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.184499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.156425 restraints weight = 154854.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.155989 restraints weight = 123725.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.156267 restraints weight = 85830.549| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.083 67779 Z= 0.207 Angle : 0.767 19.476 91441 Z= 0.375 Chirality : 0.045 0.450 10955 Planarity : 0.004 0.093 11721 Dihedral : 5.711 125.953 9295 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.79 % Favored : 94.17 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.09), residues: 8683 helix: 0.14 (0.08), residues: 4492 sheet: -1.54 (0.21), residues: 633 loop : -1.78 (0.10), residues: 3558 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20724.56 seconds wall clock time: 362 minutes 50.21 seconds (21770.21 seconds total)