Starting phenix.real_space_refine on Sun Mar 10 14:47:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znl_11313/03_2024/6znl_11313_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znl_11313/03_2024/6znl_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_11313/03_2024/6znl_11313.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znl_11313/03_2024/6znl_11313.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znl_11313/03_2024/6znl_11313_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znl_11313/03_2024/6znl_11313_neut_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 20.27, 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: 15.82 Conformation dependent library (CDL) restraints added in 7.2 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: 7.35 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: 17.36 Time building geometry restraints manager: 17.41 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: 31700 30.85 - 61.69: 877 61.69 - 92.54: 51 92.54 - 123.38: 8 123.38 - 154.22: 12 Dihedral angle restraints: 32648 sinusoidal: 12304 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 32645 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: 2.970 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: 18.370 Check model and map are aligned: 0.620 Set scattering table: 0.380 Process input model: 111.760 Find NCS groups from input model: 3.210 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.970 ------------------------------------------------------------------------------- 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 : 14.197 154.225 19472 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 % Allowed : 4.30 % Favored : 95.68 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.003 TRP G 357 HIS 0.018 0.002 HIS G 372 PHE 0.028 0.002 PHE E 376 TYR 0.063 0.003 TYR C 338 ARG 0.020 0.002 ARG D 329 *********************** 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 : 4.582 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 REVERT: A 116 ASN cc_start: 0.7121 (m-40) cc_final: 0.6784 (m110) REVERT: A 189 ASP cc_start: 0.8893 (m-30) cc_final: 0.8538 (m-30) REVERT: A 299 VAL cc_start: 0.9529 (t) cc_final: 0.9228 (m) REVERT: A 325 ASP cc_start: 0.8178 (m-30) cc_final: 0.7724 (t0) REVERT: B 268 ILE cc_start: 0.8826 (tp) cc_final: 0.8492 (tp) REVERT: D 37 ASN cc_start: 0.8897 (t0) cc_final: 0.8537 (t0) REVERT: D 94 TYR cc_start: 0.7706 (m-80) cc_final: 0.7271 (m-80) REVERT: E 120 ASN cc_start: 0.8834 (t0) cc_final: 0.8561 (t0) REVERT: E 176 MET cc_start: 0.8252 (mpp) cc_final: 0.8049 (mtm) REVERT: F 9 ASN cc_start: 0.7619 (m-40) cc_final: 0.7354 (m110) REVERT: F 10 GLN cc_start: 0.8199 (pt0) cc_final: 0.7696 (pt0) REVERT: F 79 ILE cc_start: 0.9138 (mt) cc_final: 0.8459 (mt) REVERT: F 181 MET cc_start: 0.8291 (mmm) cc_final: 0.7884 (mmt) REVERT: F 197 TYR cc_start: 0.7085 (m-10) cc_final: 0.6762 (m-80) REVERT: F 356 MET cc_start: 0.8602 (mtt) cc_final: 0.8279 (mtp) REVERT: G 55 ASP cc_start: 0.8766 (m-30) cc_final: 0.8434 (p0) REVERT: G 86 MET cc_start: 0.8972 (tpp) cc_final: 0.8185 (tpp) REVERT: G 115 LEU cc_start: 0.9250 (mt) cc_final: 0.8986 (tp) REVERT: G 196 LEU cc_start: 0.7482 (tp) cc_final: 0.7249 (tt) REVERT: G 227 ASN cc_start: 0.9045 (m-40) cc_final: 0.8782 (t0) REVERT: H 325 MET cc_start: 0.6577 (mmm) cc_final: 0.6095 (mmm) REVERT: I 37 ASN cc_start: 0.7393 (t0) cc_final: 0.6239 (t0) REVERT: K 157 CYS cc_start: 0.7368 (m) cc_final: 0.6899 (p) REVERT: K 245 GLU cc_start: 0.9186 (tt0) cc_final: 0.8882 (tm-30) REVERT: L 88 MET cc_start: 0.7801 (ptp) cc_final: 0.7184 (mmt) REVERT: L 153 VAL cc_start: 0.9384 (m) cc_final: 0.9172 (p) REVERT: L 173 VAL cc_start: 0.8966 (t) cc_final: 0.8675 (p) REVERT: L 189 LEU cc_start: 0.8801 (mt) cc_final: 0.8464 (mp) REVERT: L 221 GLU cc_start: 0.8852 (tp30) cc_final: 0.8571 (mt-10) REVERT: M 364 ILE cc_start: 0.7799 (mt) cc_final: 0.7148 (mm) REVERT: N 364 ILE cc_start: 0.8055 (mm) cc_final: 0.7831 (mm) REVERT: O 134 ILE cc_start: 0.7672 (mt) cc_final: 0.7441 (mm) REVERT: U 55 LEU cc_start: 0.4821 (pp) cc_final: 0.4277 (pp) REVERT: V 37 ASN cc_start: 0.5480 (p0) cc_final: 0.5069 (t0) REVERT: Z 1212 ASP cc_start: 0.6939 (t70) cc_final: 0.6508 (t0) REVERT: n 20 TYR cc_start: 0.8514 (m-80) cc_final: 0.8288 (m-80) outliers start: 1 outliers final: 0 residues processed: 1197 average time/residue: 0.5565 time to fit residues: 1069.9620 Evaluate side-chains 564 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 564 time to evaluate : 4.573 ------------------------------------------------------------------------------- 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: 0.6980 chunk 330 optimal weight: 2.9990 chunk 404 optimal weight: 1.9990 chunk 629 optimal weight: 7.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 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: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 53884 Z= 0.257 Angle : 0.651 11.250 73158 Z= 0.328 Chirality : 0.043 0.189 8356 Planarity : 0.004 0.049 9480 Dihedral : 8.639 162.102 7650 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.22 % Favored : 96.70 % Rotamer: Outliers : 1.90 % Allowed : 11.11 % Favored : 86.99 % 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: -0.55 (0.09), residues: 6919 helix: 0.94 (0.09), residues: 3176 sheet: -1.14 (0.17), residues: 855 loop : -1.59 (0.10), residues: 2888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 122 HIS 0.010 0.001 HIS Z1173 PHE 0.025 0.002 PHE G 353 TYR 0.021 0.002 TYR B 171 ARG 0.010 0.001 ARG U 24 *********************** 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 676 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 577 time to evaluate : 4.683 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: A 91 GLN cc_start: 0.9112 (mm-40) cc_final: 0.8903 (mm-40) REVERT: A 142 GLN cc_start: 0.7240 (mt0) cc_final: 0.6979 (mp10) REVERT: A 306 LEU cc_start: 0.9345 (mp) cc_final: 0.9076 (mp) REVERT: A 325 ASP cc_start: 0.8208 (m-30) cc_final: 0.7952 (t0) REVERT: B 86 MET cc_start: 0.7902 (tpt) cc_final: 0.7697 (tpt) REVERT: D 37 ASN cc_start: 0.8996 (t0) cc_final: 0.8529 (t0) REVERT: E 176 MET cc_start: 0.8530 (mpp) cc_final: 0.8002 (mpp) REVERT: F 9 ASN cc_start: 0.7799 (m-40) cc_final: 0.7577 (m110) REVERT: F 181 MET cc_start: 0.8363 (mmm) cc_final: 0.8029 (mmt) REVERT: F 356 MET cc_start: 0.8722 (mtt) cc_final: 0.8376 (mtp) REVERT: F 365 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7310 (mm-30) REVERT: G 55 ASP cc_start: 0.8884 (m-30) cc_final: 0.8494 (p0) REVERT: G 75 MET cc_start: 0.8172 (ptp) cc_final: 0.7873 (ptm) REVERT: G 176 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7415 (mtp) REVERT: G 179 SER cc_start: 0.8029 (OUTLIER) cc_final: 0.7290 (t) REVERT: G 357 TRP cc_start: 0.6884 (m-10) cc_final: 0.6548 (m-10) REVERT: K 59 MET cc_start: 0.9157 (mtp) cc_final: 0.8615 (mpp) REVERT: L 88 MET cc_start: 0.7748 (ptp) cc_final: 0.7233 (mmt) REVERT: L 122 TRP cc_start: 0.8112 (p-90) cc_final: 0.7636 (p-90) REVERT: L 149 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.7913 (p0) REVERT: L 174 MET cc_start: 0.7243 (mpp) cc_final: 0.6262 (mpp) REVERT: Z 1209 LYS cc_start: 0.7889 (mmmt) cc_final: 0.7131 (tppt) REVERT: z 1113 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8307 (tm-30) outliers start: 99 outliers final: 44 residues processed: 645 average time/residue: 0.5288 time to fit residues: 573.3651 Evaluate side-chains 487 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 439 time to evaluate : 4.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 176 MET Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 27 CYS Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 141 CYS Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 57 ASP Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain N residue 3 ASP Chi-restraints excluded: chain N residue 358 ASP Chi-restraints excluded: chain N residue 378 VAL Chi-restraints excluded: chain N residue 397 ASP Chi-restraints excluded: chain V residue 3 LEU Chi-restraints excluded: chain V residue 83 PHE Chi-restraints excluded: chain Y residue 238 ASP Chi-restraints excluded: chain Z residue 1205 ASP Chi-restraints excluded: chain Z residue 1207 ILE Chi-restraints excluded: chain Z residue 1219 VAL Chi-restraints excluded: chain m residue 100 THR Chi-restraints excluded: chain m residue 183 LEU Chi-restraints excluded: chain n residue 8 ASP Chi-restraints excluded: chain n residue 61 ASP Chi-restraints excluded: chain o residue 21 VAL Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain z residue 1113 GLN Chi-restraints excluded: chain z residue 1268 HIS Chi-restraints excluded: chain z residue 1278 HIS 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: 1.9990 chunk 523 optimal weight: 20.0000 chunk 428 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 630 optimal weight: 0.0020 chunk 681 optimal weight: 2.9990 chunk 561 optimal weight: 10.0000 chunk 625 optimal weight: 40.0000 chunk 214 optimal weight: 0.6980 chunk 505 optimal weight: 7.9990 overall best weight: 1.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN C 372 HIS F 16 ASN H 12 ASN H 59 GLN ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 161 HIS M 371 ASN M 385 ASN N 356 HIS ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 44 HIS m 269 GLN ** n 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 103 GLN o 137 GLN ** z1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z1276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 53884 Z= 0.307 Angle : 0.622 13.422 73158 Z= 0.307 Chirality : 0.043 0.257 8356 Planarity : 0.004 0.044 9480 Dihedral : 8.370 166.163 7650 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.02 % Favored : 95.87 % Rotamer: Outliers : 2.34 % Allowed : 11.78 % Favored : 85.88 % 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: -0.04 (0.10), residues: 6919 helix: 1.35 (0.09), residues: 3176 sheet: -0.91 (0.17), residues: 859 loop : -1.30 (0.11), residues: 2884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 357 HIS 0.007 0.001 HIS B 44 PHE 0.018 0.002 PHE o 86 TYR 0.024 0.002 TYR K 247 ARG 0.014 0.001 ARG Z1241 *********************** 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 594 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 472 time to evaluate : 4.590 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: A 91 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8758 (mm-40) REVERT: A 100 GLN cc_start: 0.8662 (tm130) cc_final: 0.8416 (tm-30) REVERT: A 119 LYS cc_start: 0.8975 (mtmm) cc_final: 0.8738 (tptp) REVERT: A 142 GLN cc_start: 0.7207 (mt0) cc_final: 0.6811 (mp10) REVERT: A 325 ASP cc_start: 0.8247 (m-30) cc_final: 0.7886 (t0) REVERT: C 197 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.7444 (t80) REVERT: D 176 MET cc_start: 0.8585 (mpp) cc_final: 0.8315 (mpp) REVERT: D 197 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.7440 (t80) REVERT: E 94 TYR cc_start: 0.8599 (m-80) cc_final: 0.8368 (m-10) REVERT: F 9 ASN cc_start: 0.7906 (m-40) cc_final: 0.7616 (m110) REVERT: F 75 MET cc_start: 0.9026 (ptm) cc_final: 0.8729 (ptp) REVERT: F 181 MET cc_start: 0.8421 (mmm) cc_final: 0.8074 (mmt) REVERT: F 197 TYR cc_start: 0.7987 (OUTLIER) cc_final: 0.7488 (m-10) REVERT: F 356 MET cc_start: 0.8513 (mtt) cc_final: 0.8255 (mtp) REVERT: F 365 GLU cc_start: 0.7380 (mm-30) cc_final: 0.7149 (mm-30) REVERT: G 55 ASP cc_start: 0.8920 (m-30) cc_final: 0.8550 (p0) REVERT: G 75 MET cc_start: 0.8257 (ptp) cc_final: 0.7797 (ptm) REVERT: J 298 GLN cc_start: 0.8515 (tp40) cc_final: 0.8269 (tp-100) REVERT: K 59 MET cc_start: 0.9251 (mtp) cc_final: 0.8661 (mpp) REVERT: L 88 MET cc_start: 0.7871 (ptp) cc_final: 0.7297 (mmt) REVERT: L 149 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.7842 (p0) REVERT: L 174 MET cc_start: 0.7299 (mpp) cc_final: 0.6279 (mpp) REVERT: L 187 MET cc_start: 0.8781 (ttm) cc_final: 0.8522 (ttm) REVERT: O 112 ASP cc_start: 0.6218 (OUTLIER) cc_final: 0.5972 (p0) REVERT: U 55 LEU cc_start: 0.5146 (tt) cc_final: 0.4857 (tt) REVERT: U 168 MET cc_start: 0.6547 (OUTLIER) cc_final: 0.5985 (mmm) REVERT: o 94 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7645 (tt) outliers start: 122 outliers final: 58 residues processed: 557 average time/residue: 0.4894 time to fit residues: 465.6749 Evaluate side-chains 476 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 411 time to evaluate : 4.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 27 CYS Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 141 CYS Chi-restraints excluded: chain J residue 364 LEU Chi-restraints excluded: chain K residue 283 MET Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain N residue 3 ASP Chi-restraints excluded: chain N residue 358 ASP Chi-restraints excluded: chain N residue 378 VAL Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 168 MET Chi-restraints excluded: chain V residue 3 LEU Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 238 ASP Chi-restraints excluded: chain Z residue 1199 GLN Chi-restraints excluded: chain Z residue 1205 ASP Chi-restraints excluded: chain Z residue 1207 ILE Chi-restraints excluded: chain Z residue 1219 VAL Chi-restraints excluded: chain Z residue 1257 THR Chi-restraints excluded: chain m residue 24 ASP Chi-restraints excluded: chain m residue 100 THR Chi-restraints excluded: chain m residue 167 ASN Chi-restraints excluded: chain m residue 183 LEU Chi-restraints excluded: chain m residue 244 CYS Chi-restraints excluded: chain n residue 8 ASP Chi-restraints excluded: chain n residue 61 ASP Chi-restraints excluded: chain n residue 149 GLN Chi-restraints excluded: chain o residue 21 VAL Chi-restraints excluded: chain o residue 94 ILE Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain z residue 1278 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 693 random chunks: chunk 622 optimal weight: 7.9990 chunk 474 optimal weight: 7.9990 chunk 327 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 300 optimal weight: 8.9990 chunk 423 optimal weight: 0.0670 chunk 632 optimal weight: 2.9990 chunk 669 optimal weight: 0.0570 chunk 330 optimal weight: 7.9990 chunk 599 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 overall best weight: 1.4040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 372 HIS C 142 GLN D 9 ASN E 229 GLN F 16 ASN ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 ASN O 164 GLN ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1113 GLN Z1173 HIS ** m 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 314 HIS n 102 GLN ** z1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z1276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 53884 Z= 0.237 Angle : 0.578 10.954 73158 Z= 0.284 Chirality : 0.041 0.178 8356 Planarity : 0.004 0.048 9480 Dihedral : 8.019 169.515 7650 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.57 % Favored : 96.37 % Rotamer: Outliers : 2.01 % Allowed : 13.31 % Favored : 84.67 % 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: 0.24 (0.10), residues: 6919 helix: 1.57 (0.09), residues: 3154 sheet: -0.74 (0.17), residues: 853 loop : -1.12 (0.11), residues: 2912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 357 HIS 0.006 0.001 HIS B 206 PHE 0.043 0.001 PHE Y 296 TYR 0.016 0.001 TYR B 38 ARG 0.010 0.000 ARG N 383 *********************** 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 562 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 457 time to evaluate : 4.642 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: A 29 GLN cc_start: 0.8874 (pm20) cc_final: 0.8622 (pm20) REVERT: A 119 LYS cc_start: 0.9010 (mtmm) cc_final: 0.8786 (tptp) REVERT: A 142 GLN cc_start: 0.7221 (mt0) cc_final: 0.6797 (mp10) REVERT: A 325 ASP cc_start: 0.8279 (m-30) cc_final: 0.7868 (t0) REVERT: B 197 TYR cc_start: 0.7838 (OUTLIER) cc_final: 0.7622 (t80) REVERT: C 197 TYR cc_start: 0.8050 (OUTLIER) cc_final: 0.7327 (t80) REVERT: C 229 GLN cc_start: 0.7890 (mp10) cc_final: 0.7686 (mp10) REVERT: D 37 ASN cc_start: 0.8799 (t0) cc_final: 0.8355 (t0) REVERT: D 176 MET cc_start: 0.8747 (mpp) cc_final: 0.8528 (mpp) REVERT: D 197 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.7366 (t80) REVERT: E 94 TYR cc_start: 0.8602 (m-80) cc_final: 0.8399 (m-10) REVERT: F 181 MET cc_start: 0.8408 (mmm) cc_final: 0.8015 (mmt) REVERT: F 197 TYR cc_start: 0.7946 (OUTLIER) cc_final: 0.7384 (m-10) REVERT: F 365 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7179 (mm-30) REVERT: G 55 ASP cc_start: 0.8833 (m-30) cc_final: 0.8460 (p0) REVERT: G 75 MET cc_start: 0.8162 (ptp) cc_final: 0.7775 (ptm) REVERT: J 126 MET cc_start: 0.7657 (mmm) cc_final: 0.7397 (mmm) REVERT: J 298 GLN cc_start: 0.8447 (tp40) cc_final: 0.8193 (tp-100) REVERT: K 173 TRP cc_start: 0.7843 (t-100) cc_final: 0.7327 (t60) REVERT: L 88 MET cc_start: 0.7847 (ptp) cc_final: 0.7386 (mmt) REVERT: L 149 ASP cc_start: 0.8973 (OUTLIER) cc_final: 0.7848 (p0) REVERT: L 174 MET cc_start: 0.7435 (mpp) cc_final: 0.6238 (mpp) REVERT: L 187 MET cc_start: 0.8759 (ttm) cc_final: 0.8499 (ttm) REVERT: U 55 LEU cc_start: 0.5634 (tt) cc_final: 0.5393 (tt) REVERT: m 172 ASP cc_start: 0.6624 (p0) cc_final: 0.6275 (p0) REVERT: o 110 MET cc_start: 0.7533 (ppp) cc_final: 0.7110 (ppp) outliers start: 105 outliers final: 60 residues processed: 534 average time/residue: 0.4950 time to fit residues: 452.7336 Evaluate side-chains 473 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 408 time to evaluate : 4.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain F residue 227 ASN Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain J residue 27 CYS Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 141 CYS Chi-restraints excluded: chain J residue 364 LEU Chi-restraints excluded: chain K residue 70 TYR Chi-restraints excluded: chain K residue 283 MET Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain N residue 3 ASP Chi-restraints excluded: chain N residue 358 ASP Chi-restraints excluded: chain N residue 378 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain V residue 3 LEU Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 238 ASP Chi-restraints excluded: chain Y residue 278 ILE Chi-restraints excluded: chain Z residue 1205 ASP Chi-restraints excluded: chain Z residue 1219 VAL Chi-restraints excluded: chain m residue 24 ASP Chi-restraints excluded: chain m residue 100 THR Chi-restraints excluded: chain m residue 167 ASN Chi-restraints excluded: chain n residue 8 ASP Chi-restraints excluded: chain n residue 61 ASP Chi-restraints excluded: chain n residue 63 ARG Chi-restraints excluded: chain n residue 149 GLN Chi-restraints excluded: chain o residue 21 VAL Chi-restraints excluded: chain o residue 33 VAL Chi-restraints excluded: chain o residue 116 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 693 random chunks: chunk 557 optimal weight: 7.9990 chunk 380 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 498 optimal weight: 0.9980 chunk 276 optimal weight: 1.9990 chunk 571 optimal weight: 5.9990 chunk 463 optimal weight: 30.0000 chunk 0 optimal weight: 7.9990 chunk 342 optimal weight: 5.9990 chunk 601 optimal weight: 6.9990 chunk 169 optimal weight: 0.5980 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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** F 16 ASN ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 GLN I 178 HIS I 240 GLN J 344 HIS K 79 HIS K 240 GLN L 166 HIS L 241 ASN ** N 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 155 ASN ** U 54 ASN ** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 53884 Z= 0.331 Angle : 0.625 11.743 73158 Z= 0.307 Chirality : 0.043 0.179 8356 Planarity : 0.004 0.061 9480 Dihedral : 7.919 167.264 7650 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.48 % Favored : 95.46 % Rotamer: Outliers : 2.32 % Allowed : 14.25 % Favored : 83.43 % 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: 0.31 (0.10), residues: 6919 helix: 1.58 (0.09), residues: 3141 sheet: -0.62 (0.18), residues: 851 loop : -1.06 (0.11), residues: 2927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 83 HIS 0.007 0.001 HIS B 276 PHE 0.019 0.002 PHE F 256 TYR 0.020 0.002 TYR B 38 ARG 0.010 0.001 ARG N 383 *********************** 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 538 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 417 time to evaluate : 4.611 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: A 128 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8041 (t80) REVERT: A 142 GLN cc_start: 0.7334 (mt0) cc_final: 0.6883 (mp10) REVERT: C 132 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.8356 (m-10) REVERT: C 197 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.7468 (t80) REVERT: C 229 GLN cc_start: 0.8069 (mp10) cc_final: 0.7867 (mp10) REVERT: D 176 MET cc_start: 0.8792 (mpp) cc_final: 0.8543 (mpp) REVERT: D 197 TYR cc_start: 0.7946 (OUTLIER) cc_final: 0.7407 (t80) REVERT: F 75 MET cc_start: 0.9094 (ptm) cc_final: 0.8767 (ptp) REVERT: F 197 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7465 (m-10) REVERT: F 365 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7055 (mm-30) REVERT: G 75 MET cc_start: 0.8094 (ptp) cc_final: 0.7817 (ptm) REVERT: G 229 GLN cc_start: 0.8964 (pm20) cc_final: 0.8706 (pm20) REVERT: H 171 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8859 (mt) REVERT: I 176 MET cc_start: 0.7709 (mpp) cc_final: 0.7493 (mtm) REVERT: I 288 MET cc_start: 0.7821 (tpp) cc_final: 0.7399 (tpp) REVERT: J 126 MET cc_start: 0.7678 (mmm) cc_final: 0.7435 (mmt) REVERT: L 88 MET cc_start: 0.7940 (ptp) cc_final: 0.7346 (mmt) REVERT: N 398 GLU cc_start: 0.6151 (OUTLIER) cc_final: 0.5367 (pt0) REVERT: U 168 MET cc_start: 0.6654 (mmm) cc_final: 0.6393 (mmm) REVERT: m 172 ASP cc_start: 0.6126 (p0) cc_final: 0.5599 (p0) REVERT: n 63 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7102 (ptp90) REVERT: o 105 GLU cc_start: 0.8127 (pp20) cc_final: 0.7683 (pp20) outliers start: 121 outliers final: 80 residues processed: 507 average time/residue: 0.4917 time to fit residues: 429.7443 Evaluate side-chains 470 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 382 time to evaluate : 4.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 197 TYR Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain F residue 227 ASN Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain I residue 76 GLU Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain I residue 275 ILE Chi-restraints excluded: chain J residue 27 CYS Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 141 CYS Chi-restraints excluded: chain J residue 364 LEU Chi-restraints excluded: chain K residue 70 TYR Chi-restraints excluded: chain K residue 255 PHE Chi-restraints excluded: chain K residue 283 MET Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 387 SER Chi-restraints excluded: chain N residue 3 ASP Chi-restraints excluded: chain N residue 358 ASP Chi-restraints excluded: chain N residue 378 VAL Chi-restraints excluded: chain N residue 398 GLU Chi-restraints excluded: chain O residue 80 ASP Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 155 ASN Chi-restraints excluded: chain O residue 156 LYS Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain V residue 3 LEU Chi-restraints excluded: chain V residue 83 PHE Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 238 ASP Chi-restraints excluded: chain Y residue 278 ILE Chi-restraints excluded: chain Z residue 1207 ILE Chi-restraints excluded: chain Z residue 1219 VAL Chi-restraints excluded: chain m residue 24 ASP Chi-restraints excluded: chain m residue 100 THR Chi-restraints excluded: chain m residue 138 VAL Chi-restraints excluded: chain m residue 167 ASN Chi-restraints excluded: chain m residue 183 LEU Chi-restraints excluded: chain n residue 8 ASP Chi-restraints excluded: chain n residue 61 ASP Chi-restraints excluded: chain n residue 63 ARG Chi-restraints excluded: chain n residue 149 GLN Chi-restraints excluded: chain o residue 41 GLN Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain z residue 1278 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 693 random chunks: chunk 225 optimal weight: 0.2980 chunk 603 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 393 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 670 optimal weight: 5.9990 chunk 556 optimal weight: 0.4980 chunk 310 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 352 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 F 16 ASN G 44 HIS ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 GLN J 344 HIS L 255 GLN ** M 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 ASN N 395 ASN ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 262 GLN ** Y 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 314 HIS ** n 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z1276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 53884 Z= 0.165 Angle : 0.559 10.766 73158 Z= 0.273 Chirality : 0.040 0.161 8356 Planarity : 0.004 0.061 9480 Dihedral : 7.542 169.135 7650 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.38 % Favored : 96.56 % Rotamer: Outliers : 1.67 % Allowed : 15.25 % Favored : 83.08 % 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: 0.52 (0.10), residues: 6919 helix: 1.74 (0.09), residues: 3158 sheet: -0.48 (0.18), residues: 845 loop : -0.97 (0.11), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 357 HIS 0.014 0.001 HIS N 214 PHE 0.046 0.001 PHE Y 296 TYR 0.019 0.001 TYR V 13 ARG 0.011 0.000 ARG N 383 *********************** REFINEMENT MACRO_CYCLE 6 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 516 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 429 time to evaluate : 4.612 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: A 142 GLN cc_start: 0.7277 (mt0) cc_final: 0.6774 (mp10) REVERT: B 32 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6932 (tptt) REVERT: B 174 PHE cc_start: 0.5705 (m-80) cc_final: 0.5386 (m-80) REVERT: B 197 TYR cc_start: 0.7552 (OUTLIER) cc_final: 0.7314 (t80) REVERT: B 270 GLU cc_start: 0.7027 (mp0) cc_final: 0.6384 (mp0) REVERT: C 188 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7953 (ttp-170) REVERT: C 197 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7409 (t80) REVERT: D 176 MET cc_start: 0.8734 (mpp) cc_final: 0.8476 (mpp) REVERT: D 197 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.7359 (t80) REVERT: F 197 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7402 (m-10) REVERT: F 365 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7074 (mm-30) REVERT: G 75 MET cc_start: 0.8103 (ptp) cc_final: 0.7714 (ptm) REVERT: I 176 MET cc_start: 0.7784 (mpp) cc_final: 0.7550 (mtm) REVERT: I 181 MET cc_start: 0.8372 (tpp) cc_final: 0.8131 (tpp) REVERT: I 288 MET cc_start: 0.7693 (tpp) cc_final: 0.7233 (tpp) REVERT: J 126 MET cc_start: 0.7540 (mmm) cc_final: 0.7139 (mmm) REVERT: L 88 MET cc_start: 0.7805 (ptp) cc_final: 0.7172 (mmt) REVERT: m 172 ASP cc_start: 0.6677 (p0) cc_final: 0.6155 (p0) outliers start: 87 outliers final: 57 residues processed: 491 average time/residue: 0.4888 time to fit residues: 413.9792 Evaluate side-chains 455 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 392 time to evaluate : 4.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 197 TYR Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain F residue 227 ASN Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 375 PHE Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain J residue 27 CYS Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 141 CYS Chi-restraints excluded: chain J residue 364 LEU Chi-restraints excluded: chain K residue 70 TYR Chi-restraints excluded: chain K residue 255 PHE Chi-restraints excluded: chain K residue 283 MET Chi-restraints excluded: chain L residue 209 HIS Chi-restraints excluded: chain M residue 326 ILE Chi-restraints excluded: chain M residue 387 SER Chi-restraints excluded: chain N residue 3 ASP Chi-restraints excluded: chain N residue 358 ASP Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain V residue 3 LEU Chi-restraints excluded: chain V residue 83 PHE Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 238 ASP Chi-restraints excluded: chain Z residue 1219 VAL Chi-restraints excluded: chain m residue 100 THR Chi-restraints excluded: chain m residue 167 ASN Chi-restraints excluded: chain m residue 183 LEU Chi-restraints excluded: chain m residue 337 LEU Chi-restraints excluded: chain n residue 8 ASP Chi-restraints excluded: chain n residue 61 ASP Chi-restraints excluded: chain n residue 149 GLN Chi-restraints excluded: chain o residue 21 VAL Chi-restraints excluded: chain o residue 41 GLN Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain z residue 1281 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 693 random chunks: chunk 646 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 382 optimal weight: 10.0000 chunk 489 optimal weight: 30.0000 chunk 379 optimal weight: 5.9990 chunk 564 optimal weight: 50.0000 chunk 374 optimal weight: 5.9990 chunk 667 optimal weight: 10.0000 chunk 418 optimal weight: 4.9990 chunk 407 optimal weight: 4.9990 chunk 308 optimal weight: 0.2980 overall best weight: 3.6588 ------------------------------------------------------------------------------- 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 120 ASN C 142 GLN ** D 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 ASN G 372 HIS J 344 HIS K 220 ASN K 234 HIS L 45 GLN ** L 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 ASN ** N 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 405 ASN ** Z1135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z1221 GLN m 342 GLN m 346 GLN ** n 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z1113 GLN ** z1276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 53884 Z= 0.543 Angle : 0.760 11.962 73158 Z= 0.376 Chirality : 0.046 0.227 8356 Planarity : 0.005 0.059 9480 Dihedral : 8.240 165.919 7650 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.54 % Favored : 94.41 % Rotamer: Outliers : 2.86 % Allowed : 14.98 % Favored : 82.16 % 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: 0.14 (0.10), residues: 6919 helix: 1.34 (0.09), residues: 3121 sheet: -0.64 (0.17), residues: 875 loop : -1.04 (0.11), residues: 2923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP E 83 HIS 0.012 0.002 HIS N 214 PHE 0.038 0.002 PHE Y 296 TYR 0.026 0.002 TYR B 38 ARG 0.012 0.001 ARG N 383 *********************** REFINEMENT MACRO_CYCLE 7 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 533 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 384 time to evaluate : 4.723 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: A 128 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8094 (t80) REVERT: A 142 GLN cc_start: 0.7320 (mt0) cc_final: 0.7068 (mp-120) REVERT: A 338 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.8430 (m-80) REVERT: B 197 TYR cc_start: 0.8068 (OUTLIER) cc_final: 0.7852 (t80) REVERT: B 288 MET cc_start: 0.8337 (tpp) cc_final: 0.8105 (tpp) REVERT: C 132 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8364 (m-10) REVERT: C 188 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7929 (ttp-170) REVERT: C 197 TYR cc_start: 0.8197 (OUTLIER) cc_final: 0.7522 (t80) REVERT: C 336 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.8457 (mtm-85) REVERT: D 176 MET cc_start: 0.8716 (mpp) cc_final: 0.8435 (mpp) REVERT: D 197 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7470 (t80) REVERT: E 342 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9003 (mt) REVERT: H 171 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9046 (mp) REVERT: I 86 MET cc_start: 0.7043 (tpt) cc_final: 0.6528 (tpt) REVERT: I 176 MET cc_start: 0.7718 (mpp) cc_final: 0.7517 (mtm) REVERT: I 288 MET cc_start: 0.8039 (tpp) cc_final: 0.7588 (tpp) REVERT: J 126 MET cc_start: 0.7710 (mmm) cc_final: 0.7458 (mmm) REVERT: K 211 ASP cc_start: 0.9385 (OUTLIER) cc_final: 0.9009 (p0) REVERT: L 88 MET cc_start: 0.7996 (ptp) cc_final: 0.7435 (mmm) REVERT: L 149 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8046 (p0) REVERT: N 398 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.5953 (pt0) REVERT: m 172 ASP cc_start: 0.6376 (p0) cc_final: 0.5721 (p0) REVERT: z 1255 LYS cc_start: 0.6673 (OUTLIER) cc_final: 0.5275 (mtmm) outliers start: 149 outliers final: 92 residues processed: 498 average time/residue: 0.4997 time to fit residues: 426.5891 Evaluate side-chains 466 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 360 time to evaluate : 4.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 338 TYR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain F residue 227 ASN Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 274 ILE Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 354 GLN Chi-restraints excluded: chain H residue 375 PHE Chi-restraints excluded: chain I residue 76 GLU Chi-restraints excluded: chain I residue 268 ILE Chi-restraints excluded: chain I residue 356 MET Chi-restraints excluded: chain J residue 27 CYS Chi-restraints excluded: chain J residue 37 CYS Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 76 TYR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 141 CYS Chi-restraints excluded: chain J residue 364 LEU Chi-restraints excluded: chain K residue 70 TYR Chi-restraints excluded: chain K residue 211 ASP Chi-restraints excluded: chain K residue 255 PHE Chi-restraints excluded: chain K residue 283 MET Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 209 HIS Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 326 ILE Chi-restraints excluded: chain M residue 387 SER Chi-restraints excluded: chain N residue 3 ASP Chi-restraints excluded: chain N residue 358 ASP Chi-restraints excluded: chain N residue 378 VAL Chi-restraints excluded: chain N residue 398 GLU Chi-restraints excluded: chain O residue 80 ASP Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain V residue 83 PHE Chi-restraints excluded: chain Y residue 18 LYS Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 278 ILE Chi-restraints excluded: chain Y residue 337 THR Chi-restraints excluded: chain Y residue 374 LEU Chi-restraints excluded: chain Z residue 1207 ILE Chi-restraints excluded: chain Z residue 1214 VAL Chi-restraints excluded: chain Z residue 1219 VAL Chi-restraints excluded: chain m residue 100 THR Chi-restraints excluded: chain m residue 138 VAL Chi-restraints excluded: chain m residue 167 ASN Chi-restraints excluded: chain m residue 183 LEU Chi-restraints excluded: chain n residue 8 ASP Chi-restraints excluded: chain n residue 61 ASP Chi-restraints excluded: chain n residue 149 GLN Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain z residue 1255 LYS Chi-restraints excluded: chain z residue 1278 HIS Chi-restraints excluded: chain z residue 1281 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 693 random chunks: chunk 413 optimal weight: 10.0000 chunk 266 optimal weight: 0.7980 chunk 398 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 424 optimal weight: 2.9990 chunk 455 optimal weight: 9.9990 chunk 330 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 525 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN C 142 GLN ** F 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 302 ASN K 220 ASN ** L 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 ASN ** N 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 162 GLN ** Y 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z1135 HIS Z1161 ASN ** m 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 314 HIS ** n 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z1113 GLN ** z1276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 53884 Z= 0.190 Angle : 0.585 10.603 73158 Z= 0.286 Chirality : 0.041 0.194 8356 Planarity : 0.004 0.054 9480 Dihedral : 7.670 173.889 7650 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.54 % Favored : 96.39 % Rotamer: Outliers : 1.59 % Allowed : 16.55 % Favored : 81.85 % 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: 0.50 (0.10), residues: 6919 helix: 1.67 (0.09), residues: 3150 sheet: -0.36 (0.19), residues: 806 loop : -0.93 (0.11), residues: 2963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 357 HIS 0.009 0.001 HIS N 214 PHE 0.016 0.001 PHE o 86 TYR 0.021 0.001 TYR V 107 ARG 0.012 0.000 ARG N 383 *********************** REFINEMENT MACRO_CYCLE 8 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 489 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 406 time to evaluate : 4.682 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: A 91 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8743 (mm-40) REVERT: A 128 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.8023 (t80) REVERT: B 197 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.7658 (t80) REVERT: B 288 MET cc_start: 0.8264 (tpp) cc_final: 0.8051 (tpp) REVERT: C 188 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7869 (ttp-170) REVERT: C 197 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.7551 (t80) REVERT: D 176 MET cc_start: 0.8647 (mpp) cc_final: 0.8348 (mpp) REVERT: D 197 TYR cc_start: 0.7815 (OUTLIER) cc_final: 0.7315 (t80) REVERT: E 176 MET cc_start: 0.8100 (mpp) cc_final: 0.7887 (mtm) REVERT: F 176 MET cc_start: 0.8845 (mpp) cc_final: 0.8453 (mtm) REVERT: F 181 MET cc_start: 0.8274 (mmm) cc_final: 0.8007 (mmm) REVERT: H 171 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8668 (mt) REVERT: I 288 MET cc_start: 0.7741 (tpp) cc_final: 0.7260 (tpp) REVERT: J 126 MET cc_start: 0.7513 (mmm) cc_final: 0.7150 (mmm) REVERT: K 157 CYS cc_start: 0.7341 (m) cc_final: 0.6636 (p) REVERT: K 204 VAL cc_start: 0.8980 (t) cc_final: 0.8764 (p) REVERT: L 88 MET cc_start: 0.7872 (ptp) cc_final: 0.7217 (mmt) REVERT: N 398 GLU cc_start: 0.6160 (OUTLIER) cc_final: 0.5836 (pt0) REVERT: m 172 ASP cc_start: 0.6196 (p0) cc_final: 0.5607 (p0) outliers start: 83 outliers final: 69 residues processed: 466 average time/residue: 0.5061 time to fit residues: 403.5743 Evaluate side-chains 456 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 380 time to evaluate : 4.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain F residue 227 ASN Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 375 PHE Chi-restraints excluded: chain J residue 27 CYS Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 141 CYS Chi-restraints excluded: chain J residue 364 LEU Chi-restraints excluded: chain K residue 70 TYR Chi-restraints excluded: chain K residue 255 PHE Chi-restraints excluded: chain K residue 283 MET Chi-restraints excluded: chain L residue 209 HIS Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 319 THR Chi-restraints excluded: chain M residue 387 SER Chi-restraints excluded: chain N residue 8 ASP Chi-restraints excluded: chain N residue 15 ASN Chi-restraints excluded: chain N residue 358 ASP Chi-restraints excluded: chain N residue 398 GLU Chi-restraints excluded: chain O residue 80 ASP Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain V residue 107 TYR Chi-restraints excluded: chain Y residue 18 LYS Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 321 ILE Chi-restraints excluded: chain Y residue 337 THR Chi-restraints excluded: chain Y residue 374 LEU Chi-restraints excluded: chain Z residue 1219 VAL Chi-restraints excluded: chain m residue 100 THR Chi-restraints excluded: chain m residue 138 VAL Chi-restraints excluded: chain m residue 167 ASN Chi-restraints excluded: chain m residue 183 LEU Chi-restraints excluded: chain m residue 337 LEU Chi-restraints excluded: chain n residue 8 ASP Chi-restraints excluded: chain n residue 61 ASP Chi-restraints excluded: chain n residue 149 GLN Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain z residue 1113 GLN Chi-restraints excluded: chain z residue 1281 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 693 random chunks: chunk 607 optimal weight: 0.9980 chunk 639 optimal weight: 2.9990 chunk 583 optimal weight: 0.9990 chunk 622 optimal weight: 6.9990 chunk 374 optimal weight: 7.9990 chunk 271 optimal weight: 4.9990 chunk 488 optimal weight: 30.0000 chunk 191 optimal weight: 2.9990 chunk 562 optimal weight: 40.0000 chunk 588 optimal weight: 0.6980 chunk 620 optimal weight: 0.3980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 GLN ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 302 ASN ** N 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 162 GLN Y 275 HIS ** Y 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z1161 ASN ** m 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z1113 GLN ** z1276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 53884 Z= 0.224 Angle : 0.592 11.293 73158 Z= 0.288 Chirality : 0.041 0.263 8356 Planarity : 0.004 0.063 9480 Dihedral : 7.553 170.953 7650 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.18 % Favored : 95.77 % Rotamer: Outliers : 1.65 % Allowed : 16.82 % Favored : 81.53 % 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: 0.51 (0.10), residues: 6919 helix: 1.63 (0.09), residues: 3188 sheet: -0.35 (0.19), residues: 799 loop : -0.90 (0.11), residues: 2932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 357 HIS 0.007 0.001 HIS z1108 PHE 0.018 0.001 PHE o 86 TYR 0.022 0.001 TYR V 107 ARG 0.013 0.000 ARG N 383 *********************** REFINEMENT MACRO_CYCLE 9 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 475 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 389 time to evaluate : 4.688 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: A 91 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8690 (mm-40) REVERT: A 128 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8043 (t80) REVERT: B 197 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.7666 (t80) REVERT: B 288 MET cc_start: 0.8203 (tpp) cc_final: 0.7959 (tpp) REVERT: C 188 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7925 (ttp-170) REVERT: C 197 TYR cc_start: 0.8156 (OUTLIER) cc_final: 0.7556 (t80) REVERT: D 176 MET cc_start: 0.8672 (mpp) cc_final: 0.8369 (mpp) REVERT: D 197 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.7376 (t80) REVERT: E 100 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8486 (mt0) REVERT: F 176 MET cc_start: 0.8827 (mpp) cc_final: 0.8430 (mtm) REVERT: F 181 MET cc_start: 0.8347 (mmm) cc_final: 0.8075 (mmm) REVERT: I 288 MET cc_start: 0.7746 (tpp) cc_final: 0.7279 (tpp) REVERT: J 48 MET cc_start: 0.5850 (ptp) cc_final: 0.5387 (ptp) REVERT: J 126 MET cc_start: 0.7520 (mmm) cc_final: 0.7149 (mmm) REVERT: K 204 VAL cc_start: 0.9071 (t) cc_final: 0.8854 (p) REVERT: L 88 MET cc_start: 0.7829 (ptp) cc_final: 0.7294 (mmm) REVERT: N 398 GLU cc_start: 0.6078 (OUTLIER) cc_final: 0.5811 (pt0) REVERT: m 172 ASP cc_start: 0.6213 (p0) cc_final: 0.5613 (p0) REVERT: n 24 ASP cc_start: 0.7630 (p0) cc_final: 0.7328 (p0) outliers start: 86 outliers final: 68 residues processed: 451 average time/residue: 0.4921 time to fit residues: 382.8634 Evaluate side-chains 445 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 370 time to evaluate : 4.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 120 ASN Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain F residue 227 ASN Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 375 PHE Chi-restraints excluded: chain J residue 27 CYS Chi-restraints excluded: chain J residue 37 CYS Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 141 CYS Chi-restraints excluded: chain J residue 364 LEU Chi-restraints excluded: chain K residue 70 TYR Chi-restraints excluded: chain K residue 234 HIS Chi-restraints excluded: chain K residue 255 PHE Chi-restraints excluded: chain K residue 283 MET Chi-restraints excluded: chain L residue 209 HIS Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 319 THR Chi-restraints excluded: chain M residue 387 SER Chi-restraints excluded: chain N residue 3 ASP Chi-restraints excluded: chain N residue 8 ASP Chi-restraints excluded: chain N residue 358 ASP Chi-restraints excluded: chain N residue 398 GLU Chi-restraints excluded: chain O residue 80 ASP Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain V residue 107 TYR Chi-restraints excluded: chain Y residue 18 LYS Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 278 ILE Chi-restraints excluded: chain Y residue 321 ILE Chi-restraints excluded: chain Y residue 337 THR Chi-restraints excluded: chain Y residue 374 LEU Chi-restraints excluded: chain Z residue 1219 VAL Chi-restraints excluded: chain m residue 100 THR Chi-restraints excluded: chain m residue 138 VAL Chi-restraints excluded: chain m residue 167 ASN Chi-restraints excluded: chain m residue 183 LEU Chi-restraints excluded: chain m residue 337 LEU Chi-restraints excluded: chain n residue 8 ASP Chi-restraints excluded: chain n residue 61 ASP Chi-restraints excluded: chain n residue 149 GLN Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain z residue 1281 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 693 random chunks: chunk 408 optimal weight: 4.9990 chunk 658 optimal weight: 2.9990 chunk 401 optimal weight: 4.9990 chunk 312 optimal weight: 0.9990 chunk 457 optimal weight: 3.9990 chunk 690 optimal weight: 0.0470 chunk 635 optimal weight: 1.9990 chunk 549 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 424 optimal weight: 7.9990 chunk 337 optimal weight: 4.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 GLN ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 ASN ** N 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 162 GLN ** Y 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z1161 ASN ** m 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 314 HIS ** n 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z1113 GLN ** z1276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 53884 Z= 0.237 Angle : 0.598 11.946 73158 Z= 0.290 Chirality : 0.041 0.223 8356 Planarity : 0.004 0.063 9480 Dihedral : 7.418 169.718 7650 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.00 % Favored : 95.94 % Rotamer: Outliers : 1.76 % Allowed : 16.59 % Favored : 81.64 % 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: 0.54 (0.10), residues: 6919 helix: 1.65 (0.09), residues: 3185 sheet: -0.34 (0.19), residues: 799 loop : -0.88 (0.11), residues: 2935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 357 HIS 0.005 0.001 HIS B 206 PHE 0.019 0.001 PHE o 86 TYR 0.025 0.001 TYR V 107 ARG 0.019 0.000 ARG n 63 ********************** REFINEMENT MACRO_CYCLE 10 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 475 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 383 time to evaluate : 4.649 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: A 128 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.8023 (t80) REVERT: B 197 TYR cc_start: 0.7937 (OUTLIER) cc_final: 0.7677 (t80) REVERT: B 288 MET cc_start: 0.8193 (tpp) cc_final: 0.7946 (tpp) REVERT: C 188 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7877 (ttp-170) REVERT: C 197 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.7593 (t80) REVERT: D 176 MET cc_start: 0.8655 (mpp) cc_final: 0.8355 (mpp) REVERT: D 197 TYR cc_start: 0.7860 (OUTLIER) cc_final: 0.7363 (t80) REVERT: E 100 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8453 (mt0) REVERT: F 176 MET cc_start: 0.8825 (mpp) cc_final: 0.8447 (mtm) REVERT: F 181 MET cc_start: 0.8347 (mmm) cc_final: 0.8070 (mmm) REVERT: I 288 MET cc_start: 0.7859 (tpp) cc_final: 0.7426 (tpp) REVERT: J 126 MET cc_start: 0.7514 (mmm) cc_final: 0.7126 (mmm) REVERT: K 204 VAL cc_start: 0.9070 (t) cc_final: 0.8853 (p) REVERT: K 247 TYR cc_start: 0.8662 (m-80) cc_final: 0.8247 (t80) REVERT: L 88 MET cc_start: 0.7835 (ptp) cc_final: 0.7296 (mmm) REVERT: m 172 ASP cc_start: 0.6252 (p0) cc_final: 0.5633 (p0) REVERT: n 24 ASP cc_start: 0.7616 (p0) cc_final: 0.7273 (p0) outliers start: 92 outliers final: 76 residues processed: 450 average time/residue: 0.4913 time to fit residues: 382.2165 Evaluate side-chains 457 residues out of total 6085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 375 time to evaluate : 4.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 120 ASN Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain F residue 227 ASN Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 375 PHE Chi-restraints excluded: chain J residue 27 CYS Chi-restraints excluded: chain J residue 37 CYS Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 141 CYS Chi-restraints excluded: chain J residue 364 LEU Chi-restraints excluded: chain K residue 70 TYR Chi-restraints excluded: chain K residue 234 HIS Chi-restraints excluded: chain K residue 255 PHE Chi-restraints excluded: chain K residue 283 MET Chi-restraints excluded: chain L residue 209 HIS Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 319 THR Chi-restraints excluded: chain M residue 326 ILE Chi-restraints excluded: chain M residue 364 ILE Chi-restraints excluded: chain M residue 387 SER Chi-restraints excluded: chain N residue 3 ASP Chi-restraints excluded: chain N residue 8 ASP Chi-restraints excluded: chain N residue 358 ASP Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain V residue 107 TYR Chi-restraints excluded: chain Y residue 18 LYS Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Y residue 278 ILE Chi-restraints excluded: chain Y residue 321 ILE Chi-restraints excluded: chain Y residue 337 THR Chi-restraints excluded: chain Y residue 374 LEU Chi-restraints excluded: chain Z residue 1219 VAL Chi-restraints excluded: chain Z residue 1231 PHE Chi-restraints excluded: chain m residue 100 THR Chi-restraints excluded: chain m residue 138 VAL Chi-restraints excluded: chain m residue 167 ASN Chi-restraints excluded: chain m residue 183 LEU Chi-restraints excluded: chain m residue 337 LEU Chi-restraints excluded: chain n residue 8 ASP Chi-restraints excluded: chain n residue 61 ASP Chi-restraints excluded: chain n residue 149 GLN Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain z residue 1113 GLN Chi-restraints excluded: chain z residue 1281 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 693 random chunks: chunk 436 optimal weight: 8.9990 chunk 585 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 506 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 550 optimal weight: 30.0000 chunk 230 optimal weight: 0.7980 chunk 565 optimal weight: 0.3980 chunk 69 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 GLN C 166 HIS ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 351 ASN ** K 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 162 GLN ** Y 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z1161 ASN ** m 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z1276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.074909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.051311 restraints weight = 196326.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.053108 restraints weight = 103002.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.053824 restraints weight = 69618.397| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 53884 Z= 0.178 Angle : 0.584 12.066 73158 Z= 0.282 Chirality : 0.041 0.204 8356 Planarity : 0.004 0.090 9480 Dihedral : 7.280 169.331 7650 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.83 % Favored : 96.11 % Rotamer: Outliers : 1.42 % Allowed : 17.11 % Favored : 81.47 % 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: 0.59 (0.10), residues: 6919 helix: 1.68 (0.09), residues: 3188 sheet: -0.30 (0.19), residues: 799 loop : -0.84 (0.11), residues: 2932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 357 HIS 0.013 0.001 HIS z1114 PHE 0.019 0.001 PHE o 86 TYR 0.021 0.001 TYR V 107 ARG 0.014 0.000 ARG N 383 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9196.32 seconds wall clock time: 163 minutes 55.81 seconds (9835.81 seconds total)