Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 02:21:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znl_11313/04_2023/6znl_11313_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znl_11313/04_2023/6znl_11313.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znl_11313/04_2023/6znl_11313.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znl_11313/04_2023/6znl_11313.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znl_11313/04_2023/6znl_11313_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znl_11313/04_2023/6znl_11313_neut_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 21 5.49 5 S 205 5.16 5 C 33429 2.51 5 N 9276 2.21 5 O 9930 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 104": "OE1" <-> "OE2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A GLU 122": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 373": "NH1" <-> "NH2" Residue "B ARG 41": "NH1" <-> "NH2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ARG 192": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B ARG 292": "NH1" <-> "NH2" Residue "C GLU 2": "OE1" <-> "OE2" Residue "C ARG 41": "NH1" <-> "NH2" Residue "C ARG 72": "NH1" <-> "NH2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C GLU 364": "OE1" <-> "OE2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "D ARG 46": "NH1" <-> "NH2" Residue "D GLU 63": "OE1" <-> "OE2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D GLU 277": "OE1" <-> "OE2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "D GLU 362": "OE1" <-> "OE2" Residue "D GLU 364": "OE1" <-> "OE2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "E GLU 64": "OE1" <-> "OE2" Residue "E ARG 121": "NH1" <-> "NH2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E ARG 123": "NH1" <-> "NH2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E GLU 232": "OE1" <-> "OE2" Residue "E ARG 257": "NH1" <-> "NH2" Residue "E GLU 277": "OE1" <-> "OE2" Residue "E GLU 362": "OE1" <-> "OE2" Residue "E ARG 373": "NH1" <-> "NH2" Residue "F ARG 41": "NH1" <-> "NH2" Residue "F ARG 72": "NH1" <-> "NH2" Residue "F ARG 118": "NH1" <-> "NH2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F GLU 122": "OE1" <-> "OE2" Residue "F GLU 130": "OE1" <-> "OE2" Residue "F ARG 182": "NH1" <-> "NH2" Residue "F ARG 220": "NH1" <-> "NH2" Residue "F GLU 260": "OE1" <-> "OE2" Residue "F GLU 273": "OE1" <-> "OE2" Residue "F ARG 313": "NH1" <-> "NH2" Residue "F GLU 362": "OE1" <-> "OE2" Residue "F ARG 373": "NH1" <-> "NH2" Residue "G GLU 87": "OE1" <-> "OE2" Residue "G ARG 121": "NH1" <-> "NH2" Residue "G ARG 199": "NH1" <-> "NH2" Residue "G GLU 237": "OE1" <-> "OE2" Residue "G GLU 270": "OE1" <-> "OE2" Residue "G ARG 291": "NH1" <-> "NH2" Residue "G ARG 329": "NH1" <-> "NH2" Residue "G ARG 369": "NH1" <-> "NH2" Residue "H TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 177": "NH1" <-> "NH2" Residue "H ARG 183": "NH1" <-> "NH2" Residue "H GLU 226": "OE1" <-> "OE2" Residue "H GLU 316": "OE1" <-> "OE2" Residue "I GLU 237": "OE1" <-> "OE2" Residue "I ARG 373": "NH1" <-> "NH2" Residue "J GLU 22": "OE1" <-> "OE2" Residue "J ARG 85": "NH1" <-> "NH2" Residue "J GLU 114": "OE1" <-> "OE2" Residue "J GLU 204": "OE1" <-> "OE2" Residue "J GLU 253": "OE1" <-> "OE2" Residue "J ARG 263": "NH1" <-> "NH2" Residue "J GLU 276": "OE1" <-> "OE2" Residue "K ARG 15": "NH1" <-> "NH2" Residue "K GLU 71": "OE1" <-> "OE2" Residue "K GLU 104": "OE1" <-> "OE2" Residue "K GLU 112": "OE1" <-> "OE2" Residue "K ARG 121": "NH1" <-> "NH2" Residue "K GLU 122": "OE1" <-> "OE2" Residue "K GLU 233": "OE1" <-> "OE2" Residue "K ARG 266": "NH1" <-> "NH2" Residue "L GLU 22": "OE1" <-> "OE2" Residue "L GLU 99": "OE1" <-> "OE2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "L GLU 158": "OE1" <-> "OE2" Residue "L GLU 198": "OE1" <-> "OE2" Residue "L GLU 201": "OE1" <-> "OE2" Residue "L ARG 215": "NH1" <-> "NH2" Residue "L GLU 218": "OE1" <-> "OE2" Residue "L ARG 225": "NH1" <-> "NH2" Residue "L ARG 268": "NH1" <-> "NH2" Residue "M ARG 74": "NH1" <-> "NH2" Residue "M GLU 84": "OE1" <-> "OE2" Residue "M GLU 184": "OE1" <-> "OE2" Residue "M GLU 384": "OE1" <-> "OE2" Residue "M ARG 399": "NH1" <-> "NH2" Residue "N ARG 322": "NH1" <-> "NH2" Residue "N ARG 336": "NH1" <-> "NH2" Residue "N ARG 399": "NH1" <-> "NH2" Residue "O GLU 91": "OE1" <-> "OE2" Residue "O GLU 142": "OE1" <-> "OE2" Residue "O GLU 152": "OE1" <-> "OE2" Residue "U GLU 22": "OE1" <-> "OE2" Residue "U GLU 44": "OE1" <-> "OE2" Residue "U GLU 52": "OE1" <-> "OE2" Residue "U GLU 58": "OE1" <-> "OE2" Residue "U GLU 91": "OE1" <-> "OE2" Residue "U GLU 135": "OE1" <-> "OE2" Residue "U GLU 139": "OE1" <-> "OE2" Residue "U ARG 151": "NH1" <-> "NH2" Residue "V ARG 24": "NH1" <-> "NH2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "Y ARG 31": "NH1" <-> "NH2" Residue "Y ARG 37": "NH1" <-> "NH2" Residue "Y GLU 45": "OE1" <-> "OE2" Residue "Y GLU 56": "OE1" <-> "OE2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ARG 119": "NH1" <-> "NH2" Residue "Y GLU 149": "OE1" <-> "OE2" Residue "Y GLU 161": "OE1" <-> "OE2" Residue "Y ARG 164": "NH1" <-> "NH2" Residue "Y ARG 255": "NH1" <-> "NH2" Residue "Y ARG 272": "NH1" <-> "NH2" Residue "Y ARG 280": "NH1" <-> "NH2" Residue "Y ARG 285": "NH1" <-> "NH2" Residue "Z ARG 1158": "NH1" <-> "NH2" Residue "Z GLU 1213": "OE1" <-> "OE2" Residue "Z ARG 1269": "NH1" <-> "NH2" Residue "m GLU 16": "OE1" <-> "OE2" Residue "m GLU 89": "OE1" <-> "OE2" Residue "m GLU 99": "OE1" <-> "OE2" Residue "m GLU 120": "OE1" <-> "OE2" Residue "m GLU 128": "OE1" <-> "OE2" Residue "m GLU 133": "OE1" <-> "OE2" Residue "m GLU 157": "OE1" <-> "OE2" Residue "m ARG 243": "NH1" <-> "NH2" Residue "m GLU 332": "OE1" <-> "OE2" Residue "n GLU 16": "OE1" <-> "OE2" Residue "n GLU 21": "OE1" <-> "OE2" Residue "n GLU 99": "OE1" <-> "OE2" Residue "n ARG 107": "NH1" <-> "NH2" Residue "n GLU 212": "OE1" <-> "OE2" Residue "n GLU 230": "OE1" <-> "OE2" Residue "n ARG 234": "NH1" <-> "NH2" Residue "n ARG 336": "NH1" <-> "NH2" Residue "o ARG 9": "NH1" <-> "NH2" Residue "o ARG 31": "NH1" <-> "NH2" Residue "z ARG 1106": "NH1" <-> "NH2" Residue "z GLU 1115": "OE1" <-> "OE2" Residue "z ARG 1267": "NH1" <-> "NH2" Residue "z ARG 1269": "NH1" <-> "NH2" Residue "z ARG 1283": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 52864 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2944 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2956 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "C" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2998 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "D" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2956 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "E" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2956 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "F" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2956 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "G" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2956 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "H" Number of atoms: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2885 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "I" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2941 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "J" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2932 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 24, 'TRANS': 354} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "K" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2264 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 267} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2122 Classifications: {'peptide': 269} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 259} Chain: "M" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2238 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 11, 'TRANS': 328} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 448 Unresolved non-hydrogen angles: 562 Unresolved non-hydrogen dihedrals: 347 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 214 Chain: "N" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 1767 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 11, 'TRANS': 268} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 443 Unresolved non-hydrogen angles: 558 Unresolved non-hydrogen dihedrals: 341 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 210 Chain: "O" Number of atoms: 1183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1183 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 5, 'TRANS': 173} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 139 Chain: "U" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1224 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 154} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "V" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1260 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 10, 'TRANS': 168} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 85 Chain: "Y" Number of atoms: 2960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 2960 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 30, 'TRANS': 379} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 331 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 14, 'PHE:plan': 3, 'GLU:plan': 20, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 215 Chain: "Z" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1444 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 180} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "m" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2262 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain breaks: 2 Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 154 Chain: "n" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2349 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'PTRANS': 14, 'TRANS': 328} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 16, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 188 Chain: "o" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1082 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 5, 'TRANS': 164} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 295 Unresolved non-hydrogen angles: 374 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 168 Chain: "z" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 952 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 9, 'TRANS': 145} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 360 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 4, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 139 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} 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: "G" 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 41801 SG CYS Y 33 202.380 59.589 41.914 1.00 25.44 S ATOM 43362 SG CYS Y 287 201.788 56.002 42.416 1.00 26.99 S ATOM 41936 SG CYS Y 51 222.354 27.863 45.658 1.00 9.26 S ATOM 42080 SG CYS Y 70 220.424 24.210 46.719 1.00 15.93 S ATOM 42121 SG CYS Y 76 234.462 28.032 50.831 1.00 17.99 S ATOM 42276 SG CYS Y 114 239.113 27.659 51.014 1.00 14.81 S Time building chain proxies: 20.30, per 1000 atoms: 0.38 Number of scatterers: 52864 At special positions: 0 Unit cell: (290.78, 148.74, 313.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 205 16.00 P 21 15.00 O 9930 8.00 N 9276 7.00 C 33429 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: 16.39 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y 501 " pdb="ZN ZN Y 501 " - pdb=" SG CYS Y 287 " pdb="ZN ZN Y 501 " - pdb=" SG CYS Y 33 " pdb=" ZN Y 502 " pdb="ZN ZN Y 502 " - pdb=" SG CYS Y 51 " pdb="ZN ZN Y 502 " - pdb=" SG CYS Y 70 " pdb=" ZN Y 503 " pdb="ZN ZN Y 503 " - pdb=" SG CYS Y 114 " pdb="ZN ZN Y 503 " - pdb=" SG CYS Y 76 " 13838 Ramachandran restraints generated. 6919 Oldfield, 0 Emsley, 6919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13176 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 257 helices and 57 sheets defined 45.2% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.61 Creating SS restraints... Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 83 through 94 removed outlier: 3.581A pdb=" N TYR A 94 " --> pdb=" O TRP A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 142 through 150 removed outlier: 3.705A pdb=" N TYR A 148 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 201 Processing helix chain 'A' and resid 208 through 220 removed outlier: 3.851A pdb=" N GLU A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 removed outlier: 3.622A pdb=" N THR A 233 " --> pdb=" O GLN A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.662A pdb=" N ARG A 255 " --> pdb=" O GLY A 252 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 257 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA A 258 " --> pdb=" O ARG A 255 " (cutoff:3.500A) Proline residue: A 259 - end of helix Processing helix chain 'A' and resid 275 through 285 removed outlier: 3.587A pdb=" N VAL A 280 " --> pdb=" O HIS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 removed outlier: 4.344A pdb=" N ARG A 292 " --> pdb=" O ASP A 289 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE A 295 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 296 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 310 through 321 removed outlier: 3.522A pdb=" N LYS A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 360 through 366 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'B' and resid 59 through 64 removed outlier: 4.003A pdb=" N GLU B 64 " --> pdb=" O LYS B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 142 through 150 removed outlier: 3.513A pdb=" N TYR B 148 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 150 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 201 Processing helix chain 'B' and resid 208 through 220 removed outlier: 3.766A pdb=" N GLU B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE B 213 " --> pdb=" O SER B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.713A pdb=" N PHE B 256 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG B 257 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA B 258 " --> pdb=" O ARG B 255 " (cutoff:3.500A) Proline residue: B 259 - end of helix Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 275 through 285 removed outlier: 3.619A pdb=" N VAL B 280 " --> pdb=" O HIS B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 310 through 321 removed outlier: 3.560A pdb=" N LYS B 320 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 321 " --> pdb=" O GLU B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 360 through 366 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'C' and resid 59 through 64 removed outlier: 4.013A pdb=" N GLU C 64 " --> pdb=" O LYS C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 93 Processing helix chain 'C' and resid 118 through 130 Processing helix chain 'C' and resid 142 through 150 removed outlier: 3.507A pdb=" N TYR C 148 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR C 150 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 201 Processing helix chain 'C' and resid 208 through 220 removed outlier: 3.773A pdb=" N GLU C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE C 213 " --> pdb=" O SER C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 233 Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.710A pdb=" N PHE C 256 " --> pdb=" O PRO C 253 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG C 257 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA C 258 " --> pdb=" O ARG C 255 " (cutoff:3.500A) Proline residue: C 259 - end of helix Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'C' and resid 275 through 285 removed outlier: 3.612A pdb=" N VAL C 280 " --> pdb=" O HIS C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 removed outlier: 4.344A pdb=" N ARG C 292 " --> pdb=" O ASP C 289 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 295 " --> pdb=" O ARG C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 310 through 321 removed outlier: 3.555A pdb=" N LYS C 320 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 321 " --> pdb=" O GLU C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 349 Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 360 through 366 Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'D' and resid 59 through 64 removed outlier: 3.907A pdb=" N GLU D 64 " --> pdb=" O LYS D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 93 Processing helix chain 'D' and resid 118 through 130 Processing helix chain 'D' and resid 142 through 150 removed outlier: 3.507A pdb=" N TYR D 148 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR D 150 " --> pdb=" O SER D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 201 Processing helix chain 'D' and resid 208 through 220 removed outlier: 3.764A pdb=" N GLU D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE D 213 " --> pdb=" O SER D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 234 removed outlier: 3.515A pdb=" N LEU D 234 " --> pdb=" O LYS D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 262 removed outlier: 3.715A pdb=" N PHE D 256 " --> pdb=" O PRO D 253 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG D 257 " --> pdb=" O SER D 254 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA D 258 " --> pdb=" O ARG D 255 " (cutoff:3.500A) Proline residue: D 259 - end of helix Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 285 removed outlier: 3.606A pdb=" N VAL D 280 " --> pdb=" O HIS D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 296 removed outlier: 4.327A pdb=" N ARG D 292 " --> pdb=" O ASP D 289 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE D 295 " --> pdb=" O ARG D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 305 No H-bonds generated for 'chain 'D' and resid 303 through 305' Processing helix chain 'D' and resid 310 through 321 removed outlier: 3.556A pdb=" N LYS D 320 " --> pdb=" O SER D 316 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 321 " --> pdb=" O GLU D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 349 Processing helix chain 'D' and resid 351 through 356 Processing helix chain 'D' and resid 360 through 366 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'E' and resid 59 through 64 removed outlier: 4.016A pdb=" N GLU E 64 " --> pdb=" O LYS E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 93 Processing helix chain 'E' and resid 118 through 130 Processing helix chain 'E' and resid 142 through 150 removed outlier: 3.512A pdb=" N TYR E 148 " --> pdb=" O VAL E 144 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR E 150 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 201 Processing helix chain 'E' and resid 208 through 220 removed outlier: 3.768A pdb=" N GLU E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE E 213 " --> pdb=" O SER E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 233 Processing helix chain 'E' and resid 252 through 262 removed outlier: 3.712A pdb=" N PHE E 256 " --> pdb=" O PRO E 253 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG E 257 " --> pdb=" O SER E 254 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA E 258 " --> pdb=" O ARG E 255 " (cutoff:3.500A) Proline residue: E 259 - end of helix Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 285 removed outlier: 3.607A pdb=" N VAL E 280 " --> pdb=" O HIS E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 296 removed outlier: 4.083A pdb=" N ARG E 292 " --> pdb=" O ASP E 289 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE E 295 " --> pdb=" O ARG E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 305 No H-bonds generated for 'chain 'E' and resid 303 through 305' Processing helix chain 'E' and resid 310 through 321 removed outlier: 3.556A pdb=" N LYS E 320 " --> pdb=" O SER E 316 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU E 321 " --> pdb=" O GLU E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 349 Processing helix chain 'E' and resid 351 through 356 Processing helix chain 'E' and resid 360 through 366 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'F' and resid 60 through 64 Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.580A pdb=" N TYR F 94 " --> pdb=" O TRP F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 142 through 150 removed outlier: 3.693A pdb=" N TYR F 148 " --> pdb=" O VAL F 144 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR F 150 " --> pdb=" O SER F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 201 Processing helix chain 'F' and resid 208 through 220 removed outlier: 3.844A pdb=" N GLU F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE F 213 " --> pdb=" O SER F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 233 removed outlier: 3.615A pdb=" N THR F 233 " --> pdb=" O GLN F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 262 removed outlier: 3.639A pdb=" N ARG F 255 " --> pdb=" O GLY F 252 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG F 257 " --> pdb=" O SER F 254 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA F 258 " --> pdb=" O ARG F 255 " (cutoff:3.500A) Proline residue: F 259 - end of helix Processing helix chain 'F' and resid 275 through 285 removed outlier: 3.570A pdb=" N VAL F 280 " --> pdb=" O HIS F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 296 removed outlier: 4.326A pdb=" N ARG F 292 " --> pdb=" O ASP F 289 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE F 295 " --> pdb=" O ARG F 292 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER F 296 " --> pdb=" O THR F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 310 through 321 removed outlier: 3.528A pdb=" N LYS F 319 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS F 320 " --> pdb=" O SER F 316 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU F 321 " --> pdb=" O GLU F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 349 Processing helix chain 'F' and resid 351 through 356 Processing helix chain 'F' and resid 360 through 366 Processing helix chain 'F' and resid 368 through 374 Processing helix chain 'G' and resid 60 through 64 Processing helix chain 'G' and resid 83 through 94 removed outlier: 3.580A pdb=" N TYR G 94 " --> pdb=" O TRP G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 130 Processing helix chain 'G' and resid 142 through 150 removed outlier: 3.688A pdb=" N TYR G 148 " --> pdb=" O VAL G 144 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR G 150 " --> pdb=" O SER G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 201 Processing helix chain 'G' and resid 208 through 220 removed outlier: 3.844A pdb=" N GLU G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE G 213 " --> pdb=" O SER G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 233 removed outlier: 3.611A pdb=" N THR G 233 " --> pdb=" O GLN G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 262 removed outlier: 3.666A pdb=" N ARG G 255 " --> pdb=" O GLY G 252 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG G 257 " --> pdb=" O SER G 254 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA G 258 " --> pdb=" O ARG G 255 " (cutoff:3.500A) Proline residue: G 259 - end of helix Processing helix chain 'G' and resid 275 through 285 removed outlier: 3.573A pdb=" N VAL G 280 " --> pdb=" O HIS G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 296 removed outlier: 4.312A pdb=" N ARG G 292 " --> pdb=" O ASP G 289 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE G 295 " --> pdb=" O ARG G 292 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER G 296 " --> pdb=" O THR G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 305 No H-bonds generated for 'chain 'G' and resid 303 through 305' Processing helix chain 'G' and resid 310 through 321 removed outlier: 3.529A pdb=" N LYS G 319 " --> pdb=" O LEU G 315 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS G 320 " --> pdb=" O SER G 316 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU G 321 " --> pdb=" O GLU G 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 349 Processing helix chain 'G' and resid 351 through 356 Processing helix chain 'G' and resid 360 through 366 Processing helix chain 'G' and resid 368 through 374 Processing helix chain 'H' and resid 56 through 60 Processing helix chain 'H' and resid 79 through 90 Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 137 through 145 removed outlier: 3.703A pdb=" N LEU H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR H 143 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA H 144 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 196 removed outlier: 3.606A pdb=" N LYS H 191 " --> pdb=" O ASP H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 216 Processing helix chain 'H' and resid 223 through 232 Processing helix chain 'H' and resid 251 through 262 removed outlier: 3.537A pdb=" N ARG H 256 " --> pdb=" O GLU H 253 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS H 257 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 274 through 284 removed outlier: 3.630A pdb=" N THR H 278 " --> pdb=" O ILE H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 289 through 295 Processing helix chain 'H' and resid 302 through 304 No H-bonds generated for 'chain 'H' and resid 302 through 304' Processing helix chain 'H' and resid 309 through 320 Processing helix chain 'H' and resid 338 through 348 removed outlier: 3.542A pdb=" N GLY H 342 " --> pdb=" O SER H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 354 removed outlier: 3.501A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 365 Processing helix chain 'H' and resid 367 through 372 Processing helix chain 'I' and resid 60 through 64 Processing helix chain 'I' and resid 83 through 93 Processing helix chain 'I' and resid 118 through 130 Processing helix chain 'I' and resid 142 through 150 removed outlier: 3.692A pdb=" N LEU I 147 " --> pdb=" O ALA I 143 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR I 148 " --> pdb=" O VAL I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 201 Processing helix chain 'I' and resid 208 through 220 removed outlier: 3.793A pdb=" N GLU I 212 " --> pdb=" O SER I 208 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE I 213 " --> pdb=" O SER I 209 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL I 214 " --> pdb=" O GLU I 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 233 Processing helix chain 'I' and resid 252 through 263 removed outlier: 3.804A pdb=" N ARG I 257 " --> pdb=" O SER I 254 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA I 258 " --> pdb=" O ARG I 255 " (cutoff:3.500A) Proline residue: I 259 - end of helix Processing helix chain 'I' and resid 275 through 285 removed outlier: 3.593A pdb=" N LEU I 279 " --> pdb=" O ILE I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 288 through 296 removed outlier: 4.604A pdb=" N ARG I 292 " --> pdb=" O MET I 288 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N THR I 293 " --> pdb=" O ASP I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 310 through 321 removed outlier: 3.505A pdb=" N SER I 316 " --> pdb=" O ASP I 312 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS I 320 " --> pdb=" O SER I 316 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU I 321 " --> pdb=" O GLU I 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 349 removed outlier: 3.505A pdb=" N GLY I 344 " --> pdb=" O THR I 340 " (cutoff:3.500A) Processing helix chain 'I' and resid 353 through 356 No H-bonds generated for 'chain 'I' and resid 353 through 356' Processing helix chain 'I' and resid 360 through 366 Processing helix chain 'I' and resid 369 through 375 Processing helix chain 'J' and resid 61 through 77 Processing helix chain 'J' and resid 99 through 111 Processing helix chain 'J' and resid 123 through 131 removed outlier: 3.584A pdb=" N LEU J 129 " --> pdb=" O LEU J 125 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR J 130 " --> pdb=" O MET J 126 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU J 131 " --> pdb=" O ALA J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 160 No H-bonds generated for 'chain 'J' and resid 158 through 160' Processing helix chain 'J' and resid 168 through 181 Processing helix chain 'J' and resid 204 through 213 Processing helix chain 'J' and resid 220 through 231 removed outlier: 3.564A pdb=" N LYS J 225 " --> pdb=" O THR J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 260 through 271 removed outlier: 3.925A pdb=" N ASP J 264 " --> pdb=" O GLY J 260 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL J 267 " --> pdb=" O ARG J 263 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLU J 268 " --> pdb=" O ASP J 264 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE J 269 " --> pdb=" O SER J 265 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LEU J 270 " --> pdb=" O VAL J 266 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE J 271 " --> pdb=" O VAL J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 290 removed outlier: 4.236A pdb=" N ILE J 284 " --> pdb=" O VAL J 280 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU J 285 " --> pdb=" O ALA J 281 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN J 290 " --> pdb=" O ASP J 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 296 through 301 Processing helix chain 'J' and resid 308 through 311 Processing helix chain 'J' and resid 315 through 328 removed outlier: 3.848A pdb=" N GLU J 328 " --> pdb=" O ARG J 324 " (cutoff:3.500A) Processing helix chain 'J' and resid 330 through 333 No H-bonds generated for 'chain 'J' and resid 330 through 333' Processing helix chain 'J' and resid 350 through 352 No H-bonds generated for 'chain 'J' and resid 350 through 352' Processing helix chain 'J' and resid 354 through 362 removed outlier: 3.635A pdb=" N GLY J 358 " --> pdb=" O ALA J 354 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 371 removed outlier: 4.041A pdb=" N SER J 370 " --> pdb=" O ASP J 366 " (cutoff:3.500A) Processing helix chain 'J' and resid 375 through 381 Processing helix chain 'K' and resid 10 through 22 removed outlier: 3.597A pdb=" N ARG K 15 " --> pdb=" O GLU K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 40 removed outlier: 3.934A pdb=" N LEU K 38 " --> pdb=" O ASN K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 61 removed outlier: 3.717A pdb=" N GLU K 48 " --> pdb=" O ASN K 44 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N HIS K 52 " --> pdb=" O GLU K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 135 removed outlier: 3.539A pdb=" N SER K 123 " --> pdb=" O SER K 119 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA K 130 " --> pdb=" O SER K 126 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR K 131 " --> pdb=" O ALA K 127 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP K 134 " --> pdb=" O ALA K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 250 removed outlier: 3.593A pdb=" N ALA K 225 " --> pdb=" O GLU K 221 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 258 removed outlier: 3.823A pdb=" N LEU K 258 " --> pdb=" O THR K 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 254 through 258' Processing helix chain 'K' and resid 271 through 276 Processing helix chain 'L' and resid 3 through 15 Processing helix chain 'L' and resid 21 through 31 removed outlier: 3.510A pdb=" N ASP L 30 " --> pdb=" O SER L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 42 Processing helix chain 'L' and resid 91 through 111 Processing helix chain 'L' and resid 209 through 243 removed outlier: 3.596A pdb=" N TYR L 232 " --> pdb=" O LEU L 228 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE L 233 " --> pdb=" O ASN L 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 249 through 268 Processing helix chain 'M' and resid 4 through 8 removed outlier: 3.584A pdb=" N ASP M 8 " --> pdb=" O PRO M 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 4 through 8' Processing helix chain 'M' and resid 52 through 59 removed outlier: 3.504A pdb=" N ASP M 57 " --> pdb=" O ASN M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 131 removed outlier: 3.756A pdb=" N MET M 124 " --> pdb=" O GLU M 120 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR M 125 " --> pdb=" O LYS M 121 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER M 129 " --> pdb=" O THR M 125 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR M 131 " --> pdb=" O LYS M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 157 Processing helix chain 'M' and resid 170 through 186 removed outlier: 4.444A pdb=" N ALA M 174 " --> pdb=" O ASP M 170 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU M 175 " --> pdb=" O PRO M 171 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS M 177 " --> pdb=" O GLY M 173 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU M 179 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU M 180 " --> pdb=" O ALA M 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 242 Processing helix chain 'M' and resid 262 through 270 Processing helix chain 'M' and resid 277 through 304 removed outlier: 4.510A pdb=" N GLN M 282 " --> pdb=" O ALA M 278 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL M 283 " --> pdb=" O VAL M 279 " (cutoff:3.500A) Processing helix chain 'M' and resid 314 through 402 Proline residue: M 325 - end of helix removed outlier: 4.034A pdb=" N SER M 328 " --> pdb=" O SER M 324 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N THR M 329 " --> pdb=" O PRO M 325 " (cutoff:3.500A) Proline residue: M 331 - end of helix removed outlier: 5.075A pdb=" N GLY M 351 " --> pdb=" O ALA M 347 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLN M 352 " --> pdb=" O MET M 348 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU M 353 " --> pdb=" O GLN M 349 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER M 387 " --> pdb=" O ARG M 383 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR M 388 " --> pdb=" O GLU M 384 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS M 402 " --> pdb=" O GLU M 398 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 7 No H-bonds generated for 'chain 'N' and resid 4 through 7' Processing helix chain 'N' and resid 104 through 108 Processing helix chain 'N' and resid 111 through 124 removed outlier: 3.726A pdb=" N MET N 124 " --> pdb=" O GLU N 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 141 through 155 removed outlier: 3.774A pdb=" N GLN N 150 " --> pdb=" O ALA N 146 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU N 151 " --> pdb=" O LEU N 147 " (cutoff:3.500A) Processing helix chain 'N' and resid 173 through 184 removed outlier: 3.507A pdb=" N LYS N 177 " --> pdb=" O GLY N 173 " (cutoff:3.500A) Processing helix chain 'N' and resid 219 through 241 removed outlier: 3.573A pdb=" N SER N 223 " --> pdb=" O GLN N 219 " (cutoff:3.500A) Processing helix chain 'N' and resid 261 through 270 Processing helix chain 'N' and resid 272 through 305 removed outlier: 3.711A pdb=" N LEU N 277 " --> pdb=" O SER N 273 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE N 297 " --> pdb=" O LYS N 293 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA N 298 " --> pdb=" O VAL N 294 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS N 300 " --> pdb=" O GLU N 296 " (cutoff:3.500A) Processing helix chain 'N' and resid 307 through 339 removed outlier: 3.564A pdb=" N THR N 319 " --> pdb=" O GLN N 315 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG N 322 " --> pdb=" O GLU N 318 " (cutoff:3.500A) Proline residue: N 325 - end of helix removed outlier: 3.640A pdb=" N THR N 329 " --> pdb=" O PRO N 325 " (cutoff:3.500A) Proline residue: N 331 - end of helix Processing helix chain 'N' and resid 341 through 402 removed outlier: 3.576A pdb=" N GLY N 351 " --> pdb=" O ALA N 347 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU N 353 " --> pdb=" O GLN N 349 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER N 387 " --> pdb=" O ARG N 383 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 18 removed outlier: 3.732A pdb=" N VAL O 7 " --> pdb=" O GLY O 3 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU O 10 " --> pdb=" O ASP O 6 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 49 Processing helix chain 'O' and resid 54 through 68 removed outlier: 4.641A pdb=" N GLU O 62 " --> pdb=" O TYR O 58 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP O 63 " --> pdb=" O LYS O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 76 Processing helix chain 'O' and resid 81 through 89 removed outlier: 4.687A pdb=" N GLN O 85 " --> pdb=" O ALA O 81 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N PHE O 86 " --> pdb=" O SER O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 91 through 107 removed outlier: 4.062A pdb=" N GLN O 103 " --> pdb=" O ALA O 99 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL O 104 " --> pdb=" O LEU O 100 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU O 105 " --> pdb=" O LEU O 101 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA O 106 " --> pdb=" O GLU O 102 " (cutoff:3.500A) Processing helix chain 'O' and resid 109 through 111 No H-bonds generated for 'chain 'O' and resid 109 through 111' Processing helix chain 'O' and resid 114 through 117 No H-bonds generated for 'chain 'O' and resid 114 through 117' Processing helix chain 'O' and resid 123 through 179 removed outlier: 3.510A pdb=" N ARG O 128 " --> pdb=" O ALA O 124 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN O 135 " --> pdb=" O GLN O 131 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL O 141 " --> pdb=" O GLN O 137 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 69 No H-bonds generated for 'chain 'U' and resid 66 through 69' Processing helix chain 'U' and resid 162 through 170 removed outlier: 3.928A pdb=" N MET U 168 " --> pdb=" O LEU U 164 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LYS U 169 " --> pdb=" O ASP U 165 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE U 170 " --> pdb=" O PHE U 166 " (cutoff:3.500A) Processing helix chain 'V' and resid 162 through 175 removed outlier: 4.140A pdb=" N ILE V 166 " --> pdb=" O GLN V 162 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP V 167 " --> pdb=" O GLU V 163 " (cutoff:3.500A) Processing helix chain 'Y' and resid 60 through 66 Processing helix chain 'Y' and resid 118 through 121 No H-bonds generated for 'chain 'Y' and resid 118 through 121' Processing helix chain 'Y' and resid 142 through 171 removed outlier: 3.516A pdb=" N GLU Y 158 " --> pdb=" O LEU Y 154 " (cutoff:3.500A) Processing helix chain 'Y' and resid 252 through 256 Processing helix chain 'Y' and resid 309 through 311 No H-bonds generated for 'chain 'Y' and resid 309 through 311' Processing helix chain 'Y' and resid 447 through 451 Processing helix chain 'Z' and resid 1099 through 1120 removed outlier: 3.606A pdb=" N SER Z1103 " --> pdb=" O LEU Z1099 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU Z1107 " --> pdb=" O SER Z1103 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS Z1108 " --> pdb=" O ALA Z1104 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU Z1119 " --> pdb=" O GLU Z1115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1122 through 1129 Processing helix chain 'Z' and resid 1143 through 1145 No H-bonds generated for 'chain 'Z' and resid 1143 through 1145' Processing helix chain 'Z' and resid 1149 through 1153 Processing helix chain 'Z' and resid 1155 through 1172 Processing helix chain 'Z' and resid 1189 through 1221 removed outlier: 3.827A pdb=" N GLN Z1196 " --> pdb=" O GLN Z1192 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL Z1197 " --> pdb=" O LEU Z1193 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR Z1206 " --> pdb=" O SER Z1202 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1237 through 1247 removed outlier: 3.669A pdb=" N GLN Z1247 " --> pdb=" O LYS Z1243 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1274 through 1284 removed outlier: 3.503A pdb=" N LEU Z1280 " --> pdb=" O GLN Z1276 " (cutoff:3.500A) Processing helix chain 'm' and resid 3 through 7 Processing helix chain 'm' and resid 101 through 134 removed outlier: 4.073A pdb=" N GLN m 106 " --> pdb=" O GLN m 102 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG m 107 " --> pdb=" O GLN m 103 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS m 127 " --> pdb=" O LYS m 123 " (cutoff:3.500A) Processing helix chain 'm' and resid 137 through 159 removed outlier: 3.611A pdb=" N HIS m 155 " --> pdb=" O LEU m 151 " (cutoff:3.500A) Processing helix chain 'm' and resid 174 through 186 removed outlier: 3.577A pdb=" N THR m 186 " --> pdb=" O GLN m 182 " (cutoff:3.500A) Processing helix chain 'm' and resid 221 through 242 removed outlier: 3.733A pdb=" N LYS m 227 " --> pdb=" O SER m 223 " (cutoff:3.500A) Processing helix chain 'm' and resid 261 through 272 Processing helix chain 'm' and resid 277 through 300 removed outlier: 3.520A pdb=" N ARG m 286 " --> pdb=" O GLN m 282 " (cutoff:3.500A) Processing helix chain 'm' and resid 306 through 324 removed outlier: 3.841A pdb=" N SER m 311 " --> pdb=" O ALA m 307 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS m 312 " --> pdb=" O ASP m 308 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN m 315 " --> pdb=" O SER m 311 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN m 321 " --> pdb=" O TYR m 317 " (cutoff:3.500A) Processing helix chain 'm' and resid 327 through 398 Proline residue: m 331 - end of helix removed outlier: 3.585A pdb=" N ARG m 336 " --> pdb=" O GLU m 332 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN m 349 " --> pdb=" O GLU m 345 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLY m 351 " --> pdb=" O ALA m 347 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN m 352 " --> pdb=" O MET m 348 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR m 355 " --> pdb=" O GLY m 351 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N HIS m 356 " --> pdb=" O GLN m 352 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET m 363 " --> pdb=" O THR m 359 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS m 366 " --> pdb=" O GLN m 362 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS m 369 " --> pdb=" O ALA m 365 " (cutoff:3.500A) Processing helix chain 'n' and resid 52 through 59 removed outlier: 3.875A pdb=" N ASP n 57 " --> pdb=" O ASN n 53 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS n 58 " --> pdb=" O ALA n 54 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE n 59 " --> pdb=" O ALA n 55 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 128 removed outlier: 3.653A pdb=" N HIS n 110 " --> pdb=" O GLN n 106 " (cutoff:3.500A) Processing helix chain 'n' and resid 136 through 154 removed outlier: 3.556A pdb=" N GLN n 149 " --> pdb=" O ALA n 145 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER n 154 " --> pdb=" O GLN n 150 " (cutoff:3.500A) Processing helix chain 'n' and resid 172 through 174 No H-bonds generated for 'chain 'n' and resid 172 through 174' Processing helix chain 'n' and resid 176 through 180 Processing helix chain 'n' and resid 184 through 188 Processing helix chain 'n' and resid 217 through 241 removed outlier: 3.587A pdb=" N LYS n 227 " --> pdb=" O SER n 223 " (cutoff:3.500A) Processing helix chain 'n' and resid 262 through 275 removed outlier: 3.895A pdb=" N ALA n 274 " --> pdb=" O ALA n 270 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU n 275 " --> pdb=" O LYS n 271 " (cutoff:3.500A) Processing helix chain 'n' and resid 280 through 298 removed outlier: 3.929A pdb=" N ARG n 286 " --> pdb=" O GLN n 282 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN n 295 " --> pdb=" O LEU n 291 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU n 296 " --> pdb=" O GLY n 292 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE n 297 " --> pdb=" O LYS n 293 " (cutoff:3.500A) Processing helix chain 'n' and resid 311 through 328 removed outlier: 3.706A pdb=" N LEU n 316 " --> pdb=" O LYS n 312 " (cutoff:3.500A) Proline residue: n 325 - end of helix Processing helix chain 'n' and resid 330 through 339 removed outlier: 3.881A pdb=" N GLN n 335 " --> pdb=" O PRO n 331 " (cutoff:3.500A) Processing helix chain 'n' and resid 341 through 392 removed outlier: 3.720A pdb=" N MET n 363 " --> pdb=" O THR n 359 " (cutoff:3.500A) Processing helix chain 'o' and resid 5 through 18 removed outlier: 3.611A pdb=" N LEU o 10 " --> pdb=" O ASP o 6 " (cutoff:3.500A) Processing helix chain 'o' and resid 33 through 46 Processing helix chain 'o' and resid 56 through 59 No H-bonds generated for 'chain 'o' and resid 56 through 59' Processing helix chain 'o' and resid 61 through 68 Processing helix chain 'o' and resid 71 through 77 Processing helix chain 'o' and resid 81 through 89 removed outlier: 3.693A pdb=" N ALA o 89 " --> pdb=" O GLN o 85 " (cutoff:3.500A) Processing helix chain 'o' and resid 92 through 112 removed outlier: 3.685A pdb=" N LEU o 100 " --> pdb=" O SER o 96 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU o 107 " --> pdb=" O GLN o 103 " (cutoff:3.500A) Proline residue: o 109 - end of helix removed outlier: 4.266A pdb=" N ASP o 112 " --> pdb=" O VAL o 108 " (cutoff:3.500A) Processing helix chain 'o' and resid 114 through 117 No H-bonds generated for 'chain 'o' and resid 114 through 117' Processing helix chain 'o' and resid 119 through 172 removed outlier: 4.016A pdb=" N ALA o 124 " --> pdb=" O PRO o 120 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG o 125 " --> pdb=" O GLU o 121 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG o 128 " --> pdb=" O ALA o 124 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN o 131 " --> pdb=" O GLN o 127 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE o 132 " --> pdb=" O ARG o 128 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS o 163 " --> pdb=" O MET o 159 " (cutoff:3.500A) Processing helix chain 'z' and resid 1096 through 1138 removed outlier: 3.637A pdb=" N ARG z1106 " --> pdb=" O ILE z1102 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER z1110 " --> pdb=" O ARG z1106 " (cutoff:3.500A) Proline residue: z1132 - end of helix Processing helix chain 'z' and resid 1140 through 1142 No H-bonds generated for 'chain 'z' and resid 1140 through 1142' Processing helix chain 'z' and resid 1159 through 1177 removed outlier: 4.304A pdb=" N LEU z1164 " --> pdb=" O THR z1160 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU z1165 " --> pdb=" O ASN z1161 " (cutoff:3.500A) Processing helix chain 'z' and resid 1181 through 1218 Proline residue: z1192 - end of helix Proline residue: z1197 - end of helix Proline residue: z1204 - end of helix Processing helix chain 'z' and resid 1275 through 1284 removed outlier: 3.945A pdb=" N GLN z1279 " --> pdb=" O GLU z1275 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP z1282 " --> pdb=" O HIS z1278 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 137 through 141 removed outlier: 7.117A pdb=" N VAL A 108 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N SER A 140 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU A 110 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL A 12 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N THR A 111 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ILE A 14 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 39 through 42 Processing sheet with id= C, first strand: chain 'A' and resid 330 through 332 removed outlier: 6.331A pdb=" N ILE A 298 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL A 156 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N SER A 301 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 158 " --> pdb=" O SER A 301 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 240 through 242 Processing sheet with id= E, first strand: chain 'B' and resid 137 through 141 removed outlier: 7.194A pdb=" N VAL B 108 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N SER B 140 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 110 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 12 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N THR B 111 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE B 14 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 39 through 42 Processing sheet with id= G, first strand: chain 'B' and resid 330 through 332 removed outlier: 6.214A pdb=" N ILE B 298 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL B 156 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N SER B 301 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU B 158 " --> pdb=" O SER B 301 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 240 through 242 Processing sheet with id= I, first strand: chain 'C' and resid 137 through 141 removed outlier: 7.186A pdb=" N VAL C 108 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N SER C 140 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU C 110 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL C 12 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N THR C 111 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ILE C 14 " --> pdb=" O THR C 111 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 39 through 42 Processing sheet with id= K, first strand: chain 'C' and resid 330 through 332 removed outlier: 6.205A pdb=" N ILE C 298 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL C 156 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N SER C 301 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU C 158 " --> pdb=" O SER C 301 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 240 through 242 Processing sheet with id= M, first strand: chain 'D' and resid 137 through 141 removed outlier: 7.197A pdb=" N VAL D 108 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N SER D 140 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU D 110 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL D 12 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N THR D 111 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE D 14 " --> pdb=" O THR D 111 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 39 through 42 Processing sheet with id= O, first strand: chain 'D' and resid 330 through 332 removed outlier: 6.209A pdb=" N ILE D 298 " --> pdb=" O SER D 331 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL D 156 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N SER D 301 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU D 158 " --> pdb=" O SER D 301 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 240 through 242 Processing sheet with id= Q, first strand: chain 'E' and resid 137 through 141 removed outlier: 7.193A pdb=" N VAL E 108 " --> pdb=" O PHE E 138 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N SER E 140 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU E 110 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL E 12 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N THR E 111 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE E 14 " --> pdb=" O THR E 111 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 39 through 42 Processing sheet with id= S, first strand: chain 'E' and resid 330 through 332 removed outlier: 6.204A pdb=" N ILE E 298 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL E 156 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N SER E 301 " --> pdb=" O VAL E 156 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU E 158 " --> pdb=" O SER E 301 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 240 through 242 Processing sheet with id= U, first strand: chain 'F' and resid 137 through 141 removed outlier: 7.130A pdb=" N VAL F 108 " --> pdb=" O PHE F 138 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N SER F 140 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU F 110 " --> pdb=" O SER F 140 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL F 12 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N THR F 111 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ILE F 14 " --> pdb=" O THR F 111 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 39 through 42 Processing sheet with id= W, first strand: chain 'F' and resid 330 through 332 removed outlier: 6.321A pdb=" N ILE F 298 " --> pdb=" O SER F 331 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL F 156 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N SER F 301 " --> pdb=" O VAL F 156 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU F 158 " --> pdb=" O SER F 301 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 240 through 242 Processing sheet with id= Y, first strand: chain 'G' and resid 137 through 141 removed outlier: 7.130A pdb=" N VAL G 108 " --> pdb=" O PHE G 138 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N SER G 140 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU G 110 " --> pdb=" O SER G 140 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL G 12 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N THR G 111 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE G 14 " --> pdb=" O THR G 111 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 39 through 42 Processing sheet with id= AA, first strand: chain 'G' and resid 330 through 332 removed outlier: 6.318A pdb=" N ILE G 298 " --> pdb=" O SER G 331 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL G 156 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N SER G 301 " --> pdb=" O VAL G 156 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU G 158 " --> pdb=" O SER G 301 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 240 through 242 Processing sheet with id= AC, first strand: chain 'H' and resid 29 through 32 removed outlier: 3.677A pdb=" N PHE H 31 " --> pdb=" O CYS H 17 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL H 10 " --> pdb=" O PRO H 102 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU H 104 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASN H 12 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR H 106 " --> pdb=" O ASN H 12 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR H 133 " --> pdb=" O VAL H 103 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 52 through 54 removed outlier: 3.576A pdb=" N VAL H 35 " --> pdb=" O LYS H 68 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG H 37 " --> pdb=" O THR H 66 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 297 through 300 removed outlier: 6.745A pdb=" N ILE H 151 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N SER H 300 " --> pdb=" O ILE H 151 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N MET H 153 " --> pdb=" O SER H 300 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE H 165 " --> pdb=" O GLY H 150 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL H 152 " --> pdb=" O VAL H 163 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 239 through 241 Processing sheet with id= AG, first strand: chain 'I' and resid 137 through 141 removed outlier: 7.236A pdb=" N VAL I 108 " --> pdb=" O PHE I 138 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N SER I 140 " --> pdb=" O VAL I 108 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU I 110 " --> pdb=" O SER I 140 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL I 12 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N THR I 111 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ILE I 14 " --> pdb=" O THR I 111 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE I 21 " --> pdb=" O PHE I 35 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR I 33 " --> pdb=" O ALA I 23 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'I' and resid 39 through 42 Processing sheet with id= AI, first strand: chain 'I' and resid 298 through 301 removed outlier: 6.230A pdb=" N VAL I 156 " --> pdb=" O VAL I 299 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N SER I 301 " --> pdb=" O VAL I 156 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU I 158 " --> pdb=" O SER I 301 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 240 through 242 Processing sheet with id= AK, first strand: chain 'J' and resid 118 through 122 removed outlier: 7.429A pdb=" N VAL J 89 " --> pdb=" O LEU J 119 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ALA J 121 " --> pdb=" O VAL J 89 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL J 91 " --> pdb=" O ALA J 121 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL J 16 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ILE J 92 " --> pdb=" O VAL J 16 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE J 18 " --> pdb=" O ILE J 92 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'J' and resid 303 through 306 removed outlier: 6.508A pdb=" N MET J 137 " --> pdb=" O VAL J 304 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE J 306 " --> pdb=" O MET J 137 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU J 139 " --> pdb=" O ILE J 306 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL J 138 " --> pdb=" O LEU J 149 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'J' and resid 246 through 250 Processing sheet with id= AN, first strand: chain 'K' and resid 63 through 65 removed outlier: 3.738A pdb=" N THR K 63 " --> pdb=" O ILE K 76 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'K' and resid 86 through 89 removed outlier: 3.737A pdb=" N LYS K 97 " --> pdb=" O ASP K 107 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ASP K 107 " --> pdb=" O LYS K 97 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ASP K 99 " --> pdb=" O ALA K 105 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ALA K 105 " --> pdb=" O ASP K 99 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'K' and resid 141 through 147 removed outlier: 3.525A pdb=" N LYS K 146 " --> pdb=" O THR K 153 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR K 180 " --> pdb=" O GLN K 187 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN K 187 " --> pdb=" O THR K 180 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU K 192 " --> pdb=" O LYS K 210 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'K' and resid 195 through 198 removed outlier: 3.500A pdb=" N VAL K 196 " --> pdb=" O LEU K 206 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'L' and resid 48 through 52 removed outlier: 4.522A pdb=" N LYS L 48 " --> pdb=" O LEU L 61 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'L' and resid 71 through 73 removed outlier: 3.637A pdb=" N LYS L 78 " --> pdb=" O SER L 73 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'L' and resid 116 through 120 Processing sheet with id= AU, first strand: chain 'U' and resid 23 through 25 removed outlier: 6.677A pdb=" N ILE U 41 " --> pdb=" O ARG U 24 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain 'U' and resid 88 through 90 removed outlier: 7.005A pdb=" N ASN U 105 " --> pdb=" O VAL U 89 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV Processing sheet with id= AW, first strand: chain 'U' and resid 141 through 143 Processing sheet with id= AX, first strand: chain 'V' and resid 8 through 10 Processing sheet with id= AY, first strand: chain 'V' and resid 15 through 17 Processing sheet with id= AZ, first strand: chain 'V' and resid 144 through 147 removed outlier: 3.623A pdb=" N GLY V 155 " --> pdb=" O VAL V 145 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N SER V 147 " --> pdb=" O PHE V 153 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N PHE V 153 " --> pdb=" O SER V 147 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'Y' and resid 84 through 86 Processing sheet with id= BB, first strand: chain 'Y' and resid 330 through 333 Processing sheet with id= BC, first strand: chain 'Y' and resid 423 through 431 Processing sheet with id= BD, first strand: chain 'Y' and resid 43 through 50 removed outlier: 3.702A pdb=" N SER Y 281 " --> pdb=" O GLU Y 45 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP Y 47 " --> pdb=" O LYS Y 279 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS Y 279 " --> pdb=" O ASP Y 47 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N HIS Y 49 " --> pdb=" O LEU Y 277 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU Y 277 " --> pdb=" O HIS Y 49 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'Y' and resid 69 through 74 removed outlier: 4.299A pdb=" N LYS Y 274 " --> pdb=" O CYS Y 70 " (cutoff:3.500A) 2211 hydrogen bonds defined for protein. 6195 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: 15.20 Time building geometry restraints manager: 17.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 10273 1.33 - 1.46: 12299 1.46 - 1.58: 30945 1.58 - 1.71: 32 1.71 - 1.83: 335 Bond restraints: 53884 Sorted by residual: bond pdb=" N ARG N 216 " pdb=" CA ARG N 216 " ideal model delta sigma weight residual 1.455 1.507 -0.052 7.00e-03 2.04e+04 5.57e+01 bond pdb=" N GLN A 98 " pdb=" CA GLN A 98 " ideal model delta sigma weight residual 1.457 1.493 -0.036 6.40e-03 2.44e+04 3.21e+01 bond pdb=" C4 ADP C 800 " pdb=" C5 ADP C 800 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" C4 ADP G 800 " pdb=" C5 ADP G 800 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C4 ADP E 800 " pdb=" C5 ADP E 800 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.91e+01 ... (remaining 53879 not shown) Histogram of bond angle deviations from ideal: 95.37 - 103.26: 346 103.26 - 111.16: 18592 111.16 - 119.06: 31719 119.06 - 126.96: 22073 126.96 - 134.86: 428 Bond angle restraints: 73158 Sorted by residual: angle pdb=" N PRO Y 438 " pdb=" CA PRO Y 438 " pdb=" CB PRO Y 438 " ideal model delta sigma weight residual 103.30 110.08 -6.78 8.00e-01 1.56e+00 7.18e+01 angle pdb=" N PRO z1143 " pdb=" CA PRO z1143 " pdb=" CB PRO z1143 " ideal model delta sigma weight residual 103.36 110.29 -6.93 8.80e-01 1.29e+00 6.20e+01 angle pdb=" N PRO z1147 " pdb=" CA PRO z1147 " pdb=" CB PRO z1147 " ideal model delta sigma weight residual 103.27 110.32 -7.05 9.00e-01 1.23e+00 6.14e+01 angle pdb=" PB ATP H 401 " pdb=" O3B ATP H 401 " pdb=" PG ATP H 401 " ideal model delta sigma weight residual 139.87 132.12 7.75 1.00e+00 1.00e+00 6.01e+01 angle pdb=" N PRO z1132 " pdb=" CA PRO z1132 " pdb=" CB PRO z1132 " ideal model delta sigma weight residual 103.08 110.50 -7.42 9.70e-01 1.06e+00 5.85e+01 ... (remaining 73153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.85: 31686 30.85 - 61.69: 863 61.69 - 92.54: 48 92.54 - 123.38: 8 123.38 - 154.22: 12 Dihedral angle restraints: 32617 sinusoidal: 12273 harmonic: 20344 Sorted by residual: dihedral pdb=" O2A ADP B 800 " pdb=" O3A ADP B 800 " pdb=" PA ADP B 800 " pdb=" PB ADP B 800 " ideal model delta sinusoidal sigma weight residual -60.00 94.23 -154.22 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" C5' ADP G 800 " pdb=" O5' ADP G 800 " pdb=" PA ADP G 800 " pdb=" O2A ADP G 800 " ideal model delta sinusoidal sigma weight residual -60.00 94.22 -154.21 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" O1B ADP B 800 " pdb=" O3A ADP B 800 " pdb=" PB ADP B 800 " pdb=" PA ADP B 800 " ideal model delta sinusoidal sigma weight residual -60.00 93.73 -153.74 1 2.00e+01 2.50e-03 4.55e+01 ... (remaining 32614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3798 0.062 - 0.125: 3219 0.125 - 0.187: 1139 0.187 - 0.250: 187 0.250 - 0.312: 13 Chirality restraints: 8356 Sorted by residual: chirality pdb=" CB ILE E 183 " pdb=" CA ILE E 183 " pdb=" CG1 ILE E 183 " pdb=" CG2 ILE E 183 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA GLU D 64 " pdb=" N GLU D 64 " pdb=" C GLU D 64 " pdb=" CB GLU D 64 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CB VAL C 47 " pdb=" CA VAL C 47 " pdb=" CG1 VAL C 47 " pdb=" CG2 VAL C 47 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 8353 not shown) Planarity restraints: 9480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 357 " 0.036 2.00e-02 2.50e+03 2.82e-02 1.99e+01 pdb=" CG TRP G 357 " -0.079 2.00e-02 2.50e+03 pdb=" CD1 TRP G 357 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP G 357 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP G 357 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP G 357 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP G 357 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 357 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 357 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP G 357 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET n 262 " 0.019 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C MET n 262 " -0.066 2.00e-02 2.50e+03 pdb=" O MET n 262 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU n 263 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 338 " 0.024 2.00e-02 2.50e+03 2.54e-02 1.29e+01 pdb=" CG TYR C 338 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR C 338 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR C 338 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR C 338 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 338 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 338 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 338 " -0.000 2.00e-02 2.50e+03 ... (remaining 9477 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 35 2.41 - 3.03: 25136 3.03 - 3.66: 80614 3.66 - 4.28: 114306 4.28 - 4.90: 194522 Nonbonded interactions: 414613 Sorted by model distance: nonbonded pdb=" NH2 ARG Y 37 " pdb="ZN ZN Y 501 " model vdw 1.790 2.310 nonbonded pdb=" NH1 ARG E 46 " pdb=" O GLU M 84 " model vdw 2.205 2.520 nonbonded pdb=" O LEU G 267 " pdb=" NE2 HIS H 173 " model vdw 2.214 2.520 nonbonded pdb=" CG MET D 48 " pdb=" CE1 TYR F 148 " model vdw 2.220 3.740 nonbonded pdb=" N ALA G 49 " pdb=" OH TYR I 148 " model vdw 2.235 2.520 ... (remaining 414608 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 7 through 361 or (resid 362 and (name N or name CA or name \ C or name O or name CB )) or resid 363 or (resid 364 through 366 and (name N or \ name CA or name C or name O or name CB )) or resid 367 through 376 or resid 800 \ )) selection = (chain 'B' and (resid 7 through 231 or (resid 232 and (name N or name CA or name \ C or name O or name CB )) or resid 233 through 234 or (resid 235 and (name N or \ name CA or name C or name O or name CB )) or resid 236 or (resid 237 and (name \ N or name CA or name C or name O or name CB )) or resid 238 through 361 or (resi \ d 362 and (name N or name CA or name C or name O or name CB )) or resid 363 or ( \ resid 364 through 366 and (name N or name CA or name C or name O or name CB )) o \ r resid 367 through 376 or resid 800)) selection = (chain 'C' and (resid 7 through 231 or (resid 232 and (name N or name CA or name \ C or name O or name CB )) or resid 233 through 234 or (resid 235 and (name N or \ name CA or name C or name O or name CB )) or resid 236 or (resid 237 and (name \ N or name CA or name C or name O or name CB )) or resid 238 through 361 or (resi \ d 362 and (name N or name CA or name C or name O or name CB )) or resid 363 or ( \ resid 364 through 366 and (name N or name CA or name C or name O or name CB )) o \ r resid 367 through 376 or resid 800)) selection = (chain 'D' and (resid 7 through 231 or (resid 232 and (name N or name CA or name \ C or name O or name CB )) or resid 233 through 234 or (resid 235 and (name N or \ name CA or name C or name O or name CB )) or resid 236 or (resid 237 and (name \ N or name CA or name C or name O or name CB )) or resid 238 through 361 or (resi \ d 362 and (name N or name CA or name C or name O or name CB )) or resid 363 or ( \ resid 364 through 366 and (name N or name CA or name C or name O or name CB )) o \ r resid 367 through 376 or resid 800)) selection = (chain 'E' and (resid 7 through 231 or (resid 232 and (name N or name CA or name \ C or name O or name CB )) or resid 233 through 234 or (resid 235 and (name N or \ name CA or name C or name O or name CB )) or resid 236 or (resid 237 and (name \ N or name CA or name C or name O or name CB )) or resid 238 through 361 or (resi \ d 362 and (name N or name CA or name C or name O or name CB )) or resid 363 or ( \ resid 364 through 366 and (name N or name CA or name C or name O or name CB )) o \ r resid 367 through 376 or resid 800)) selection = (chain 'F' and (resid 7 through 231 or (resid 232 and (name N or name CA or name \ C or name O or name CB )) or resid 233 through 234 or (resid 235 and (name N or \ name CA or name C or name O or name CB )) or resid 236 or (resid 237 and (name \ N or name CA or name C or name O or name CB )) or resid 238 through 361 or (resi \ d 362 and (name N or name CA or name C or name O or name CB )) or resid 363 or ( \ resid 364 through 366 and (name N or name CA or name C or name O or name CB )) o \ r resid 367 through 376 or resid 800)) selection = (chain 'G' and (resid 7 through 231 or (resid 232 and (name N or name CA or name \ C or name O or name CB )) or resid 233 through 234 or (resid 235 and (name N or \ name CA or name C or name O or name CB )) or resid 236 or (resid 237 and (name \ N or name CA or name C or name O or name CB )) or resid 238 through 361 or (resi \ d 362 and (name N or name CA or name C or name O or name CB )) or resid 363 or ( \ resid 364 through 366 and (name N or name CA or name C or name O or name CB )) o \ r resid 367 through 376 or resid 800)) selection = (chain 'I' and (resid 7 through 231 or (resid 232 and (name N or name CA or name \ C or name O or name CB )) or resid 233 through 234 or (resid 235 and (name N or \ name CA or name C or name O or name CB )) or resid 236 or (resid 237 and (name \ N or name CA or name C or name O or name CB )) or resid 238 through 376 or resid \ 800)) } ncs_group { reference = (chain 'M' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 26 or resid 39 or resid 44 or resid 46 or resid 56 or resid \ 65 or resid 68 or (resid 69 and (name N or name CA or name C or name O or name \ CB )) or resid 79 or resid 81 or resid 102 through 183 or (resid 184 through 187 \ and (name N or name CA or name C or name O or name CB )) or resid 209 through 3 \ 11 or (resid 312 and (name N or name CA or name C or name O or name CB )) or res \ id 313 through 314 or (resid 315 and (name N or name CA or name C or name O or n \ ame CB )) or resid 316 through 317 or (resid 318 and (name N or name CA or name \ C or name O or name CB )) or resid 319 through 365 or (resid 366 through 390 and \ (name N or name CA or name C or name O or name CB )) or resid 391 or (resid 392 \ through 393 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'm' and (resid 3 through 26 or resid 84 through 85 or resid 87 through 88 \ or resid 92 or resid 94 through 95 or resid 98 or resid 100 or (resid 102 throu \ gh 160 and (name N or name CA or name C or name O or name CB )) or resid 161 thr \ ough 162 or (resid 163 through 170 and (name N or name CA or name C or name O or \ name CB )) or resid 171 or (resid 172 and (name N or name CA or name C or name \ O or name CB )) or resid 173 through 183 or (resid 184 through 187 and (name N o \ r name CA or name C or name O or name CB )) or resid 209 through 216 or (resid 2 \ 17 through 243 and (name N or name CA or name C or name O or name CB )) or (resi \ d 261 through 291 and (name N or name CA or name C or name O or name CB )) or (r \ esid 292 through 312 and (name N or name CA or name C or name O or name CB )) or \ resid 313 through 314 or (resid 315 and (name N or name CA or name C or name O \ or name CB )) or resid 316 through 393)) selection = (chain 'n' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 26 or resid 39 or resid 44 or resid 46 or resid 56 or resid \ 65 or resid 68 through 69 or resid 98 or resid 100 or (resid 102 through 160 an \ d (name N or name CA or name C or name O or name CB )) or resid 161 through 165 \ or (resid 166 through 170 and (name N or name CA or name C or name O or name CB \ )) or resid 171 or (resid 172 and (name N or name CA or name C or name O or name \ CB )) or resid 173 through 187 or resid 209 through 215 or (resid 216 through 2 \ 43 and (name N or name CA or name C or name O or name CB )) or (resid 261 throug \ h 291 and (name N or name CA or name C or name O or name CB )) or resid 292 thro \ ugh 393)) } ncs_group { reference = (chain 'O' and (resid 4 through 79 or (resid 80 through 82 and (name N or name C \ A or name C or name O or name CB )) or resid 83 through 84 or (resid 85 and (nam \ e N or name CA or name C or name O or name CB )) or resid 86 through 89 or (resi \ d 90 through 92 and (name N or name CA or name C or name O or name CB )) or resi \ d 93 through 111 or (resid 112 and (name N or name CA or name C or name O or nam \ e CB )) or resid 113 through 120 or (resid 121 and (name N or name CA or name C \ or name O or name CB )) or resid 122 through 127 or (resid 128 and (name N or na \ me CA or name C or name O or name CB )) or resid 129 through 130 or (resid 131 a \ nd (name N or name CA or name C or name O or name CB )) or resid 132 through 137 \ or (resid 138 through 173 and (name N or name CA or name C or name O or name CB \ )))) selection = (chain 'o' and ((resid 4 through 22 and (name N or name CA or name C or name O o \ r name CB )) or resid 23 or (resid 24 and (name N or name CA or name C or name O \ or name CB )) or resid 25 through 26 or (resid 27 through 28 and (name N or nam \ e CA or name C or name O or name CB )) or resid 29 or (resid 30 through 35 and ( \ name N or name CA or name C or name O or name CB )) or resid 36 or (resid 37 thr \ ough 44 and (name N or name CA or name C or name O or name CB )) or resid 45 thr \ ough 173)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 19.570 Check model and map are aligned: 0.640 Set scattering table: 0.340 Process input model: 102.630 Find NCS groups from input model: 2.990 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 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 : 0.014 0.117 53884 Z= 0.935 Angle : 1.874 12.919 73158 Z= 1.394 Chirality : 0.089 0.312 8356 Planarity : 0.003 0.042 9480 Dihedral : 14.114 154.225 19441 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.78 % Favored : 94.00 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.29 % 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: -2.54 (0.08), residues: 6919 helix: -1.11 (0.08), residues: 3100 sheet: -1.78 (0.18), residues: 668 loop : -2.21 (0.09), residues: 3151 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13838 Ramachandran restraints generated. 6919 Oldfield, 0 Emsley, 6919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13838 Ramachandran restraints generated. 6919 Oldfield, 0 Emsley, 6919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1197 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1196 time to evaluate : 4.889 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 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: 1 outliers final: 0 residues processed: 1197 average time/residue: 0.5703 time to fit residues: 1096.3670 Evaluate side-chains 549 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 549 time to evaluate : 4.896 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.5446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 693 random chunks: chunk 585 optimal weight: 4.9990 chunk 525 optimal weight: 7.9990 chunk 291 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 354 optimal weight: 6.9990 chunk 280 optimal weight: 0.6980 chunk 543 optimal weight: 0.9990 chunk 210 optimal weight: 0.8980 chunk 330 optimal weight: 2.9990 chunk 404 optimal weight: 3.9990 chunk 629 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN B 77 HIS C 142 GLN E 37 ASN E 77 HIS E 276 HIS F 16 ASN ** F 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 ASN F 142 GLN G 120 ASN H 12 ASN ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 HIS H 371 HIS I 16 ASN J 290 GLN K 52 HIS K 170 ASN M 53 ASN M 371 ASN M 392 ASN N 356 HIS Y 49 HIS Y 254 GLN Z1268 HIS m 113 GLN m 224 GLN m 314 HIS n 150 GLN ** o 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z1113 GLN ** z1276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 53884 Z= 0.273 Angle : 0.659 11.120 73158 Z= 0.333 Chirality : 0.043 0.189 8356 Planarity : 0.004 0.049 9480 Dihedral : 8.309 161.172 7619 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.32 % Favored : 96.60 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.09), residues: 6919 helix: 0.90 (0.09), residues: 3177 sheet: -1.12 (0.17), residues: 849 loop : -1.57 (0.10), residues: 2893 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13838 Ramachandran restraints generated. 6919 Oldfield, 0 Emsley, 6919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13838 Ramachandran restraints generated. 6919 Oldfield, 0 Emsley, 6919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 558 time to evaluate : 4.858 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 49 residues processed: 630 average time/residue: 0.5344 time to fit residues: 565.3147 Evaluate side-chains 479 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 430 time to evaluate : 4.926 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.3900 time to fit residues: 43.2389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 693 random chunks: chunk 349 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 523 optimal weight: 8.9990 chunk 428 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 630 optimal weight: 6.9990 chunk 681 optimal weight: 2.9990 chunk 561 optimal weight: 2.9990 chunk 625 optimal weight: 40.0000 chunk 214 optimal weight: 3.9990 chunk 505 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 HIS C 372 HIS D 9 ASN D 37 ASN F 16 ASN ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 HIS I 297 ASN J 344 HIS K 161 HIS K 234 HIS K 240 GLN L 45 GLN L 166 HIS M 371 ASN M 385 ASN O 155 ASN ** Y 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z1113 GLN ** m 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 103 GLN o 137 GLN ** z1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z1276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.140 53884 Z= 0.476 Angle : 0.732 13.375 73158 Z= 0.365 Chirality : 0.046 0.241 8356 Planarity : 0.005 0.099 9480 Dihedral : 8.350 167.001 7619 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.74 % Favored : 95.16 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.10), residues: 6919 helix: 1.08 (0.09), residues: 3135 sheet: -1.03 (0.17), residues: 845 loop : -1.34 (0.11), residues: 2939 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13838 Ramachandran restraints generated. 6919 Oldfield, 0 Emsley, 6919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13838 Ramachandran restraints generated. 6919 Oldfield, 0 Emsley, 6919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 452 time to evaluate : 4.845 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: 105 outliers final: 44 residues processed: 530 average time/residue: 0.5170 time to fit residues: 465.4095 Evaluate side-chains 430 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 386 time to evaluate : 4.851 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.3817 time to fit residues: 38.3803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 693 random chunks: chunk 622 optimal weight: 6.9990 chunk 474 optimal weight: 1.9990 chunk 327 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 300 optimal weight: 9.9990 chunk 423 optimal weight: 0.0060 chunk 632 optimal weight: 0.6980 chunk 669 optimal weight: 0.9990 chunk 330 optimal weight: 0.9980 chunk 599 optimal weight: 10.0000 chunk 180 optimal weight: 0.4980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 GLN C 166 HIS ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 GLN F 16 ASN G 44 HIS H 59 GLN ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 240 GLN N 15 ASN ** N 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 155 ASN O 164 GLN ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 44 HIS Y 289 HIS Z1173 HIS m 15 ASN m 269 GLN m 314 HIS n 102 GLN ** z1276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 53884 Z= 0.169 Angle : 0.570 14.467 73158 Z= 0.281 Chirality : 0.041 0.170 8356 Planarity : 0.004 0.041 9480 Dihedral : 7.779 170.725 7619 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.21 % Favored : 96.73 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.10), residues: 6919 helix: 1.48 (0.09), residues: 3201 sheet: -0.75 (0.17), residues: 852 loop : -1.18 (0.11), residues: 2866 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13838 Ramachandran restraints generated. 6919 Oldfield, 0 Emsley, 6919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13838 Ramachandran restraints generated. 6919 Oldfield, 0 Emsley, 6919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 475 time to evaluate : 4.992 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 outliers start: 46 outliers final: 17 residues processed: 504 average time/residue: 0.5286 time to fit residues: 453.3358 Evaluate side-chains 423 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 406 time to evaluate : 4.957 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4060 time to fit residues: 19.5341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 693 random chunks: chunk 557 optimal weight: 2.9990 chunk 380 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 498 optimal weight: 0.8980 chunk 276 optimal weight: 5.9990 chunk 571 optimal weight: 4.9990 chunk 463 optimal weight: 30.0000 chunk 0 optimal weight: 8.9990 chunk 342 optimal weight: 5.9990 chunk 601 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 372 HIS ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 GLN K 79 HIS L 241 ASN ** N 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 395 ASN ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1135 HIS ** m 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 103 GLN ** z1276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.066 53884 Z= 0.402 Angle : 0.659 11.700 73158 Z= 0.325 Chirality : 0.043 0.192 8356 Planarity : 0.004 0.051 9480 Dihedral : 7.814 168.494 7619 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.77 % Favored : 95.17 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.10), residues: 6919 helix: 1.48 (0.09), residues: 3143 sheet: -0.82 (0.16), residues: 935 loop : -1.05 (0.11), residues: 2841 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13838 Ramachandran restraints generated. 6919 Oldfield, 0 Emsley, 6919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13838 Ramachandran restraints generated. 6919 Oldfield, 0 Emsley, 6919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 413 time to evaluate : 4.880 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: 80 outliers final: 42 residues processed: 471 average time/residue: 0.5293 time to fit residues: 423.0882 Evaluate side-chains 422 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 380 time to evaluate : 4.917 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.4197 time to fit residues: 38.8151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 693 random chunks: chunk 225 optimal weight: 0.9990 chunk 603 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 393 optimal weight: 8.9990 chunk 165 optimal weight: 0.0970 chunk 670 optimal weight: 1.9990 chunk 556 optimal weight: 0.7980 chunk 310 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 221 optimal weight: 0.8980 chunk 352 optimal weight: 0.2980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: