Starting phenix.real_space_refine on Mon Mar 18 08:22:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg9_31109/03_2024/7eg9_31109.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg9_31109/03_2024/7eg9_31109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg9_31109/03_2024/7eg9_31109.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg9_31109/03_2024/7eg9_31109.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg9_31109/03_2024/7eg9_31109.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg9_31109/03_2024/7eg9_31109.pdb" } resolution = 3.7 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= -0.002 sd= 0.037 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: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 142 5.49 5 Mg 1 5.21 5 S 469 5.16 5 C 52959 2.51 5 N 14735 2.21 5 O 16002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 400": "OE1" <-> "OE2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A GLU 481": "OE1" <-> "OE2" Residue "A GLU 653": "OE1" <-> "OE2" Residue "A GLU 682": "OE1" <-> "OE2" Residue "A ARG 706": "NH1" <-> "NH2" Residue "A GLU 721": "OE1" <-> "OE2" Residue "A PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 828": "OE1" <-> "OE2" Residue "A GLU 895": "OE1" <-> "OE2" Residue "A ARG 996": "NH1" <-> "NH2" Residue "A ARG 1008": "NH1" <-> "NH2" Residue "A GLU 1024": "OE1" <-> "OE2" Residue "A ARG 1030": "NH1" <-> "NH2" Residue "A GLU 1057": "OE1" <-> "OE2" Residue "A ARG 1181": "NH1" <-> "NH2" Residue "A GLU 1203": "OE1" <-> "OE2" Residue "B GLU 21": "OE1" <-> "OE2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B ARG 230": "NH1" <-> "NH2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 343": "NH1" <-> "NH2" Residue "B GLU 398": "OE1" <-> "OE2" Residue "B ARG 539": "NH1" <-> "NH2" Residue "B ARG 541": "NH1" <-> "NH2" Residue "B GLU 547": "OE1" <-> "OE2" Residue "B GLU 582": "OE1" <-> "OE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B ARG 597": "NH1" <-> "NH2" Residue "B ARG 598": "NH1" <-> "NH2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "B ARG 629": "NH1" <-> "NH2" Residue "B PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 688": "OE1" <-> "OE2" Residue "B ARG 725": "NH1" <-> "NH2" Residue "B GLU 770": "OE1" <-> "OE2" Residue "B ARG 817": "NH1" <-> "NH2" Residue "B GLU 831": "OE1" <-> "OE2" Residue "B ARG 966": "NH1" <-> "NH2" Residue "B TYR 975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 881": "NH1" <-> "NH2" Residue "D GLU 884": "OE1" <-> "OE2" Residue "D ARG 909": "NH1" <-> "NH2" Residue "D GLU 960": "OE1" <-> "OE2" Residue "D GLU 962": "OE1" <-> "OE2" Residue "D GLU 990": "OE1" <-> "OE2" Residue "D GLU 995": "OE1" <-> "OE2" Residue "E GLU 226": "OE1" <-> "OE2" Residue "E GLU 235": "OE1" <-> "OE2" Residue "E ARG 347": "NH1" <-> "NH2" Residue "E ARG 450": "NH1" <-> "NH2" Residue "E ARG 452": "NH1" <-> "NH2" Residue "E GLU 563": "OE1" <-> "OE2" Residue "E PHE 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 607": "NH1" <-> "NH2" Residue "E GLU 763": "OE1" <-> "OE2" Residue "F GLU 229": "OE1" <-> "OE2" Residue "F ARG 239": "NH1" <-> "NH2" Residue "F GLU 265": "OE1" <-> "OE2" Residue "F ARG 284": "NH1" <-> "NH2" Residue "F GLU 303": "OE1" <-> "OE2" Residue "F ARG 320": "NH1" <-> "NH2" Residue "F ARG 330": "NH1" <-> "NH2" Residue "F ARG 335": "NH1" <-> "NH2" Residue "F GLU 366": "OE1" <-> "OE2" Residue "F ARG 373": "NH1" <-> "NH2" Residue "F ARG 395": "NH1" <-> "NH2" Residue "G GLU 13": "OE1" <-> "OE2" Residue "G ARG 19": "NH1" <-> "NH2" Residue "G GLU 163": "OE1" <-> "OE2" Residue "H ARG 113": "NH1" <-> "NH2" Residue "H ARG 183": "NH1" <-> "NH2" Residue "H ARG 184": "NH1" <-> "NH2" Residue "I TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 119": "NH1" <-> "NH2" Residue "J GLU 124": "OE1" <-> "OE2" Residue "L GLU 74": "OE1" <-> "OE2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "P GLU 286": "OE1" <-> "OE2" Residue "R ARG 28": "NH1" <-> "NH2" Residue "R ARG 44": "NH1" <-> "NH2" Residue "R ARG 112": "NH1" <-> "NH2" Residue "R ARG 127": "NH1" <-> "NH2" Residue "R ARG 248": "NH1" <-> "NH2" Residue "R ARG 290": "NH1" <-> "NH2" Residue "U ARG 77": "NH1" <-> "NH2" Residue "U GLU 163": "OE1" <-> "OE2" Residue "U GLU 165": "OE1" <-> "OE2" Residue "U ARG 174": "NH1" <-> "NH2" Residue "U ARG 179": "NH1" <-> "NH2" Residue "U GLU 182": "OE1" <-> "OE2" Residue "U GLU 185": "OE1" <-> "OE2" Residue "U ARG 192": "NH1" <-> "NH2" Residue "U GLU 193": "OE1" <-> "OE2" Residue "V TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 173": "OE1" <-> "OE2" Residue "V GLU 230": "OE1" <-> "OE2" Residue "V GLU 234": "OE1" <-> "OE2" Residue "d GLU 847": "OE1" <-> "OE2" Residue "d GLU 848": "OE1" <-> "OE2" Residue "d ARG 851": "NH1" <-> "NH2" Residue "d GLU 858": "OE1" <-> "OE2" Residue "d ARG 865": "NH1" <-> "NH2" Residue "d GLU 870": "OE1" <-> "OE2" Residue "d ARG 881": "NH1" <-> "NH2" Residue "d ARG 909": "NH1" <-> "NH2" Residue "d GLU 954": "OE1" <-> "OE2" Residue "d ARG 1057": "NH1" <-> "NH2" Residue "e TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 250": "OE1" <-> "OE2" Residue "e GLU 257": "OE1" <-> "OE2" Residue "e GLU 335": "OE1" <-> "OE2" Residue "e ARG 365": "NH1" <-> "NH2" Residue "e ARG 450": "NH1" <-> "NH2" Residue "e ARG 452": "NH1" <-> "NH2" Residue "e ARG 607": "NH1" <-> "NH2" Residue "e ARG 634": "NH1" <-> "NH2" Residue "e GLU 706": "OE1" <-> "OE2" Residue "f GLU 17": "OE1" <-> "OE2" Residue "f ARG 63": "NH1" <-> "NH2" Residue "f PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 109": "OE1" <-> "OE2" Residue "f GLU 226": "OE1" <-> "OE2" Residue "f GLU 229": "OE1" <-> "OE2" Residue "f ARG 239": "NH1" <-> "NH2" Residue "f ARG 258": "NH1" <-> "NH2" Residue "f ARG 284": "NH1" <-> "NH2" Residue "f ARG 315": "NH1" <-> "NH2" Residue "f ARG 373": "NH1" <-> "NH2" Residue "f ARG 395": "NH1" <-> "NH2" Residue "i ARG 34": "NH1" <-> "NH2" Residue "i GLU 41": "OE1" <-> "OE2" Residue "i ARG 78": "NH1" <-> "NH2" Residue "i ARG 119": "NH1" <-> "NH2" Residue "j GLU 145": "OE1" <-> "OE2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "k GLU 167": "OE1" <-> "OE2" Residue "k GLU 174": "OE1" <-> "OE2" Residue "k ARG 192": "NH1" <-> "NH2" Residue "k ARG 193": "NH1" <-> "NH2" Residue "l ARG 106": "NH1" <-> "NH2" Residue "l GLU 121": "OE1" <-> "OE2" Residue "m ARG 30": "NH1" <-> "NH2" Residue "m ASP 45": "OD1" <-> "OD2" Residue "m ARG 80": "NH1" <-> "NH2" Residue "m GLU 109": "OE1" <-> "OE2" Residue "o PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 743": "NH1" <-> "NH2" Residue "o ARG 749": "NH1" <-> "NH2" Residue "p ARG 101": "NH1" <-> "NH2" Residue "p GLU 266": "OE1" <-> "OE2" Residue "p GLU 346": "OE1" <-> "OE2" Residue "p GLU 381": "OE1" <-> "OE2" Residue "p GLU 609": "OE1" <-> "OE2" Residue "p GLU 647": "OE1" <-> "OE2" Residue "p ARG 770": "NH1" <-> "NH2" Residue "p ARG 1078": "NH1" <-> "NH2" Residue "q ARG 10": "NH1" <-> "NH2" Residue "q PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 207": "OE1" <-> "OE2" Residue "r GLU 15": "OE1" <-> "OE2" Residue "r GLU 54": "OE1" <-> "OE2" Residue "r GLU 106": "OE1" <-> "OE2" Residue "w GLU 19": "OE1" <-> "OE2" Residue "x GLU 28": "OE1" <-> "OE2" Residue "y GLU 97": "OE1" <-> "OE2" Residue "y GLU 117": "OE1" <-> "OE2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 84318 Number of models: 1 Model: "" Number of chains: 49 Chain: "A" Number of atoms: 4927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4927 Classifications: {'peptide': 602} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 561} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 7796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 7796 Classifications: {'peptide': 963} Link IDs: {'PTRANS': 45, 'TRANS': 917} Chain breaks: 1 Chain: "D" Number of atoms: 1361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1361 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 4364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4364 Classifications: {'peptide': 546} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 524} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3081 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 379} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 73 Chain: "G" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1180 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain breaks: 2 Chain: "H" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1633 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 188} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 108} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 709 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 6, 'TRANS': 82} Chain breaks: 1 Chain: "L" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 622 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "O" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 771 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 95} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "P" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1412 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain: "Q" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 996 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1913 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 13, 'TRANS': 234} Chain breaks: 1 Chain: "S" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1101 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain breaks: 1 Chain: "T" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 789 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain breaks: 1 Chain: "U" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1476 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 4, 'TRANS': 174} Chain breaks: 1 Chain: "V" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1400 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 166} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1470 Classifications: {'DNA': 71} Link IDs: {'rna3p': 70} Chain: "Y" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1441 Classifications: {'DNA': 71} Link IDs: {'rna3p': 70} Chain: "c" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1011 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 118} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "d" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1307 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "e" Number of atoms: 4327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4327 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 516} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "f" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3081 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 378} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 57 Chain: "i" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 108} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "j" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 759 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain breaks: 1 Chain: "k" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 785 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "l" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 876 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "m" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 724 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "o" Number of atoms: 11308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1427, 11308 Classifications: {'peptide': 1427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 70, 'TRANS': 1356} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "p" Number of atoms: 9062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1134, 9062 Classifications: {'peptide': 1134} Link IDs: {'PTRANS': 53, 'TRANS': 1080} Chain breaks: 2 Chain: "q" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "r" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1005 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "s" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "t" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 635 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "v" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "w" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "x" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "y" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 937 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "z" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "u" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 29978 SG CYS R 34 147.514 219.934 161.064 1.00 0.00 S ATOM 34516 SG CYS U 132 167.670 193.285 158.813 1.00 0.00 S ATOM 34688 SG CYS U 154 170.225 195.679 157.666 1.00 0.00 S ATOM 34712 SG CYS U 157 169.109 195.893 161.143 1.00 0.00 S ATOM 53702 SG CYS o 71 150.748 198.819 149.526 1.00 46.90 S ATOM 53771 SG CYS o 81 148.499 201.616 147.294 1.00 40.48 S ATOM 54034 SG CYS o 114 147.936 169.563 110.378 1.00 63.39 S ATOM 73178 SG CYS p1119 156.967 202.458 130.546 1.00179.27 S ATOM 73200 SG CYS p1122 154.866 199.786 130.048 1.00181.25 S ATOM 73315 SG CYS p1137 157.493 200.135 133.166 1.00194.80 S ATOM 73336 SG CYS p1140 157.722 197.759 129.912 1.00200.53 S ATOM 74315 SG CYS q 90 119.739 249.654 182.763 1.00126.45 S ATOM 74350 SG CYS q 94 117.484 251.064 184.866 1.00113.16 S ATOM 74372 SG CYS q 97 116.472 250.394 181.398 1.00107.06 S ATOM 80260 SG CYS w 17 70.284 160.071 107.906 1.00165.50 S ATOM 80284 SG CYS w 20 73.196 159.328 109.881 1.00166.36 S ATOM 80445 SG CYS w 39 74.713 160.314 106.558 1.00170.94 S ATOM 80470 SG CYS w 42 72.413 157.454 107.008 1.00174.09 S ATOM 80822 SG CYS w 86 48.665 200.593 113.847 1.00138.72 S ATOM 80846 SG CYS w 89 46.037 200.278 116.396 1.00141.27 S ATOM 81050 SG CYS w 114 49.540 200.816 117.845 1.00129.58 S ATOM 81085 SG CYS w 119 48.510 197.680 116.128 1.00136.89 S ATOM 81195 SG CYS x 7 90.835 243.879 162.044 1.00 65.12 S ATOM 81219 SG CYS x 10 90.148 248.497 160.988 1.00 73.64 S ATOM 81483 SG CYS x 44 88.970 245.817 159.395 1.00 74.53 S ATOM 81489 SG CYS x 45 87.740 246.274 162.692 1.00 74.88 S ATOM 82626 SG CYS z 19 101.563 206.181 185.189 1.00111.16 S ATOM 82645 SG CYS z 22 100.082 206.648 188.299 1.00114.66 S ATOM 82762 SG CYS z 36 102.992 204.712 188.248 1.00121.32 S Time building chain proxies: 32.64, per 1000 atoms: 0.39 Number of scatterers: 84318 At special positions: 0 Unit cell: (217.3, 297.86, 239.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 10 29.99 S 469 16.00 P 142 15.00 Mg 1 11.99 O 16002 8.00 N 14735 7.00 C 52959 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 945 " - pdb=" SG CYS B 986 " distance=2.07 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: 27.90 Conformation dependent library (CDL) restraints added in 11.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 401 " pdb="ZN ZN R 401 " - pdb=" NE2 HIS R 18 " pdb="ZN ZN R 401 " - pdb=" SG CYS R 34 " pdb=" ZN U 501 " pdb="ZN ZN U 501 " - pdb=" SG CYS U 157 " pdb="ZN ZN U 501 " - pdb=" SG CYS U 132 " pdb="ZN ZN U 501 " - pdb=" SG CYS U 154 " pdb=" ZN o2001 " pdb="ZN ZN o2001 " - pdb=" SG CYS o 81 " pdb="ZN ZN o2001 " - pdb=" SG CYS o 71 " pdb=" ZN o2002 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 114 " pdb=" ZN p1201 " pdb="ZN ZN p1201 " - pdb=" SG CYS p1122 " pdb="ZN ZN p1201 " - pdb=" SG CYS p1119 " pdb="ZN ZN p1201 " - pdb=" SG CYS p1137 " pdb="ZN ZN p1201 " - pdb=" SG CYS p1140 " pdb=" ZN q 301 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 90 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 94 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 97 " pdb=" ZN w 201 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 39 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 20 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 17 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 42 " pdb=" ZN w 202 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 89 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 119 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 86 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 114 " pdb=" ZN x 101 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 45 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 44 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 7 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 10 " pdb=" ZN z 101 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 22 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 36 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 19 " Number of angles added : 24 20056 Ramachandran restraints generated. 10028 Oldfield, 0 Emsley, 10028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19340 Finding SS restraints... Secondary structure from input PDB file: 362 helices and 94 sheets defined 41.4% alpha, 14.1% beta 62 base pairs and 129 stacking pairs defined. Time for finding SS restraints: 21.30 Creating SS restraints... Processing helix chain 'A' and resid 346 through 354 Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 472 through 478 Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'A' and resid 569 through 574 removed outlier: 3.635A pdb=" N TYR A 573 " --> pdb=" O ASN A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 597 Processing helix chain 'A' and resid 608 through 614 Processing helix chain 'A' and resid 639 through 657 Processing helix chain 'A' and resid 667 through 672 removed outlier: 4.033A pdb=" N THR A 672 " --> pdb=" O GLN A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 817 Processing helix chain 'A' and resid 826 through 834 removed outlier: 3.978A pdb=" N ILE A 830 " --> pdb=" O ARG A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 848 removed outlier: 3.638A pdb=" N ILE A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 848 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 880 removed outlier: 3.854A pdb=" N VAL A 880 " --> pdb=" O ILE A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 901 Processing helix chain 'A' and resid 925 through 929 Processing helix chain 'A' and resid 930 through 944 Processing helix chain 'A' and resid 1000 through 1011 Processing helix chain 'A' and resid 1013 through 1020 removed outlier: 3.529A pdb=" N ILE A1017 " --> pdb=" O PRO A1013 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU A1020 " --> pdb=" O GLU A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1035 removed outlier: 4.141A pdb=" N ASP A1027 " --> pdb=" O TRP A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1077 Processing helix chain 'A' and resid 1187 through 1205 removed outlier: 3.610A pdb=" N ALA A1193 " --> pdb=" O ALA A1189 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 117 removed outlier: 3.737A pdb=" N PHE B 106 " --> pdb=" O ASN B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 185 through 189 removed outlier: 3.548A pdb=" N PHE B 188 " --> pdb=" O SER B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 273 through 281 Processing helix chain 'B' and resid 283 through 295 removed outlier: 3.719A pdb=" N VAL B 287 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU B 295 " --> pdb=" O TYR B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 330 No H-bonds generated for 'chain 'B' and resid 328 through 330' Processing helix chain 'B' and resid 338 through 356 Processing helix chain 'B' and resid 366 through 409 removed outlier: 4.080A pdb=" N LEU B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL B 388 " --> pdb=" O LYS B 384 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N ASN B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU B 390 " --> pdb=" O PHE B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 441 removed outlier: 3.558A pdb=" N LEU B 441 " --> pdb=" O PRO B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 464 Processing helix chain 'B' and resid 465 through 484 Processing helix chain 'B' and resid 492 through 495 removed outlier: 3.541A pdb=" N GLN B 495 " --> pdb=" O MET B 492 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 492 through 495' Processing helix chain 'B' and resid 499 through 512 Processing helix chain 'B' and resid 515 through 523 Processing helix chain 'B' and resid 595 through 600 removed outlier: 3.820A pdb=" N ASN B 599 " --> pdb=" O LYS B 595 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 600 " --> pdb=" O SER B 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 595 through 600' Processing helix chain 'B' and resid 645 through 656 removed outlier: 3.800A pdb=" N GLU B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 669 Processing helix chain 'B' and resid 670 through 672 No H-bonds generated for 'chain 'B' and resid 670 through 672' Processing helix chain 'B' and resid 674 through 686 Processing helix chain 'B' and resid 691 through 709 removed outlier: 3.545A pdb=" N ARG B 695 " --> pdb=" O PHE B 691 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE B 700 " --> pdb=" O MET B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 728 removed outlier: 3.721A pdb=" N CYS B 728 " --> pdb=" O THR B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 758 Proline residue: B 754 - end of helix Processing helix chain 'B' and resid 768 through 781 removed outlier: 3.534A pdb=" N THR B 773 " --> pdb=" O LYS B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 805 removed outlier: 3.507A pdb=" N SER B 805 " --> pdb=" O ALA B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 822 Processing helix chain 'B' and resid 823 through 843 removed outlier: 4.204A pdb=" N LEU B 828 " --> pdb=" O PRO B 824 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 829 " --> pdb=" O ASP B 825 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 842 " --> pdb=" O ASN B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 864 Processing helix chain 'B' and resid 871 through 878 Processing helix chain 'B' and resid 883 through 901 Processing helix chain 'B' and resid 903 through 916 removed outlier: 3.521A pdb=" N LEU B 907 " --> pdb=" O SER B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 933 Processing helix chain 'B' and resid 946 through 959 removed outlier: 3.562A pdb=" N VAL B 950 " --> pdb=" O ASN B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 980 Processing helix chain 'D' and resid 874 through 886 removed outlier: 3.682A pdb=" N ARG D 880 " --> pdb=" O ALA D 876 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE D 885 " --> pdb=" O ARG D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 898 through 922 removed outlier: 3.635A pdb=" N SER D 903 " --> pdb=" O VAL D 899 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN D 912 " --> pdb=" O GLN D 908 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS D 916 " --> pdb=" O ASN D 912 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR D 920 " --> pdb=" O LYS D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 969 removed outlier: 3.745A pdb=" N MET D 967 " --> pdb=" O ARG D 963 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG D 968 " --> pdb=" O GLU D 964 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 1011 removed outlier: 3.889A pdb=" N GLN D 993 " --> pdb=" O LYS D 989 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ALA D 997 " --> pdb=" O GLN D 993 " (cutoff:3.500A) Processing helix chain 'D' and resid 1059 through 1066 removed outlier: 3.621A pdb=" N LEU D1063 " --> pdb=" O ASN D1059 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS D1066 " --> pdb=" O ASP D1062 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1083 Processing helix chain 'E' and resid 210 through 212 No H-bonds generated for 'chain 'E' and resid 210 through 212' Processing helix chain 'E' and resid 213 through 227 removed outlier: 3.839A pdb=" N SER E 219 " --> pdb=" O GLU E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 237 removed outlier: 3.811A pdb=" N ALA E 234 " --> pdb=" O ASP E 230 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU E 235 " --> pdb=" O CYS E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 254 removed outlier: 3.695A pdb=" N LEU E 243 " --> pdb=" O LEU E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 268 removed outlier: 3.749A pdb=" N SER E 262 " --> pdb=" O ASN E 258 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE E 263 " --> pdb=" O GLU E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 274 No H-bonds generated for 'chain 'E' and resid 272 through 274' Processing helix chain 'E' and resid 275 through 285 removed outlier: 3.655A pdb=" N ARG E 280 " --> pdb=" O GLN E 276 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL E 281 " --> pdb=" O ASP E 277 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU E 282 " --> pdb=" O ASP E 278 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER E 284 " --> pdb=" O ARG E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 292 removed outlier: 3.801A pdb=" N MET E 291 " --> pdb=" O LYS E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 303 removed outlier: 3.710A pdb=" N THR E 302 " --> pdb=" O LEU E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 319 removed outlier: 4.310A pdb=" N LEU E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 337 Processing helix chain 'E' and resid 348 through 353 Processing helix chain 'E' and resid 433 through 449 removed outlier: 3.536A pdb=" N LYS E 440 " --> pdb=" O ASP E 436 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE E 441 " --> pdb=" O LYS E 437 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET E 442 " --> pdb=" O LEU E 438 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS E 445 " --> pdb=" O ILE E 441 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU E 446 " --> pdb=" O MET E 442 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS E 449 " --> pdb=" O LYS E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 516 removed outlier: 3.698A pdb=" N LEU E 515 " --> pdb=" O SER E 511 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE E 516 " --> pdb=" O ASP E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 764 through 768 Processing helix chain 'F' and resid 15 through 25 removed outlier: 3.749A pdb=" N MET F 19 " --> pdb=" O PRO F 15 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL F 21 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 60 removed outlier: 3.554A pdb=" N LEU F 39 " --> pdb=" O THR F 35 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR F 40 " --> pdb=" O CYS F 36 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU F 42 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER F 44 " --> pdb=" O THR F 40 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS F 56 " --> pdb=" O GLN F 52 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE F 57 " --> pdb=" O ASP F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 78 removed outlier: 4.198A pdb=" N ILE F 71 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 120 removed outlier: 3.531A pdb=" N THR F 120 " --> pdb=" O ASP F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 231 Processing helix chain 'F' and resid 235 through 249 Processing helix chain 'F' and resid 250 through 253 removed outlier: 4.355A pdb=" N TYR F 253 " --> pdb=" O PRO F 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 250 through 253' Processing helix chain 'F' and resid 255 through 270 Processing helix chain 'F' and resid 275 through 291 Processing helix chain 'F' and resid 300 through 309 Proline residue: F 306 - end of helix Processing helix chain 'F' and resid 323 through 344 Processing helix chain 'F' and resid 351 through 364 Processing helix chain 'F' and resid 371 through 382 removed outlier: 4.135A pdb=" N ILE F 377 " --> pdb=" O ARG F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 392 removed outlier: 4.250A pdb=" N ILE F 388 " --> pdb=" O GLY F 384 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS F 389 " --> pdb=" O HIS F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 409 Processing helix chain 'F' and resid 415 through 438 Proline residue: F 433 - end of helix Processing helix chain 'F' and resid 446 through 452 removed outlier: 3.596A pdb=" N PHE F 452 " --> pdb=" O ARG F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 473 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 37 through 43 removed outlier: 3.681A pdb=" N ASP G 41 " --> pdb=" O VAL G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 175 Processing helix chain 'H' and resid 27 through 45 removed outlier: 4.760A pdb=" N ARG H 33 " --> pdb=" O TYR H 29 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR H 36 " --> pdb=" O ALA H 32 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL H 39 " --> pdb=" O ARG H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 83 removed outlier: 3.516A pdb=" N LYS H 77 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR H 83 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 103 through 105 No H-bonds generated for 'chain 'H' and resid 103 through 105' Processing helix chain 'H' and resid 106 through 112 removed outlier: 3.873A pdb=" N LYS H 112 " --> pdb=" O PRO H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 160 removed outlier: 4.363A pdb=" N TYR H 159 " --> pdb=" O ASP H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 197 Processing helix chain 'H' and resid 221 through 228 removed outlier: 3.968A pdb=" N THR H 225 " --> pdb=" O ILE H 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 26 removed outlier: 3.575A pdb=" N MET I 18 " --> pdb=" O LYS I 14 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA I 20 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN I 21 " --> pdb=" O GLN I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 62 removed outlier: 4.412A pdb=" N ILE I 36 " --> pdb=" O GLU I 32 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASN I 37 " --> pdb=" O PRO I 33 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN I 38 " --> pdb=" O ARG I 34 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP I 52 " --> pdb=" O THR I 48 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP I 53 " --> pdb=" O THR I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 77 removed outlier: 3.550A pdb=" N VAL I 71 " --> pdb=" O ASP I 67 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN I 76 " --> pdb=" O ARG I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 100 removed outlier: 3.674A pdb=" N ASP I 94 " --> pdb=" O ASP I 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 121 Processing helix chain 'J' and resid 131 through 141 removed outlier: 3.690A pdb=" N TYR J 137 " --> pdb=" O ALA J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 170 removed outlier: 3.624A pdb=" N ILE J 152 " --> pdb=" O ASP J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 176 removed outlier: 3.727A pdb=" N MET J 176 " --> pdb=" O GLN J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 204 Proline residue: J 202 - end of helix Processing helix chain 'L' and resid 61 through 71 removed outlier: 3.952A pdb=" N VAL L 70 " --> pdb=" O LEU L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 106 removed outlier: 3.672A pdb=" N MET L 83 " --> pdb=" O ASP L 79 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA L 98 " --> pdb=" O SER L 94 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN L 101 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU L 102 " --> pdb=" O ALA L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 123 removed outlier: 3.948A pdb=" N VAL L 116 " --> pdb=" O GLU L 112 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS L 119 " --> pdb=" O ASP L 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 8 removed outlier: 4.241A pdb=" N TYR O 6 " --> pdb=" O TYR O 3 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG O 7 " --> pdb=" O GLN O 4 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN O 8 " --> pdb=" O LEU O 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 3 through 8' Processing helix chain 'O' and resid 9 through 26 Processing helix chain 'O' and resid 31 through 50 Processing helix chain 'P' and resid 179 through 187 removed outlier: 3.517A pdb=" N ILE P 183 " --> pdb=" O ASP P 179 " (cutoff:3.500A) Processing helix chain 'P' and resid 226 through 245 removed outlier: 3.628A pdb=" N LEU P 244 " --> pdb=" O VAL P 240 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY P 245 " --> pdb=" O VAL P 241 " (cutoff:3.500A) Processing helix chain 'P' and resid 269 through 277 removed outlier: 3.577A pdb=" N LEU P 273 " --> pdb=" O ARG P 269 " (cutoff:3.500A) Processing helix chain 'P' and resid 317 through 335 removed outlier: 4.035A pdb=" N ILE P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR P 322 " --> pdb=" O ARG P 318 " (cutoff:3.500A) Proline residue: P 330 - end of helix Processing helix chain 'Q' and resid 10 through 33 removed outlier: 4.802A pdb=" N ASP Q 27 " --> pdb=" O ASN Q 23 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ILE Q 28 " --> pdb=" O ASP Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 35 through 54 removed outlier: 3.731A pdb=" N LEU Q 39 " --> pdb=" O ASP Q 35 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU Q 50 " --> pdb=" O TRP Q 46 " (cutoff:3.500A) Processing helix chain 'Q' and resid 58 through 63 Processing helix chain 'Q' and resid 323 through 328 Processing helix chain 'R' and resid 111 through 129 removed outlier: 4.159A pdb=" N ARG R 127 " --> pdb=" O THR R 123 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE R 128 " --> pdb=" O MET R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 149 removed outlier: 3.602A pdb=" N ASP R 136 " --> pdb=" O ARG R 132 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG R 137 " --> pdb=" O ASN R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 171 Processing helix chain 'R' and resid 176 through 183 removed outlier: 3.513A pdb=" N VAL R 183 " --> pdb=" O GLU R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 203 Processing helix chain 'R' and resid 211 through 222 removed outlier: 3.849A pdb=" N SER R 216 " --> pdb=" O GLY R 212 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ARG R 217 " --> pdb=" O ASP R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 242 Processing helix chain 'R' and resid 249 through 264 Processing helix chain 'R' and resid 270 through 278 Processing helix chain 'R' and resid 281 through 293 removed outlier: 3.998A pdb=" N ILE R 285 " --> pdb=" O ALA R 281 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER R 288 " --> pdb=" O THR R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 300 removed outlier: 3.886A pdb=" N PHE R 300 " --> pdb=" O ALA R 296 " (cutoff:3.500A) Processing helix chain 'R' and resid 309 through 313 Processing helix chain 'S' and resid 6 through 10 Processing helix chain 'S' and resid 34 through 36 No H-bonds generated for 'chain 'S' and resid 34 through 36' Processing helix chain 'S' and resid 38 through 42 Processing helix chain 'S' and resid 156 through 173 Processing helix chain 'T' and resid 9 through 14 Processing helix chain 'T' and resid 25 through 32 Processing helix chain 'U' and resid 12 through 25 removed outlier: 3.604A pdb=" N ARG U 23 " --> pdb=" O LYS U 19 " (cutoff:3.500A) Processing helix chain 'U' and resid 27 through 37 removed outlier: 3.773A pdb=" N ALA U 33 " --> pdb=" O GLU U 29 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE U 36 " --> pdb=" O LEU U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 53 Processing helix chain 'U' and resid 55 through 69 Processing helix chain 'U' and resid 102 through 119 removed outlier: 3.840A pdb=" N LEU U 107 " --> pdb=" O VAL U 103 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP U 108 " --> pdb=" O LYS U 104 " (cutoff:3.500A) Processing helix chain 'U' and resid 138 through 145 removed outlier: 3.565A pdb=" N LEU U 144 " --> pdb=" O GLU U 140 " (cutoff:3.500A) Processing helix chain 'U' and resid 170 through 179 Processing helix chain 'U' and resid 185 through 202 removed outlier: 4.350A pdb=" N LEU U 190 " --> pdb=" O PRO U 186 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU U 191 " --> pdb=" O ILE U 187 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 92 removed outlier: 4.340A pdb=" N ASN V 83 " --> pdb=" O ALA V 79 " (cutoff:3.500A) Processing helix chain 'V' and resid 98 through 106 Processing helix chain 'V' and resid 112 through 122 Processing helix chain 'V' and resid 122 through 127 Processing helix chain 'V' and resid 151 through 156 Processing helix chain 'V' and resid 176 through 187 removed outlier: 3.996A pdb=" N LYS V 180 " --> pdb=" O PRO V 176 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS V 183 " --> pdb=" O GLN V 179 " (cutoff:3.500A) Processing helix chain 'V' and resid 214 through 222 Processing helix chain 'V' and resid 230 through 239 removed outlier: 3.587A pdb=" N GLU V 235 " --> pdb=" O GLU V 231 " (cutoff:3.500A) Processing helix chain 'c' and resid 2 through 16 Processing helix chain 'c' and resid 16 through 21 removed outlier: 3.552A pdb=" N ALA c 20 " --> pdb=" O GLN c 16 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU c 21 " --> pdb=" O ILE c 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 16 through 21' Processing helix chain 'c' and resid 28 through 56 removed outlier: 3.562A pdb=" N HIS c 32 " --> pdb=" O LEU c 28 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU c 33 " --> pdb=" O SER c 29 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU c 34 " --> pdb=" O ALA c 30 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP c 36 " --> pdb=" O HIS c 32 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN c 43 " --> pdb=" O GLN c 39 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER c 53 " --> pdb=" O CYS c 49 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR c 56 " --> pdb=" O TYR c 52 " (cutoff:3.500A) Processing helix chain 'c' and resid 62 through 74 removed outlier: 3.934A pdb=" N GLN c 71 " --> pdb=" O GLY c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 76 through 87 removed outlier: 3.605A pdb=" N GLU c 81 " --> pdb=" O LEU c 77 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP c 82 " --> pdb=" O HIS c 78 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN c 86 " --> pdb=" O ASP c 82 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE c 87 " --> pdb=" O TYR c 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 844 through 849 removed outlier: 3.526A pdb=" N GLU d 848 " --> pdb=" O ASN d 844 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER d 849 " --> pdb=" O LEU d 845 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 844 through 849' Processing helix chain 'd' and resid 849 through 855 removed outlier: 4.155A pdb=" N LEU d 853 " --> pdb=" O SER d 849 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR d 855 " --> pdb=" O ARG d 851 " (cutoff:3.500A) Processing helix chain 'd' and resid 856 through 858 No H-bonds generated for 'chain 'd' and resid 856 through 858' Processing helix chain 'd' and resid 874 through 885 removed outlier: 3.676A pdb=" N ARG d 880 " --> pdb=" O ALA d 876 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU d 883 " --> pdb=" O GLN d 879 " (cutoff:3.500A) Processing helix chain 'd' and resid 898 through 922 removed outlier: 3.547A pdb=" N HIS d 904 " --> pdb=" O SER d 900 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN d 907 " --> pdb=" O SER d 903 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU d 913 " --> pdb=" O ARG d 909 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU d 919 " --> pdb=" O GLU d 915 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR d 920 " --> pdb=" O LYS d 916 " (cutoff:3.500A) Processing helix chain 'd' and resid 923 through 926 Processing helix chain 'd' and resid 945 through 954 Processing helix chain 'd' and resid 954 through 966 removed outlier: 3.502A pdb=" N LYS d 958 " --> pdb=" O GLU d 954 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU d 962 " --> pdb=" O LYS d 958 " (cutoff:3.500A) Processing helix chain 'd' and resid 1059 through 1069 removed outlier: 3.755A pdb=" N LEU d1063 " --> pdb=" O ASN d1059 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS d1066 " --> pdb=" O ASP d1062 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN d1069 " --> pdb=" O PHE d1065 " (cutoff:3.500A) Processing helix chain 'd' and resid 1076 through 1083 removed outlier: 3.688A pdb=" N TYR d1080 " --> pdb=" O SER d1076 " (cutoff:3.500A) Processing helix chain 'e' and resid 210 through 212 No H-bonds generated for 'chain 'e' and resid 210 through 212' Processing helix chain 'e' and resid 213 through 218 removed outlier: 3.642A pdb=" N TYR e 217 " --> pdb=" O MET e 213 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR e 218 " --> pdb=" O TYR e 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 213 through 218' Processing helix chain 'e' and resid 220 through 227 Processing helix chain 'e' and resid 236 through 240 removed outlier: 3.711A pdb=" N LEU e 239 " --> pdb=" O LEU e 236 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE e 240 " --> pdb=" O SER e 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 236 through 240' Processing helix chain 'e' and resid 243 through 248 Processing helix chain 'e' and resid 257 through 268 removed outlier: 4.228A pdb=" N SER e 262 " --> pdb=" O ASN e 258 " (cutoff:3.500A) Processing helix chain 'e' and resid 281 through 285 Processing helix chain 'e' and resid 287 through 292 removed outlier: 3.906A pdb=" N MET e 291 " --> pdb=" O LYS e 287 " (cutoff:3.500A) Processing helix chain 'e' and resid 310 through 322 removed outlier: 3.604A pdb=" N GLN e 315 " --> pdb=" O ARG e 311 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU e 316 " --> pdb=" O ASP e 312 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU e 317 " --> pdb=" O SER e 313 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN e 322 " --> pdb=" O LYS e 318 " (cutoff:3.500A) Processing helix chain 'e' and resid 329 through 334 removed outlier: 3.926A pdb=" N VAL e 333 " --> pdb=" O ILE e 329 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN e 334 " --> pdb=" O TRP e 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 329 through 334' Processing helix chain 'e' and resid 433 through 438 Processing helix chain 'e' and resid 438 through 446 removed outlier: 3.503A pdb=" N GLU e 446 " --> pdb=" O MET e 442 " (cutoff:3.500A) Processing helix chain 'e' and resid 511 through 515 Processing helix chain 'e' and resid 522 through 527 removed outlier: 3.504A pdb=" N ARG e 526 " --> pdb=" O ASP e 522 " (cutoff:3.500A) Processing helix chain 'f' and resid 16 through 27 removed outlier: 3.719A pdb=" N LYS f 20 " --> pdb=" O SER f 16 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL f 21 " --> pdb=" O GLU f 17 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL f 22 " --> pdb=" O SER f 18 " (cutoff:3.500A) Processing helix chain 'f' and resid 32 through 61 removed outlier: 3.535A pdb=" N ASP f 41 " --> pdb=" O GLN f 37 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU f 42 " --> pdb=" O LEU f 38 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR f 45 " --> pdb=" O ASP f 41 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS f 48 " --> pdb=" O SER f 44 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP f 53 " --> pdb=" O GLU f 49 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS f 56 " --> pdb=" O GLN f 52 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE f 57 " --> pdb=" O ASP f 53 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 76 removed outlier: 4.017A pdb=" N ILE f 71 " --> pdb=" O THR f 67 " (cutoff:3.500A) Processing helix chain 'f' and resid 114 through 119 Processing helix chain 'f' and resid 217 through 231 removed outlier: 3.540A pdb=" N CYS f 231 " --> pdb=" O ILE f 227 " (cutoff:3.500A) Processing helix chain 'f' and resid 235 through 248 removed outlier: 3.627A pdb=" N ARG f 239 " --> pdb=" O CYS f 235 " (cutoff:3.500A) Processing helix chain 'f' and resid 255 through 269 Processing helix chain 'f' and resid 275 through 291 removed outlier: 3.527A pdb=" N LEU f 279 " --> pdb=" O ASN f 275 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP f 291 " --> pdb=" O LYS f 287 " (cutoff:3.500A) Processing helix chain 'f' and resid 300 through 314 removed outlier: 3.632A pdb=" N LEU f 304 " --> pdb=" O TYR f 300 " (cutoff:3.500A) Proline residue: f 306 - end of helix Processing helix chain 'f' and resid 325 through 341 removed outlier: 4.120A pdb=" N LEU f 329 " --> pdb=" O ASN f 325 " (cutoff:3.500A) Processing helix chain 'f' and resid 350 through 364 Processing helix chain 'f' and resid 369 through 384 removed outlier: 4.059A pdb=" N GLY f 384 " --> pdb=" O LEU f 380 " (cutoff:3.500A) Processing helix chain 'f' and resid 384 through 391 removed outlier: 3.546A pdb=" N ILE f 388 " --> pdb=" O GLY f 384 " (cutoff:3.500A) Processing helix chain 'f' and resid 392 through 396 removed outlier: 3.690A pdb=" N LEU f 396 " --> pdb=" O LEU f 393 " (cutoff:3.500A) Processing helix chain 'f' and resid 397 through 404 removed outlier: 3.694A pdb=" N GLU f 401 " --> pdb=" O GLN f 397 " (cutoff:3.500A) Processing helix chain 'f' and resid 417 through 438 Proline residue: f 433 - end of helix Processing helix chain 'f' and resid 445 through 450 Processing helix chain 'f' and resid 454 through 473 Processing helix chain 'i' and resid 18 through 26 Processing helix chain 'i' and resid 33 through 61 removed outlier: 4.307A pdb=" N ASN i 37 " --> pdb=" O PRO i 33 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU i 41 " --> pdb=" O ASN i 37 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA i 43 " --> pdb=" O MET i 39 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP i 52 " --> pdb=" O THR i 48 " (cutoff:3.500A) Processing helix chain 'i' and resid 67 through 77 removed outlier: 3.510A pdb=" N VAL i 71 " --> pdb=" O ASP i 67 " (cutoff:3.500A) Processing helix chain 'i' and resid 88 through 100 removed outlier: 3.967A pdb=" N ASP i 94 " --> pdb=" O ASP i 90 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN i 98 " --> pdb=" O ASP i 94 " (cutoff:3.500A) Processing helix chain 'j' and resid 115 through 121 removed outlier: 3.723A pdb=" N LEU j 120 " --> pdb=" O LEU j 116 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET j 121 " --> pdb=" O VAL j 117 " (cutoff:3.500A) Processing helix chain 'j' and resid 131 through 139 Processing helix chain 'j' and resid 151 through 175 removed outlier: 3.761A pdb=" N LEU j 157 " --> pdb=" O ARG j 153 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE j 162 " --> pdb=" O ALA j 158 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE j 163 " --> pdb=" O ALA j 159 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN j 168 " --> pdb=" O SER j 164 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU j 171 " --> pdb=" O ALA j 167 " (cutoff:3.500A) Processing helix chain 'j' and resid 196 through 205 Proline residue: j 202 - end of helix removed outlier: 3.571A pdb=" N SER j 205 " --> pdb=" O THR j 201 " (cutoff:3.500A) Processing helix chain 'k' and resid 116 through 127 removed outlier: 3.503A pdb=" N ARG k 125 " --> pdb=" O TYR k 121 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER k 127 " --> pdb=" O MET k 123 " (cutoff:3.500A) Processing helix chain 'k' and resid 130 through 143 removed outlier: 4.102A pdb=" N ARG k 136 " --> pdb=" O ALA k 132 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE k 141 " --> pdb=" O LEU k 137 " (cutoff:3.500A) Processing helix chain 'k' and resid 147 through 176 removed outlier: 3.608A pdb=" N ALA k 153 " --> pdb=" O ASN k 149 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER k 158 " --> pdb=" O MET k 154 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS k 159 " --> pdb=" O SER k 155 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU k 167 " --> pdb=" O GLY k 163 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU k 168 " --> pdb=" O GLU k 164 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP k 171 " --> pdb=" O GLU k 167 " (cutoff:3.500A) Processing helix chain 'k' and resid 184 through 197 removed outlier: 3.610A pdb=" N LYS k 197 " --> pdb=" O ARG k 193 " (cutoff:3.500A) Processing helix chain 'l' and resid 61 through 69 Processing helix chain 'l' and resid 77 through 106 removed outlier: 3.599A pdb=" N MET l 83 " --> pdb=" O ASP l 79 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA l 98 " --> pdb=" O SER l 94 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLN l 101 " --> pdb=" O THR l 97 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU l 102 " --> pdb=" O ALA l 98 " (cutoff:3.500A) Processing helix chain 'l' and resid 113 through 123 removed outlier: 3.894A pdb=" N LEU l 118 " --> pdb=" O LYS l 114 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS l 119 " --> pdb=" O ASP l 115 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU l 120 " --> pdb=" O VAL l 116 " (cutoff:3.500A) Processing helix chain 'l' and resid 145 through 161 removed outlier: 3.794A pdb=" N ALA l 153 " --> pdb=" O LYS l 149 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU l 154 " --> pdb=" O GLN l 150 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE l 155 " --> pdb=" O ARG l 151 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG l 156 " --> pdb=" O MET l 152 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS l 157 " --> pdb=" O ALA l 153 " (cutoff:3.500A) Processing helix chain 'm' and resid 34 through 43 removed outlier: 3.733A pdb=" N CYS m 38 " --> pdb=" O LYS m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 67 removed outlier: 3.603A pdb=" N ILE m 56 " --> pdb=" O GLU m 52 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP m 59 " --> pdb=" O ASP m 55 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) Processing helix chain 'm' and resid 93 through 99 removed outlier: 3.878A pdb=" N PHE m 97 " --> pdb=" O ASP m 93 " (cutoff:3.500A) Processing helix chain 'm' and resid 100 through 106 Processing helix chain 'o' and resid 27 through 35 removed outlier: 3.711A pdb=" N SER o 35 " --> pdb=" O LEU o 31 " (cutoff:3.500A) Processing helix chain 'o' and resid 99 through 110 Processing helix chain 'o' and resid 123 through 132 Processing helix chain 'o' and resid 136 through 148 removed outlier: 3.528A pdb=" N ARG o 140 " --> pdb=" O GLN o 136 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP o 146 " --> pdb=" O THR o 142 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU o 147 " --> pdb=" O HIS o 143 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS o 148 " --> pdb=" O VAL o 144 " (cutoff:3.500A) Processing helix chain 'o' and resid 217 through 226 Processing helix chain 'o' and resid 231 through 237 Processing helix chain 'o' and resid 244 through 247 Processing helix chain 'o' and resid 276 through 296 removed outlier: 3.964A pdb=" N ASP o 282 " --> pdb=" O HIS o 278 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG o 292 " --> pdb=" O ASN o 288 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN o 293 " --> pdb=" O GLN o 289 " (cutoff:3.500A) Processing helix chain 'o' and resid 303 through 316 removed outlier: 4.051A pdb=" N LEU o 309 " --> pdb=" O GLU o 305 " (cutoff:3.500A) Processing helix chain 'o' and resid 338 through 343 Processing helix chain 'o' and resid 398 through 408 Processing helix chain 'o' and resid 434 through 438 Processing helix chain 'o' and resid 488 through 493 removed outlier: 3.887A pdb=" N TYR o 492 " --> pdb=" O VAL o 488 " (cutoff:3.500A) Processing helix chain 'o' and resid 508 through 517 removed outlier: 3.588A pdb=" N ARG o 512 " --> pdb=" O SER o 508 " (cutoff:3.500A) Processing helix chain 'o' and resid 521 through 525 removed outlier: 3.575A pdb=" N MET o 524 " --> pdb=" O VAL o 521 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE o 525 " --> pdb=" O PRO o 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 521 through 525' Processing helix chain 'o' and resid 539 through 549 removed outlier: 3.717A pdb=" N THR o 543 " --> pdb=" O GLN o 539 " (cutoff:3.500A) Processing helix chain 'o' and resid 556 through 565 Processing helix chain 'o' and resid 588 through 593 Processing helix chain 'o' and resid 641 through 646 Processing helix chain 'o' and resid 651 through 660 Processing helix chain 'o' and resid 662 through 684 removed outlier: 3.921A pdb=" N LEU o 667 " --> pdb=" O ASP o 663 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE o 682 " --> pdb=" O ASN o 678 " (cutoff:3.500A) Processing helix chain 'o' and resid 689 through 693 removed outlier: 4.072A pdb=" N ILE o 693 " --> pdb=" O GLY o 690 " (cutoff:3.500A) Processing helix chain 'o' and resid 695 through 723 Processing helix chain 'o' and resid 732 through 758 removed outlier: 3.562A pdb=" N PHE o 737 " --> pdb=" O LEU o 733 " (cutoff:3.500A) Processing helix chain 'o' and resid 766 through 771 Processing helix chain 'o' and resid 777 through 786 removed outlier: 3.724A pdb=" N ILE o 781 " --> pdb=" O SER o 777 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER o 782 " --> pdb=" O LYS o 778 " (cutoff:3.500A) Processing helix chain 'o' and resid 832 through 869 removed outlier: 4.688A pdb=" N PHE o 838 " --> pdb=" O THR o 834 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY o 846 " --> pdb=" O GLY o 842 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA o 855 " --> pdb=" O ALA o 851 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR o 859 " --> pdb=" O ALA o 855 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN o 861 " --> pdb=" O THR o 857 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ARG o 862 " --> pdb=" O GLY o 858 " (cutoff:3.500A) Processing helix chain 'o' and resid 890 through 894 Processing helix chain 'o' and resid 912 through 920 removed outlier: 3.762A pdb=" N GLU o 917 " --> pdb=" O ASN o 913 " (cutoff:3.500A) Processing helix chain 'o' and resid 928 through 934 Processing helix chain 'o' and resid 935 through 946 Processing helix chain 'o' and resid 946 through 970 Processing helix chain 'o' and resid 982 through 994 removed outlier: 3.859A pdb=" N ALA o 990 " --> pdb=" O MET o 986 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS o 992 " --> pdb=" O TRP o 988 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE o 994 " --> pdb=" O ALA o 990 " (cutoff:3.500A) Processing helix chain 'o' and resid 1005 through 1020 removed outlier: 3.590A pdb=" N VAL o1009 " --> pdb=" O HIS o1005 " (cutoff:3.500A) Processing helix chain 'o' and resid 1027 through 1038 removed outlier: 3.643A pdb=" N ALA o1033 " --> pdb=" O LEU o1029 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR o1038 " --> pdb=" O GLN o1034 " (cutoff:3.500A) Processing helix chain 'o' and resid 1039 through 1049 Processing helix chain 'o' and resid 1050 through 1056 Processing helix chain 'o' and resid 1061 through 1080 removed outlier: 3.616A pdb=" N ILE o1080 " --> pdb=" O PHE o1076 " (cutoff:3.500A) Processing helix chain 'o' and resid 1086 through 1097 Processing helix chain 'o' and resid 1097 through 1102 removed outlier: 3.648A pdb=" N GLN o1101 " --> pdb=" O GLU o1097 " (cutoff:3.500A) Processing helix chain 'o' and resid 1120 through 1128 removed outlier: 3.631A pdb=" N LEU o1124 " --> pdb=" O GLY o1120 " (cutoff:3.500A) Processing helix chain 'o' and resid 1145 through 1149 Processing helix chain 'o' and resid 1150 through 1162 removed outlier: 3.733A pdb=" N ALA o1154 " --> pdb=" O ASP o1150 " (cutoff:3.500A) Processing helix chain 'o' and resid 1165 through 1168 Processing helix chain 'o' and resid 1191 through 1199 removed outlier: 4.264A pdb=" N MET o1199 " --> pdb=" O VAL o1195 " (cutoff:3.500A) Processing helix chain 'o' and resid 1217 through 1223 Processing helix chain 'o' and resid 1227 through 1235 Processing helix chain 'o' and resid 1263 through 1266 Processing helix chain 'o' and resid 1280 through 1293 Processing helix chain 'o' and resid 1314 through 1318 removed outlier: 3.532A pdb=" N LYS o1317 " --> pdb=" O THR o1314 " (cutoff:3.500A) Processing helix chain 'o' and resid 1342 through 1348 removed outlier: 3.656A pdb=" N VAL o1346 " --> pdb=" O SER o1342 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER o1348 " --> pdb=" O MET o1344 " (cutoff:3.500A) Processing helix chain 'o' and resid 1361 through 1369 Processing helix chain 'o' and resid 1371 through 1387 Processing helix chain 'o' and resid 1394 through 1406 removed outlier: 4.066A pdb=" N LEU o1398 " --> pdb=" O ASN o1394 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR o1406 " --> pdb=" O CYS o1402 " (cutoff:3.500A) Processing helix chain 'o' and resid 1415 through 1420 removed outlier: 3.735A pdb=" N VAL o1419 " --> pdb=" O THR o1415 " (cutoff:3.500A) Processing helix chain 'o' and resid 1425 through 1430 removed outlier: 3.738A pdb=" N LYS o1429 " --> pdb=" O GLY o1425 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS o1430 " --> pdb=" O PRO o1426 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 1425 through 1430' Processing helix chain 'o' and resid 1434 through 1446 Processing helix chain 'p' and resid 21 through 37 removed outlier: 4.342A pdb=" N TRP p 27 " --> pdb=" O GLN p 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE p 28 " --> pdb=" O GLU p 24 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL p 29 " --> pdb=" O ALA p 25 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER p 31 " --> pdb=" O TRP p 27 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER p 32 " --> pdb=" O ILE p 28 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU p 36 " --> pdb=" O SER p 32 " (cutoff:3.500A) Processing helix chain 'p' and resid 40 through 53 removed outlier: 4.079A pdb=" N SER p 46 " --> pdb=" O GLN p 42 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE p 47 " --> pdb=" O GLN p 43 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP p 48 " --> pdb=" O LEU p 44 " (cutoff:3.500A) Processing helix chain 'p' and resid 55 through 61 removed outlier: 3.697A pdb=" N VAL p 59 " --> pdb=" O VAL p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 109 through 116 removed outlier: 3.567A pdb=" N ARG p 114 " --> pdb=" O PRO p 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 167 through 172 Processing helix chain 'p' and resid 248 through 253 Processing helix chain 'p' and resid 269 through 275 Processing helix chain 'p' and resid 280 through 285 removed outlier: 3.817A pdb=" N LEU p 285 " --> pdb=" O ASP p 281 " (cutoff:3.500A) Processing helix chain 'p' and resid 294 through 302 removed outlier: 3.527A pdb=" N MET p 298 " --> pdb=" O ASP p 294 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET p 300 " --> pdb=" O GLU p 296 " (cutoff:3.500A) Processing helix chain 'p' and resid 303 through 309 removed outlier: 4.352A pdb=" N ASP p 306 " --> pdb=" O PRO p 303 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU p 307 " --> pdb=" O SER p 304 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE p 309 " --> pdb=" O ASP p 306 " (cutoff:3.500A) Processing helix chain 'p' and resid 313 through 323 Processing helix chain 'p' and resid 332 through 346 removed outlier: 3.657A pdb=" N LYS p 340 " --> pdb=" O ILE p 336 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU p 341 " --> pdb=" O LYS p 337 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL p 342 " --> pdb=" O TYR p 338 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU p 343 " --> pdb=" O ALA p 339 " (cutoff:3.500A) Processing helix chain 'p' and resid 359 through 375 removed outlier: 3.511A pdb=" N LEU p 374 " --> pdb=" O HIS p 370 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA p 375 " --> pdb=" O ARG p 371 " (cutoff:3.500A) Processing helix chain 'p' and resid 387 through 389 No H-bonds generated for 'chain 'p' and resid 387 through 389' Processing helix chain 'p' and resid 396 through 424 removed outlier: 4.122A pdb=" N PHE p 402 " --> pdb=" O PRO p 398 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY p 406 " --> pdb=" O PHE p 402 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET p 407 " --> pdb=" O LEU p 403 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN p 410 " --> pdb=" O GLY p 406 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU p 411 " --> pdb=" O MET p 407 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU p 414 " --> pdb=" O ASN p 410 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL p 415 " --> pdb=" O LEU p 411 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG p 416 " --> pdb=" O LEU p 412 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE p 417 " --> pdb=" O LYS p 413 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR p 418 " --> pdb=" O GLU p 414 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS p 421 " --> pdb=" O ILE p 417 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE p 422 " --> pdb=" O TYR p 418 " (cutoff:3.500A) Processing helix chain 'p' and resid 437 through 451 removed outlier: 3.791A pdb=" N SER p 441 " --> pdb=" O THR p 437 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP p 442 " --> pdb=" O ARG p 438 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER p 447 " --> pdb=" O GLY p 443 " (cutoff:3.500A) Processing helix chain 'p' and resid 455 through 459 removed outlier: 3.695A pdb=" N ALA p 459 " --> pdb=" O GLN p 456 " (cutoff:3.500A) Processing helix chain 'p' and resid 474 through 480 removed outlier: 3.514A pdb=" N LEU p 479 " --> pdb=" O PHE p 475 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER p 480 " --> pdb=" O ALA p 476 " (cutoff:3.500A) Processing helix chain 'p' and resid 502 through 506 removed outlier: 3.565A pdb=" N TRP p 506 " --> pdb=" O ASN p 503 " (cutoff:3.500A) Processing helix chain 'p' and resid 538 through 547 removed outlier: 3.539A pdb=" N PHE p 544 " --> pdb=" O PRO p 540 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU p 547 " --> pdb=" O GLU p 543 " (cutoff:3.500A) Processing helix chain 'p' and resid 579 through 592 removed outlier: 3.584A pdb=" N LEU p 583 " --> pdb=" O ASP p 579 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN p 585 " --> pdb=" O GLU p 581 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS p 589 " --> pdb=" O ASN p 585 " (cutoff:3.500A) Processing helix chain 'p' and resid 636 through 641 removed outlier: 3.985A pdb=" N ILE p 640 " --> pdb=" O LYS p 636 " (cutoff:3.500A) Processing helix chain 'p' and resid 645 through 649 removed outlier: 3.839A pdb=" N ASN p 649 " --> pdb=" O ARG p 646 " (cutoff:3.500A) Processing helix chain 'p' and resid 653 through 658 Processing helix chain 'p' and resid 668 through 672 Processing helix chain 'p' and resid 678 through 683 Processing helix chain 'p' and resid 713 through 717 removed outlier: 3.555A pdb=" N HIS p 716 " --> pdb=" O PHE p 713 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN p 717 " --> pdb=" O PRO p 714 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 713 through 717' Processing helix chain 'p' and resid 718 through 727 removed outlier: 3.800A pdb=" N ASN p 722 " --> pdb=" O GLN p 718 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR p 723 " --> pdb=" O SER p 719 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER p 726 " --> pdb=" O ASN p 722 " (cutoff:3.500A) Processing helix chain 'p' and resid 761 through 765 removed outlier: 4.042A pdb=" N GLU p 765 " --> pdb=" O ARG p 762 " (cutoff:3.500A) Processing helix chain 'p' and resid 798 through 802 Processing helix chain 'p' and resid 970 through 976 removed outlier: 4.564A pdb=" N SER p 974 " --> pdb=" O HIS p 970 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG p 975 " --> pdb=" O ALA p 971 " (cutoff:3.500A) Processing helix chain 'p' and resid 978 through 994 removed outlier: 3.509A pdb=" N GLU p 983 " --> pdb=" O GLY p 979 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N CYS p 984 " --> pdb=" O HIS p 980 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU p 985 " --> pdb=" O LEU p 981 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS p 988 " --> pdb=" O CYS p 984 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL p 989 " --> pdb=" O LEU p 985 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN p 992 " --> pdb=" O LYS p 988 " (cutoff:3.500A) Processing helix chain 'p' and resid 1008 through 1016 removed outlier: 3.587A pdb=" N LEU p1014 " --> pdb=" O LYS p1010 " (cutoff:3.500A) Processing helix chain 'p' and resid 1054 through 1058 removed outlier: 3.672A pdb=" N ASP p1057 " --> pdb=" O MET p1054 " (cutoff:3.500A) Processing helix chain 'p' and resid 1089 through 1098 removed outlier: 3.710A pdb=" N GLN p1094 " --> pdb=" O GLU p1090 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE p1095 " --> pdb=" O ARG p1091 " (cutoff:3.500A) Processing helix chain 'p' and resid 1099 through 1108 removed outlier: 3.627A pdb=" N LEU p1103 " --> pdb=" O ALA p1099 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU p1107 " --> pdb=" O LEU p1103 " (cutoff:3.500A) Processing helix chain 'p' and resid 1152 through 1164 removed outlier: 3.532A pdb=" N LYS p1156 " --> pdb=" O PRO p1152 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU p1158 " --> pdb=" O ALA p1154 " (cutoff:3.500A) Processing helix chain 'q' and resid 27 through 34 Processing helix chain 'q' and resid 60 through 70 removed outlier: 3.509A pdb=" N ILE q 64 " --> pdb=" O HIS q 60 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS q 66 " --> pdb=" O GLU q 62 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY q 69 " --> pdb=" O ALA q 65 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU q 70 " --> pdb=" O HIS q 66 " (cutoff:3.500A) Processing helix chain 'q' and resid 118 through 120 No H-bonds generated for 'chain 'q' and resid 118 through 120' Processing helix chain 'q' and resid 242 through 265 removed outlier: 3.501A pdb=" N LEU q 246 " --> pdb=" O GLU q 242 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS q 254 " --> pdb=" O SER q 250 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP q 258 " --> pdb=" O LYS q 254 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR q 261 " --> pdb=" O SER q 257 " (cutoff:3.500A) Processing helix chain 'r' and resid 33 through 50 removed outlier: 3.504A pdb=" N LEU r 40 " --> pdb=" O GLU r 36 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU r 42 " --> pdb=" O HIS r 38 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS r 43 " --> pdb=" O MET r 39 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER r 50 " --> pdb=" O GLN r 46 " (cutoff:3.500A) Processing helix chain 'r' and resid 59 through 71 removed outlier: 3.703A pdb=" N ARG r 70 " --> pdb=" O ASN r 66 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE r 71 " --> pdb=" O TYR r 67 " (cutoff:3.500A) Processing helix chain 'r' and resid 76 through 87 removed outlier: 3.790A pdb=" N SER r 85 " --> pdb=" O ALA r 81 " (cutoff:3.500A) Processing helix chain 'r' and resid 93 through 102 removed outlier: 3.774A pdb=" N LEU r 97 " --> pdb=" O HIS r 93 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA r 98 " --> pdb=" O LYS r 94 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU r 100 " --> pdb=" O GLU r 96 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN r 102 " --> pdb=" O ALA r 98 " (cutoff:3.500A) Processing helix chain 'r' and resid 107 through 115 Processing helix chain 'r' and resid 123 through 138 removed outlier: 4.055A pdb=" N LEU r 127 " --> pdb=" O GLU r 123 " (cutoff:3.500A) Processing helix chain 's' and resid 3 through 24 removed outlier: 3.562A pdb=" N TRP s 11 " --> pdb=" O THR s 7 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN s 19 " --> pdb=" O LYS s 15 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS s 22 " --> pdb=" O MET s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 29 through 34 removed outlier: 3.900A pdb=" N LEU s 33 " --> pdb=" O THR s 29 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP s 34 " --> pdb=" O GLN s 30 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 29 through 34' Processing helix chain 's' and resid 36 through 44 Processing helix chain 's' and resid 84 through 98 Processing helix chain 's' and resid 111 through 119 removed outlier: 3.867A pdb=" N VAL s 119 " --> pdb=" O LYS s 115 " (cutoff:3.500A) Processing helix chain 's' and resid 133 through 137 removed outlier: 3.972A pdb=" N ILE s 137 " --> pdb=" O GLU s 134 " (cutoff:3.500A) Processing helix chain 's' and resid 138 through 142 removed outlier: 3.588A pdb=" N GLU s 141 " --> pdb=" O ASN s 138 " (cutoff:3.500A) Processing helix chain 's' and resid 155 through 163 removed outlier: 3.556A pdb=" N LEU s 160 " --> pdb=" O VAL s 156 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA s 161 " --> pdb=" O THR s 157 " (cutoff:3.500A) Processing helix chain 's' and resid 177 through 183 Processing helix chain 't' and resid 58 through 75 removed outlier: 3.681A pdb=" N ALA t 63 " --> pdb=" O LYS t 59 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY t 67 " --> pdb=" O ALA t 63 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET t 75 " --> pdb=" O LEU t 71 " (cutoff:3.500A) Processing helix chain 't' and resid 88 through 98 removed outlier: 3.824A pdb=" N ALA t 93 " --> pdb=" O PRO t 89 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET t 94 " --> pdb=" O LEU t 90 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS t 95 " --> pdb=" O LEU t 91 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU t 97 " --> pdb=" O ALA t 93 " (cutoff:3.500A) Processing helix chain 't' and resid 121 through 123 No H-bonds generated for 'chain 't' and resid 121 through 123' Processing helix chain 'w' and resid 63 through 67 Processing helix chain 'w' and resid 69 through 75 removed outlier: 3.716A pdb=" N VAL w 72 " --> pdb=" O ILE w 69 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER w 73 " --> pdb=" O ALA w 70 " (cutoff:3.500A) Processing helix chain 'x' and resid 14 through 16 No H-bonds generated for 'chain 'x' and resid 14 through 16' Processing helix chain 'x' and resid 17 through 27 Processing helix chain 'x' and resid 30 through 39 Processing helix chain 'x' and resid 42 through 51 removed outlier: 3.641A pdb=" N ARG x 47 " --> pdb=" O TYR x 43 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N MET x 48 " --> pdb=" O CYS x 44 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU x 49 " --> pdb=" O CYS x 45 " (cutoff:3.500A) Processing helix chain 'x' and resid 54 through 58 removed outlier: 3.904A pdb=" N GLU x 57 " --> pdb=" O ASP x 54 " (cutoff:3.500A) Processing helix chain 'y' and resid 5 through 10 Processing helix chain 'y' and resid 39 through 51 removed outlier: 4.113A pdb=" N ILE y 45 " --> pdb=" O THR y 41 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE y 46 " --> pdb=" O LEU y 42 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS y 47 " --> pdb=" O GLY y 43 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN y 49 " --> pdb=" O ILE y 45 " (cutoff:3.500A) Processing helix chain 'y' and resid 82 through 110 removed outlier: 3.559A pdb=" N ASP y 93 " --> pdb=" O ASN y 89 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU y 100 " --> pdb=" O SER y 96 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS y 110 " --> pdb=" O ARG y 106 " (cutoff:3.500A) Processing helix chain 'y' and resid 111 through 113 No H-bonds generated for 'chain 'y' and resid 111 through 113' Processing helix chain 'u' and resid 14 through 18 removed outlier: 3.792A pdb=" N PHE u 18 " --> pdb=" O PRO u 15 " (cutoff:3.500A) Processing helix chain 'u' and resid 21 through 33 removed outlier: 3.661A pdb=" N THR u 25 " --> pdb=" O ASN u 21 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS u 27 " --> pdb=" O LEU u 23 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR u 32 " --> pdb=" O GLN u 28 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU u 33 " --> pdb=" O LYS u 29 " (cutoff:3.500A) Processing helix chain 'u' and resid 111 through 113 No H-bonds generated for 'chain 'u' and resid 111 through 113' Processing sheet with id=AA1, first strand: chain 'A' and resid 786 through 787 removed outlier: 6.509A pdb=" N LEU A 680 " --> pdb=" O PHE A 780 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL A 782 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU A 682 " --> pdb=" O VAL A 782 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 680 through 683 current: chain 'G' and resid 54 through 58 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 44 through 47 current: chain 'A' and resid 771 through 775 removed outlier: 7.811A pdb=" N GLN G 15 " --> pdb=" O GLN G 93 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N LEU G 95 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE G 17 " --> pdb=" O LEU G 95 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N SER G 97 " --> pdb=" O ILE G 17 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ARG G 19 " --> pdb=" O SER G 97 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE G 85 " --> pdb=" O THR A 698 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR A 698 " --> pdb=" O PHE G 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 786 through 787 removed outlier: 6.509A pdb=" N LEU A 680 " --> pdb=" O PHE A 780 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL A 782 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU A 682 " --> pdb=" O VAL A 782 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 680 through 683 current: chain 'G' and resid 85 through 98 removed outlier: 4.218A pdb=" N PHE G 85 " --> pdb=" O THR A 698 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR A 698 " --> pdb=" O PHE G 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 786 through 787 removed outlier: 4.291A pdb=" N GLN A 741 " --> pdb=" O ILE A 752 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N LEU A 754 " --> pdb=" O LEU A 739 " (cutoff:3.500A) removed outlier: 12.852A pdb=" N LEU A 739 " --> pdb=" O LEU A 754 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 824 through 825 Processing sheet with id=AA5, first strand: chain 'A' and resid 947 through 948 Processing sheet with id=AA6, first strand: chain 'A' and resid 1180 through 1185 removed outlier: 3.613A pdb=" N LYS A1166 " --> pdb=" O GLU G 182 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU G 182 " --> pdb=" O LYS A1166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 80 through 81 removed outlier: 5.552A pdb=" N ILE B 72 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N SER B 151 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 74 " --> pdb=" O ASN B 149 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL B 46 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASN B 37 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N PHE B 48 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ILE B 35 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLU B 50 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL B 33 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N THR B 52 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLN B 31 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N PHE B 54 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N THR B 29 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 9.634A pdb=" N THR B 201 " --> pdb=" O LYS B 27 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR B 29 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N LYS B 203 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLN B 31 " --> pdb=" O LYS B 203 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU B 205 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL B 33 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N THR B 207 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE B 35 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N ASP B 209 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 10.420A pdb=" N ASN B 37 " --> pdb=" O ASP B 209 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N CYS B 200 " --> pdb=" O ILE B 240 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE B 240 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU B 222 " --> pdb=" O HIS B 235 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET B 237 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LEU B 220 " --> pdb=" O MET B 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 63 through 65 removed outlier: 4.057A pdb=" N ALA B 83 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 159 through 162 removed outlier: 5.756A pdb=" N LEU B 249 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 255 through 258 removed outlier: 6.356A pdb=" N LYS B 305 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N PHE B 325 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N VAL B 307 " --> pdb=" O PHE B 325 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET B 322 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 360 through 361 removed outlier: 6.562A pdb=" N SER B 360 " --> pdb=" O VAL B 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 587 through 591 removed outlier: 4.571A pdb=" N PHE B 535 " --> pdb=" O GLU B 643 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 573 through 580 removed outlier: 7.406A pdb=" N LYS B 565 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ILE B 630 " --> pdb=" O LYS B 565 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR B 567 " --> pdb=" O ILE B 628 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE B 628 " --> pdb=" O THR B 567 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLN B 569 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 604 through 605 Processing sheet with id=AB6, first strand: chain 'D' and resid 934 through 936 Processing sheet with id=AB7, first strand: chain 'E' and resid 308 through 310 Processing sheet with id=AB8, first strand: chain 'E' and resid 782 through 785 Processing sheet with id=AB9, first strand: chain 'E' and resid 473 through 478 removed outlier: 3.997A pdb=" N THR E 493 " --> pdb=" O PHE E 489 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 504 through 507 removed outlier: 3.716A pdb=" N SER E 506 " --> pdb=" O THR E 532 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N THR E 532 " --> pdb=" O SER E 506 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 546 through 550 removed outlier: 3.507A pdb=" N SER E 562 " --> pdb=" O THR E 566 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR E 566 " --> pdb=" O SER E 562 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL E 579 " --> pdb=" O LEU E 569 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 588 through 593 Processing sheet with id=AC4, first strand: chain 'E' and resid 634 through 635 removed outlier: 3.615A pdb=" N ARG E 663 " --> pdb=" O LEU E 653 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP E 655 " --> pdb=" O CYS E 661 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N CYS E 661 " --> pdb=" O ASP E 655 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 672 through 677 Processing sheet with id=AC6, first strand: chain 'E' and resid 714 through 719 removed outlier: 6.477A pdb=" N LEU E 737 " --> pdb=" O LEU E 770 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 86 through 88 Processing sheet with id=AC8, first strand: chain 'H' and resid 200 through 201 Processing sheet with id=AC9, first strand: chain 'O' and resid 60 through 68 removed outlier: 4.802A pdb=" N LEU O 62 " --> pdb=" O ASN O 77 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ASN O 77 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN Q 333 " --> pdb=" O LYS O 92 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL Q 334 " --> pdb=" O MET Q 358 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N MET Q 358 " --> pdb=" O VAL Q 334 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL Q 336 " --> pdb=" O GLY Q 356 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY Q 356 " --> pdb=" O VAL Q 336 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N HIS Q 352 " --> pdb=" O ASP Q 340 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE Q 342 " --> pdb=" O LYS Q 350 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS Q 350 " --> pdb=" O ILE Q 342 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG Q 344 " --> pdb=" O LYS Q 348 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LYS Q 348 " --> pdb=" O ARG Q 344 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LYS Q 348 " --> pdb=" O GLU Q 375 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLU Q 375 " --> pdb=" O LYS Q 348 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LYS Q 350 " --> pdb=" O ASP Q 373 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASP Q 373 " --> pdb=" O LYS Q 350 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N HIS Q 352 " --> pdb=" O ILE Q 371 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE Q 371 " --> pdb=" O HIS Q 352 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LYS Q 354 " --> pdb=" O LYS Q 369 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LYS Q 369 " --> pdb=" O LYS Q 354 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU Q 375 " --> pdb=" O GLY O 60 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU O 62 " --> pdb=" O GLU Q 375 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 190 through 191 removed outlier: 3.838A pdb=" N THR P 209 " --> pdb=" O ILE P 204 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS P 218 " --> pdb=" O PHE P 214 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY P 223 " --> pdb=" O ILE P 168 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ILE P 168 " --> pdb=" O GLY P 223 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL P 259 " --> pdb=" O GLN P 166 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE P 168 " --> pdb=" O ASN P 257 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN P 257 " --> pdb=" O ILE P 168 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N SER P 170 " --> pdb=" O ILE P 255 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE P 255 " --> pdb=" O SER P 170 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL P 172 " --> pdb=" O PHE P 253 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N PHE P 253 " --> pdb=" O VAL P 172 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N MET P 258 " --> pdb=" O GLY P 314 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY P 314 " --> pdb=" O MET P 258 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'R' and resid 24 through 26 removed outlier: 3.672A pdb=" N ILE R 33 " --> pdb=" O VAL R 24 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY R 42 " --> pdb=" O MET R 32 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'S' and resid 45 through 49 removed outlier: 3.862A pdb=" N ASN S 142 " --> pdb=" O TYR S 26 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA S 30 " --> pdb=" O TYR S 144 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASN S 32 " --> pdb=" O PHE S 146 " (cutoff:3.500A) removed outlier: 11.721A pdb=" N GLN T 91 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N VAL T 111 " --> pdb=" O GLN T 91 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU T 93 " --> pdb=" O ILE T 109 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE T 109 " --> pdb=" O LEU T 93 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL T 95 " --> pdb=" O GLU T 107 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG T 113 " --> pdb=" O GLN T 86 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL T 54 " --> pdb=" O PHE T 83 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LEU T 85 " --> pdb=" O THR T 52 " (cutoff:3.500A) removed outlier: 11.178A pdb=" N THR T 52 " --> pdb=" O LEU T 85 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG T 51 " --> pdb=" O THR T 48 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N PHE S 135 " --> pdb=" O GLU S 13 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL S 15 " --> pdb=" O PHE S 135 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA S 137 " --> pdb=" O VAL S 15 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ARG S 17 " --> pdb=" O ALA S 137 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLN S 129 " --> pdb=" O GLY T 17 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N GLY T 17 " --> pdb=" O GLN S 129 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N VAL T 18 " --> pdb=" O VAL T 110 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'U' and resid 75 through 76 Processing sheet with id=AD5, first strand: chain 'U' and resid 126 through 129 removed outlier: 3.558A pdb=" N SER U 134 " --> pdb=" O CYS U 129 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'V' and resid 131 through 132 Processing sheet with id=AD7, first strand: chain 'V' and resid 191 through 192 removed outlier: 4.020A pdb=" N LEU V 201 " --> pdb=" O VAL V 192 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'f' and resid 111 through 113 removed outlier: 8.242A pdb=" N SER c 25 " --> pdb=" O LEU j 195 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'd' and resid 893 through 894 removed outlier: 7.792A pdb=" N GLU d 893 " --> pdb=" O LEU l 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'd' and resid 934 through 936 Processing sheet with id=AE2, first strand: chain 'e' and resid 461 through 466 removed outlier: 6.410A pdb=" N ILE e 461 " --> pdb=" O LEU f 136 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'e' and resid 473 through 478 removed outlier: 3.849A pdb=" N THR e 493 " --> pdb=" O PHE e 489 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'e' and resid 506 through 507 removed outlier: 4.284A pdb=" N SER e 506 " --> pdb=" O ASP e 529 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'e' and resid 546 through 550 removed outlier: 6.693A pdb=" N SER e 561 " --> pdb=" O TYR e 547 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA e 549 " --> pdb=" O LEU e 559 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU e 559 " --> pdb=" O ALA e 549 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL e 579 " --> pdb=" O LEU e 569 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'e' and resid 588 through 593 Processing sheet with id=AE7, first strand: chain 'e' and resid 632 through 635 removed outlier: 3.634A pdb=" N ARG e 652 " --> pdb=" O THR e 644 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG e 663 " --> pdb=" O LEU e 653 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP e 655 " --> pdb=" O CYS e 661 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N CYS e 661 " --> pdb=" O ASP e 655 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'e' and resid 672 through 677 removed outlier: 6.678A pdb=" N GLY e 687 " --> pdb=" O HIS e 673 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU e 675 " --> pdb=" O ALA e 685 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA e 685 " --> pdb=" O LEU e 675 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N PHE e 677 " --> pdb=" O PHE e 683 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE e 683 " --> pdb=" O PHE e 677 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP e 697 " --> pdb=" O MET e 703 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N MET e 703 " --> pdb=" O ASP e 697 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'e' and resid 716 through 719 Processing sheet with id=AF1, first strand: chain 'e' and resid 782 through 785 removed outlier: 4.237A pdb=" N HIS e 782 " --> pdb=" O ALA e 794 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA e 794 " --> pdb=" O HIS e 782 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'f' and resid 95 through 97 removed outlier: 3.504A pdb=" N LEU f 104 " --> pdb=" O ALA f 97 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'o' and resid 20 through 22 removed outlier: 4.084A pdb=" N ARG o 20 " --> pdb=" O MET p1172 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET p1172 " --> pdb=" O ARG o 20 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'o' and resid 86 through 95 removed outlier: 3.708A pdb=" N GLY o 86 " --> pdb=" O VAL o 255 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N THR o 251 " --> pdb=" O LEU o 90 " (cutoff:3.500A) removed outlier: 10.536A pdb=" N LYS o 92 " --> pdb=" O ILE o 249 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N ILE o 249 " --> pdb=" O LYS o 92 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'o' and resid 193 through 194 removed outlier: 4.294A pdb=" N LEU o 198 " --> pdb=" O LEU o 216 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'o' and resid 264 through 266 removed outlier: 3.856A pdb=" N ALA o 270 " --> pdb=" O MET o 266 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'o' and resid 329 through 331 removed outlier: 4.351A pdb=" N LYS o 331 " --> pdb=" O ARG o 334 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'o' and resid 357 through 359 removed outlier: 4.025A pdb=" N LYS o 357 " --> pdb=" O PHE p1086 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'o' and resid 469 through 470 removed outlier: 3.741A pdb=" N MET o 501 " --> pdb=" O THR o 365 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR o 365 " --> pdb=" O MET o 501 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N PHE o 482 " --> pdb=" O ARG o 364 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL o 366 " --> pdb=" O PHE o 482 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU o 484 " --> pdb=" O VAL o 366 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N THR o 368 " --> pdb=" O LEU o 484 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL o 378 " --> pdb=" O ARG o 475 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'o' and resid 389 through 393 removed outlier: 4.373A pdb=" N TYR o 418 " --> pdb=" O GLU o 447 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N HIS o 449 " --> pdb=" O ALA o 416 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ALA o 416 " --> pdb=" O HIS o 449 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'o' and resid 554 through 555 Processing sheet with id=AG3, first strand: chain 'o' and resid 602 through 603 removed outlier: 6.921A pdb=" N VAL o 629 " --> pdb=" O ILE o 636 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'o' and resid 789 through 790 removed outlier: 3.507A pdb=" N GLY o 789 " --> pdb=" O VAL o 823 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'o' and resid 792 through 793 Processing sheet with id=AG6, first strand: chain 'o' and resid 872 through 873 Processing sheet with id=AG7, first strand: chain 'o' and resid 902 through 905 Processing sheet with id=AG8, first strand: chain 'o' and resid 1139 through 1140 removed outlier: 3.881A pdb=" N THR o1358 " --> pdb=" O THR o1140 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'o' and resid 1243 through 1247 removed outlier: 4.478A pdb=" N LEU o1255 " --> pdb=" O LEU o1216 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU o1211 " --> pdb=" O ILE o1175 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE o1175 " --> pdb=" O LEU o1211 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG o1213 " --> pdb=" O THR o1173 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR o1173 " --> pdb=" O ARG o1213 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLU o1215 " --> pdb=" O ALA o1171 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'o' and resid 1319 through 1322 Processing sheet with id=AH2, first strand: chain 't' and resid 115 through 119 removed outlier: 3.931A pdb=" N ASP o1472 " --> pdb=" O ARG t 107 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU o1473 " --> pdb=" O ILE u 59 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY u 57 " --> pdb=" O LEU o1475 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL u 66 " --> pdb=" O LEU u 13 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE u 5 " --> pdb=" O ALA u 74 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 't' and resid 115 through 119 removed outlier: 3.931A pdb=" N ASP o1472 " --> pdb=" O ARG t 107 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU o1473 " --> pdb=" O ILE u 59 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY u 57 " --> pdb=" O LEU o1475 " (cutoff:3.500A) removed outlier: 11.236A pdb=" N LEU u 67 " --> pdb=" O ILE u 54 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N ILE u 54 " --> pdb=" O LEU u 67 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N ASP u 52 " --> pdb=" O PRO u 69 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LYS u 71 " --> pdb=" O THR u 50 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N THR u 50 " --> pdb=" O LYS u 71 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LYS u 73 " --> pdb=" O VAL u 48 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL u 48 " --> pdb=" O LYS u 73 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ILE u 75 " --> pdb=" O ILE u 46 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE u 46 " --> pdb=" O ILE u 75 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'p' and resid 83 through 84 removed outlier: 4.861A pdb=" N LEU p 93 " --> pdb=" O PRO p 123 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR p 125 " --> pdb=" O ILE p 91 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ILE p 91 " --> pdb=" O TYR p 125 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP p 127 " --> pdb=" O GLU p 89 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'p' and resid 83 through 84 removed outlier: 6.603A pdb=" N ALA p 122 " --> pdb=" O GLY p 150 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLY p 150 " --> pdb=" O ALA p 122 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU p 124 " --> pdb=" O PHE p 148 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE p 148 " --> pdb=" O LEU p 124 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N VAL p 126 " --> pdb=" O LYS p 146 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU p 140 " --> pdb=" O VAL p 132 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'p' and resid 97 through 99 Processing sheet with id=AH7, first strand: chain 'p' and resid 185 through 187 Processing sheet with id=AH8, first strand: chain 'p' and resid 391 through 394 removed outlier: 3.560A pdb=" N LYS p 524 " --> pdb=" O LEU p 485 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'p' and resid 206 through 208 removed outlier: 6.850A pdb=" N MET p 239 " --> pdb=" O ALA p 216 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR p 218 " --> pdb=" O VAL p 237 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL p 237 " --> pdb=" O THR p 218 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU p 220 " --> pdb=" O ILE p 235 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE p 235 " --> pdb=" O GLU p 220 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ARG p 222 " --> pdb=" O SER p 233 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER p 233 " --> pdb=" O ARG p 222 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP p 236 " --> pdb=" O THR p 259 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'p' and resid 531 through 532 Processing sheet with id=AI2, first strand: chain 'p' and resid 572 through 573 removed outlier: 3.548A pdb=" N ILE p 614 " --> pdb=" O PHE p 568 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU p 611 " --> pdb=" O ASP p 606 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP p 606 " --> pdb=" O GLU p 611 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER p 602 " --> pdb=" O TYR p 615 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'p' and resid 662 through 664 Processing sheet with id=AI4, first strand: chain 'p' and resid 748 through 751 removed outlier: 3.564A pdb=" N VAL p 750 " --> pdb=" O VAL p 809 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N PHE p 918 " --> pdb=" O VAL p 909 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL p 909 " --> pdb=" O PHE p 918 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS p 920 " --> pdb=" O VAL p 907 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL p 907 " --> pdb=" O LYS p 920 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG p 922 " --> pdb=" O ASP p 905 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N VAL p 907 " --> pdb=" O LYS z 46 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'p' and resid 759 through 760 removed outlier: 3.516A pdb=" N THR p 760 " --> pdb=" O GLY p 997 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'p' and resid 1025 through 1026 removed outlier: 7.442A pdb=" N VAL p 794 " --> pdb=" O GLY p 946 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLN p 948 " --> pdb=" O VAL p 794 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N MET p 796 " --> pdb=" O GLN p 948 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N ILE p 965 " --> pdb=" O ASN p 777 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE p 779 " --> pdb=" O ILE p 965 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE p 967 " --> pdb=" O ILE p 779 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA p 781 " --> pdb=" O ILE p 967 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE p1042 " --> pdb=" O ILE p 782 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'p' and resid 827 through 829 removed outlier: 3.916A pdb=" N ILE p 867 " --> pdb=" O THR p 894 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'p' and resid 1115 through 1119 Processing sheet with id=AI9, first strand: chain 'p' and resid 1127 through 1129 Processing sheet with id=AJ1, first strand: chain 'q' and resid 8 through 14 removed outlier: 6.520A pdb=" N LYS q 20 " --> pdb=" O THR q 12 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU q 14 " --> pdb=" O ASN q 18 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASN q 18 " --> pdb=" O LEU q 14 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE q 21 " --> pdb=" O TYR q 231 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'q' and resid 121 through 122 removed outlier: 3.517A pdb=" N ALA q 163 " --> pdb=" O PHE q 101 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLU q 158 " --> pdb=" O ALA q 54 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA q 54 " --> pdb=" O GLU q 158 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ARG q 160 " --> pdb=" O ILE q 52 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ILE q 52 " --> pdb=" O ARG q 160 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ARG q 162 " --> pdb=" O VAL q 50 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL q 50 " --> pdb=" O ARG q 162 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TYR q 164 " --> pdb=" O ASP q 48 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'q' and resid 113 through 116 removed outlier: 3.643A pdb=" N VAL q 151 " --> pdb=" O VAL q 115 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 's' and resid 60 through 63 removed outlier: 3.751A pdb=" N VAL s 60 " --> pdb=" O VAL s 74 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG s 101 " --> pdb=" O GLN s 71 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 's' and resid 81 through 82 Processing sheet with id=AJ6, first strand: chain 's' and resid 147 through 150 removed outlier: 3.807A pdb=" N GLU s 147 " --> pdb=" O ILE s 194 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 't' and resid 56 through 57 Processing sheet with id=AJ8, first strand: chain 'v' and resid 4 through 14 removed outlier: 6.912A pdb=" N HIS v 29 " --> pdb=" O LYS v 13 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU v 122 " --> pdb=" O ASP v 42 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY v 127 " --> pdb=" O LEU v 112 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER v 113 " --> pdb=" O GLU v 100 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG v 98 " --> pdb=" O TYR v 115 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER v 117 " --> pdb=" O VAL v 96 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N VAL v 96 " --> pdb=" O SER v 117 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'w' and resid 25 through 28 Processing sheet with id=AK1, first strand: chain 'w' and resid 80 through 81 Processing sheet with id=AK2, first strand: chain 'y' and resid 21 through 23 removed outlier: 6.628A pdb=" N ILE y 72 " --> pdb=" O TYR y 61 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR y 61 " --> pdb=" O ILE y 72 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG y 74 " --> pdb=" O ALA y 59 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA y 59 " --> pdb=" O ARG y 74 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN y 76 " --> pdb=" O LEU y 57 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'u' and resid 169 through 170 removed outlier: 3.666A pdb=" N LYS u 146 " --> pdb=" O SER u 162 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE u 160 " --> pdb=" O VAL u 148 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR u 150 " --> pdb=" O PHE u 158 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE u 158 " --> pdb=" O THR u 150 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL u 152 " --> pdb=" O ASP u 156 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP u 156 " --> pdb=" O VAL u 152 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER u 105 " --> pdb=" O ALA u 159 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N GLY u 161 " --> pdb=" O SER u 105 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N PHE u 107 " --> pdb=" O GLY u 161 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLY u 96 " --> pdb=" O VAL u 92 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VAL u 92 " --> pdb=" O GLY u 96 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE u 98 " --> pdb=" O THR u 90 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'u' and resid 118 through 120 3152 hydrogen bonds defined for protein. 8946 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 163 hydrogen bonds 326 hydrogen bond angles 0 basepair planarities 62 basepair parallelities 129 stacking parallelities Total time for adding SS restraints: 45.44 Time building geometry restraints manager: 30.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 13788 1.28 - 1.43: 22108 1.43 - 1.57: 49372 1.57 - 1.71: 285 1.71 - 1.85: 739 Bond restraints: 86292 Sorted by residual: bond pdb=" C PHE A 762 " pdb=" O PHE A 762 " ideal model delta sigma weight residual 1.234 1.141 0.093 1.28e-02 6.10e+03 5.33e+01 bond pdb=" C ASN B 61 " pdb=" O ASN B 61 " ideal model delta sigma weight residual 1.239 1.180 0.059 9.60e-03 1.09e+04 3.81e+01 bond pdb=" C GLU o 964 " pdb=" O GLU o 964 " ideal model delta sigma weight residual 1.237 1.304 -0.067 1.17e-02 7.31e+03 3.31e+01 bond pdb=" C ARG F 395 " pdb=" O ARG F 395 " ideal model delta sigma weight residual 1.237 1.316 -0.079 1.39e-02 5.18e+03 3.27e+01 bond pdb=" N ARG O 59 " pdb=" CA ARG O 59 " ideal model delta sigma weight residual 1.455 1.518 -0.063 1.25e-02 6.40e+03 2.55e+01 ... (remaining 86287 not shown) Histogram of bond angle deviations from ideal: 95.81 - 103.62: 1612 103.62 - 111.43: 35880 111.43 - 119.24: 37008 119.24 - 127.05: 41569 127.05 - 134.85: 1189 Bond angle restraints: 117258 Sorted by residual: angle pdb=" C PHE B 883 " pdb=" N VAL B 884 " pdb=" CA VAL B 884 " ideal model delta sigma weight residual 121.97 104.04 17.93 1.80e+00 3.09e-01 9.92e+01 angle pdb=" N HIS B 491 " pdb=" CA HIS B 491 " pdb=" C HIS B 491 " ideal model delta sigma weight residual 111.28 100.89 10.39 1.09e+00 8.42e-01 9.09e+01 angle pdb=" O ILE U 94 " pdb=" C ILE U 94 " pdb=" N ASN U 95 " ideal model delta sigma weight residual 123.10 133.29 -10.19 1.07e+00 8.73e-01 9.08e+01 angle pdb=" O PRO f 149 " pdb=" C PRO f 149 " pdb=" N PRO f 150 " ideal model delta sigma weight residual 121.31 125.55 -4.24 4.60e-01 4.73e+00 8.50e+01 angle pdb=" N ARG R 112 " pdb=" CA ARG R 112 " pdb=" C ARG R 112 " ideal model delta sigma weight residual 111.28 101.25 10.03 1.09e+00 8.42e-01 8.46e+01 ... (remaining 117253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.39: 47903 23.39 - 46.78: 3583 46.78 - 70.17: 737 70.17 - 93.56: 76 93.56 - 116.95: 1 Dihedral angle restraints: 52300 sinusoidal: 22507 harmonic: 29793 Sorted by residual: dihedral pdb=" C THR O 29 " pdb=" N THR O 29 " pdb=" CA THR O 29 " pdb=" CB THR O 29 " ideal model delta harmonic sigma weight residual -122.00 -142.85 20.85 0 2.50e+00 1.60e-01 6.95e+01 dihedral pdb=" C ASP Q 330 " pdb=" N ASP Q 330 " pdb=" CA ASP Q 330 " pdb=" CB ASP Q 330 " ideal model delta harmonic sigma weight residual -122.60 -142.75 20.15 0 2.50e+00 1.60e-01 6.50e+01 dihedral pdb=" C LEU V 175 " pdb=" N LEU V 175 " pdb=" CA LEU V 175 " pdb=" CB LEU V 175 " ideal model delta harmonic sigma weight residual -122.60 -141.93 19.33 0 2.50e+00 1.60e-01 5.98e+01 ... (remaining 52297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 12372 0.159 - 0.317: 644 0.317 - 0.476: 52 0.476 - 0.634: 11 0.634 - 0.793: 3 Chirality restraints: 13082 Sorted by residual: chirality pdb=" CA LEU V 175 " pdb=" N LEU V 175 " pdb=" C LEU V 175 " pdb=" CB LEU V 175 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.57e+01 chirality pdb=" CA ASP Q 330 " pdb=" N ASP Q 330 " pdb=" C ASP Q 330 " pdb=" CB ASP Q 330 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CA THR O 29 " pdb=" N THR O 29 " pdb=" C THR O 29 " pdb=" CB THR O 29 " both_signs ideal model delta sigma weight residual False 2.53 1.86 0.67 2.00e-01 2.50e+01 1.12e+01 ... (remaining 13079 not shown) Planarity restraints: 14642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU O 17 " -0.036 2.00e-02 2.50e+03 7.28e-02 5.30e+01 pdb=" C GLU O 17 " 0.126 2.00e-02 2.50e+03 pdb=" O GLU O 17 " -0.049 2.00e-02 2.50e+03 pdb=" N SER O 18 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL U 161 " -0.032 2.00e-02 2.50e+03 6.15e-02 3.78e+01 pdb=" C VAL U 161 " 0.106 2.00e-02 2.50e+03 pdb=" O VAL U 161 " -0.040 2.00e-02 2.50e+03 pdb=" N GLU U 162 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 942 " -0.027 2.00e-02 2.50e+03 5.42e-02 2.94e+01 pdb=" C ALA D 942 " 0.094 2.00e-02 2.50e+03 pdb=" O ALA D 942 " -0.035 2.00e-02 2.50e+03 pdb=" N GLN D 943 " -0.032 2.00e-02 2.50e+03 ... (remaining 14639 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 118 2.19 - 2.87: 30304 2.87 - 3.55: 111599 3.55 - 4.22: 198549 4.22 - 4.90: 334318 Nonbonded interactions: 674888 Sorted by model distance: nonbonded pdb=" OE2 GLU D 948 " pdb=" NE2 GLN D 952 " model vdw 1.514 2.520 nonbonded pdb=" OE1 GLU F 81 " pdb=" NH2 ARG I 45 " model vdw 1.523 2.520 nonbonded pdb=" CD1 ILE F 280 " pdb=" CE1 HIS F 326 " model vdw 1.523 3.680 nonbonded pdb=" OE2 GLU R 36 " pdb="ZN ZN R 401 " model vdw 1.592 2.230 nonbonded pdb=" CE MET R 114 " pdb=" CE2 PHE R 142 " model vdw 1.679 3.760 ... (remaining 674883 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 'E' and (resid 209 through 343 or resid 363 through 798)) selection = (chain 'e' and (resid 209 through 378 or resid 417 through 747 or resid 754 thro \ ugh 798)) } ncs_group { reference = (chain 'F' and (resid 14 through 150 or resid 210 or resid 214 through 473)) selection = (chain 'f' and (resid 14 through 106 or (resid 107 through 108 and (name N or na \ me CA or name C or name O or name CB )) or resid 109 through 123 or (resid 124 a \ nd (name N or name CA or name C or name O or name CB )) or resid 125 through 473 \ )) } ncs_group { reference = chain 'I' selection = (chain 'i' and resid 13 through 132) } ncs_group { reference = chain 'J' selection = (chain 'j' and (resid 114 through 177 or resid 192 through 216)) } 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: 6.270 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: 0.100 Extract box with map and model: 24.470 Check model and map are aligned: 0.970 Set scattering table: 0.610 Process input model: 214.660 Find NCS groups from input model: 2.600 Set up NCS constraints: 0.340 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 252.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3039 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 : 0.008 0.099 86292 Z= 0.532 Angle : 1.154 17.926 117258 Z= 0.767 Chirality : 0.079 0.793 13082 Planarity : 0.007 0.105 14642 Dihedral : 16.439 116.946 32957 Min Nonbonded Distance : 1.514 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.69 % Favored : 92.62 % Rotamer: Outliers : 4.37 % Allowed : 7.05 % Favored : 88.58 % Cbeta Deviations : 0.56 % Peptide Plane: Cis-proline : 0.61 % 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: -3.68 (0.07), residues: 10028 helix: -2.56 (0.07), residues: 3943 sheet: -1.55 (0.14), residues: 1270 loop : -2.55 (0.08), residues: 4815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.003 TRP T 19 HIS 0.015 0.001 HIS F 385 PHE 0.054 0.003 PHE B 883 TYR 0.036 0.002 TYR p1048 ARG 0.049 0.001 ARG u 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20056 Ramachandran restraints generated. 10028 Oldfield, 0 Emsley, 10028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20056 Ramachandran restraints generated. 10028 Oldfield, 0 Emsley, 10028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1147 residues out of total 9048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 391 poor density : 756 time to evaluate : 7.617 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: A 500 LEU cc_start: -0.2636 (OUTLIER) cc_final: -0.3328 (tp) REVERT: A 505 ASN cc_start: 0.1605 (OUTLIER) cc_final: 0.1121 (p0) REVERT: A 511 LEU cc_start: -0.0266 (OUTLIER) cc_final: -0.1251 (mp) REVERT: A 649 MET cc_start: -0.1069 (ttm) cc_final: -0.1312 (ppp) REVERT: A 757 MET cc_start: -0.2059 (mmm) cc_final: -0.3030 (ttp) REVERT: A 942 MET cc_start: 0.2647 (mmm) cc_final: 0.2407 (mmm) REVERT: B 614 MET cc_start: -0.2414 (mtt) cc_final: -0.2953 (ttm) REVERT: B 819 LEU cc_start: -0.0049 (OUTLIER) cc_final: -0.0257 (tp) REVERT: D 883 LEU cc_start: 0.5914 (mt) cc_final: 0.5713 (mt) REVERT: D 1000 ARG cc_start: 0.0268 (OUTLIER) cc_final: -0.0039 (tpp-160) REVERT: E 747 LEU cc_start: -0.1243 (OUTLIER) cc_final: -0.1707 (mm) REVERT: F 261 THR cc_start: 0.2181 (OUTLIER) cc_final: 0.1786 (m) REVERT: F 283 MET cc_start: -0.2071 (mmm) cc_final: -0.3597 (tpt) REVERT: F 296 TYR cc_start: 0.0667 (t80) cc_final: -0.0182 (p90) REVERT: G 154 LYS cc_start: -0.1140 (OUTLIER) cc_final: -0.1909 (mttm) REVERT: G 161 ASP cc_start: -0.0151 (OUTLIER) cc_final: -0.2358 (p0) REVERT: G 181 TRP cc_start: 0.0518 (OUTLIER) cc_final: -0.1260 (p90) REVERT: H 205 LYS cc_start: 0.3174 (OUTLIER) cc_final: 0.0916 (mptt) REVERT: J 197 MET cc_start: -0.2187 (mmm) cc_final: -0.2612 (mtt) REVERT: R 248 ARG cc_start: 0.0339 (OUTLIER) cc_final: -0.0026 (mmm-85) REVERT: U 76 MET cc_start: 0.0928 (OUTLIER) cc_final: -0.0102 (ppp) REVERT: U 111 ARG cc_start: 0.1675 (OUTLIER) cc_final: 0.0039 (ptt90) REVERT: U 113 ARG cc_start: 0.1301 (OUTLIER) cc_final: 0.0934 (tmt-80) REVERT: U 171 LYS cc_start: 0.0976 (OUTLIER) cc_final: 0.0495 (mmtm) REVERT: V 120 MET cc_start: 0.4843 (tpt) cc_final: 0.4252 (tpt) REVERT: V 142 LYS cc_start: 0.0181 (OUTLIER) cc_final: -0.0798 (mptt) REVERT: V 146 ARG cc_start: -0.2759 (OUTLIER) cc_final: -0.3987 (mmp-170) REVERT: V 169 GLU cc_start: 0.2267 (OUTLIER) cc_final: 0.2016 (pm20) REVERT: V 228 MET cc_start: 0.1946 (mtm) cc_final: -0.0326 (tpt) REVERT: c 24 ASP cc_start: 0.2140 (OUTLIER) cc_final: 0.1203 (m-30) REVERT: d 933 ARG cc_start: -0.1244 (ptt-90) cc_final: -0.2187 (ttt90) REVERT: e 291 MET cc_start: 0.1142 (ttm) cc_final: 0.0744 (ttt) REVERT: f 421 ASP cc_start: 0.3512 (OUTLIER) cc_final: 0.3220 (p0) REVERT: o 114 CYS cc_start: 0.5955 (OUTLIER) cc_final: 0.5153 (m) REVERT: o 728 THR cc_start: 0.7004 (OUTLIER) cc_final: 0.6787 (p) REVERT: p 239 MET cc_start: 0.7019 (ttm) cc_final: 0.6768 (ttp) REVERT: p 315 ASN cc_start: 0.9255 (m-40) cc_final: 0.9027 (m-40) REVERT: p 508 MET cc_start: 0.8031 (mtt) cc_final: 0.7778 (mtt) REVERT: p 908 MET cc_start: 0.7861 (ttp) cc_final: 0.7539 (tmm) REVERT: s 110 MET cc_start: 0.7250 (ttp) cc_final: 0.6983 (ttp) outliers start: 391 outliers final: 60 residues processed: 1115 average time/residue: 0.8205 time to fit residues: 1531.6338 Evaluate side-chains 501 residues out of total 9048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 418 time to evaluate : 7.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 970 ASN Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1026 ILE Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 559 LYS Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain D residue 993 GLN Chi-restraints excluded: chain D residue 1000 ARG Chi-restraints excluded: chain E residue 526 ARG Chi-restraints excluded: chain E residue 747 LEU Chi-restraints excluded: chain F residue 221 GLN Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 354 ARG Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain F residue 433 PRO Chi-restraints excluded: chain G residue 154 LYS Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 181 TRP Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain I residue 110 TYR Chi-restraints excluded: chain O residue 23 ILE Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 58 PHE Chi-restraints excluded: chain O residue 65 TYR Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 286 GLU Chi-restraints excluded: chain P residue 311 VAL Chi-restraints excluded: chain P residue 317 VAL Chi-restraints excluded: chain Q residue 320 VAL Chi-restraints excluded: chain Q residue 343 HIS Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 189 LYS Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 248 ARG Chi-restraints excluded: chain R residue 252 SER Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 76 MET Chi-restraints excluded: chain U residue 77 ARG Chi-restraints excluded: chain U residue 111 ARG Chi-restraints excluded: chain U residue 113 ARG Chi-restraints excluded: chain U residue 171 LYS Chi-restraints excluded: chain U residue 174 ARG Chi-restraints excluded: chain U residue 176 LEU Chi-restraints excluded: chain U residue 191 LEU Chi-restraints excluded: chain V residue 142 LYS Chi-restraints excluded: chain V residue 146 ARG Chi-restraints excluded: chain V residue 147 ASP Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain V residue 163 LEU Chi-restraints excluded: chain V residue 169 GLU Chi-restraints excluded: chain V residue 175 LEU Chi-restraints excluded: chain V residue 188 GLN Chi-restraints excluded: chain V residue 204 ASN Chi-restraints excluded: chain V residue 208 CYS Chi-restraints excluded: chain c residue 24 ASP Chi-restraints excluded: chain f residue 253 TYR Chi-restraints excluded: chain f residue 323 VAL Chi-restraints excluded: chain f residue 356 THR Chi-restraints excluded: chain f residue 421 ASP Chi-restraints excluded: chain o residue 114 CYS Chi-restraints excluded: chain o residue 265 VAL Chi-restraints excluded: chain o residue 437 ASP Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 947 HIS Chi-restraints excluded: chain o residue 1356 ARG Chi-restraints excluded: chain o residue 1482 TYR Chi-restraints excluded: chain x residue 26 GLN Chi-restraints excluded: chain x residue 30 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 852 optimal weight: 0.4980 chunk 765 optimal weight: 8.9990 chunk 424 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 516 optimal weight: 40.0000 chunk 408 optimal weight: 20.0000 chunk 791 optimal weight: 0.5980 chunk 306 optimal weight: 8.9990 chunk 481 optimal weight: 30.0000 chunk 589 optimal weight: 7.9990 chunk 917 optimal weight: 7.9990 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 ASN A 489 GLN A 616 HIS A 634 HIS A 637 GLN A 642 HIS A 896 GLN A 970 ASN A1073 GLN B 30 HIS B 137 HIS B 176 HIS B 235 HIS B 348 GLN B 415 HIS B 432 HIS B 450 GLN B 509 ASN B 521 GLN B 750 GLN B 813 ASN B 908 GLN B 916 ASN D 936 GLN D 949 GLN D 952 GLN D 994 GLN ** D1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 ASN E 351 GLN ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 585 ASN E 605 HIS E 636 HIS E 673 HIS F 52 GLN F 119 ASN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN F 273 GLN ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 ASN ** F 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 HIS G 10 HIS G 48 HIS ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 HIS H 201 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN I 126 ASN ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 HIS L 117 GLN O 16 GLN ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 343 HIS Q 352 HIS Q 361 ASN R 139 ASN S 172 ASN U 123 ASN V 95 HIS V 117 GLN V 158 HIS c 32 HIS c 85 HIS d 912 ASN d1069 ASN e 223 HIS e 246 HIS e 294 ASN e 336 HIS f 325 ASN f 422 HIS i 81 GLN k 139 GLN k 186 HIS o 143 HIS o 222 HIS o 293 ASN o 353 ASN o 465 HIS o 502 ASN ** o 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 671 ASN o 673 GLN o 678 ASN o 721 HIS o 739 ASN o 861 GLN o 926 ASN o 947 HIS ** o1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1316 ASN o1397 HIS o1420 ASN o1462 GLN p 111 ASN ** p 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 287 HIS p 370 HIS ** p 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 570 ASN p 639 HIS p 941 GLN p1021 HIS p1073 GLN p1097 HIS p1115 GLN ** p1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 131 ASN ** w 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 26 GLN y 29 ASN ** u 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 122 ASN Total number of N/Q/H flips: 102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3277 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 86292 Z= 0.340 Angle : 0.756 14.875 117258 Z= 0.394 Chirality : 0.046 0.383 13082 Planarity : 0.006 0.108 14642 Dihedral : 13.944 115.535 12797 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.65 % Favored : 94.21 % Rotamer: Outliers : 2.64 % Allowed : 12.45 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: -2.41 (0.08), residues: 10028 helix: -1.14 (0.08), residues: 4008 sheet: -1.10 (0.14), residues: 1294 loop : -2.12 (0.08), residues: 4726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP T 19 HIS 0.023 0.001 HIS L 105 PHE 0.030 0.002 PHE s 130 TYR 0.026 0.002 TYR R 27 ARG 0.016 0.001 ARG L 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20056 Ramachandran restraints generated. 10028 Oldfield, 0 Emsley, 10028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20056 Ramachandran restraints generated. 10028 Oldfield, 0 Emsley, 10028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 9048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 428 time to evaluate : 7.640 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: A 511 LEU cc_start: -0.0404 (OUTLIER) cc_final: -0.1509 (mp) REVERT: A 649 MET cc_start: -0.1433 (ttm) cc_final: -0.1903 (ppp) REVERT: A 757 MET cc_start: -0.2698 (mmm) cc_final: -0.3147 (ttt) REVERT: A 950 VAL cc_start: -0.0949 (OUTLIER) cc_final: -0.1176 (p) REVERT: A 1024 GLU cc_start: 0.4783 (OUTLIER) cc_final: 0.4496 (pt0) REVERT: B 262 MET cc_start: -0.2215 (mtp) cc_final: -0.2499 (mtm) REVERT: E 528 MET cc_start: 0.2151 (tpp) cc_final: 0.1199 (mmm) REVERT: E 747 LEU cc_start: -0.0951 (OUTLIER) cc_final: -0.1153 (mm) REVERT: F 290 MET cc_start: 0.2727 (mtt) cc_final: 0.1959 (tmm) REVERT: F 296 TYR cc_start: 0.1190 (t80) cc_final: -0.0267 (p90) REVERT: G 74 MET cc_start: 0.0158 (mpp) cc_final: -0.0375 (mpp) REVERT: H 166 ARG cc_start: 0.0169 (tpt170) cc_final: -0.0237 (ppt170) REVERT: J 197 MET cc_start: -0.1940 (mmm) cc_final: -0.2701 (mtt) REVERT: P 197 PHE cc_start: -0.3368 (OUTLIER) cc_final: -0.3686 (t80) REVERT: U 76 MET cc_start: 0.1170 (mtp) cc_final: 0.0252 (ppp) REVERT: U 113 ARG cc_start: 0.1477 (OUTLIER) cc_final: 0.0033 (tmt170) REVERT: V 142 LYS cc_start: 0.0973 (OUTLIER) cc_final: 0.0321 (mptt) REVERT: V 146 ARG cc_start: -0.2386 (OUTLIER) cc_final: -0.3599 (mmp-170) REVERT: V 228 MET cc_start: 0.1961 (mtm) cc_final: 0.0247 (tpt) REVERT: d 933 ARG cc_start: -0.1227 (ptt-90) cc_final: -0.1975 (ttt-90) REVERT: j 176 MET cc_start: 0.0541 (mmt) cc_final: 0.0258 (mmt) REVERT: m 39 MET cc_start: -0.1441 (tpp) cc_final: -0.2092 (tpt) REVERT: o 365 THR cc_start: 0.8090 (t) cc_final: 0.7632 (t) REVERT: o 986 MET cc_start: 0.6516 (ttt) cc_final: 0.4491 (tpp) REVERT: p 239 MET cc_start: 0.6906 (ttm) cc_final: 0.6664 (ttp) REVERT: p 594 MET cc_start: 0.8644 (mmt) cc_final: 0.8136 (mmm) REVERT: s 72 MET cc_start: 0.8613 (ttp) cc_final: 0.8356 (ttm) outliers start: 236 outliers final: 113 residues processed: 634 average time/residue: 0.7442 time to fit residues: 825.7409 Evaluate side-chains 498 residues out of total 9048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 377 time to evaluate : 7.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 416 TRP Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 804 ARG Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 970 ASN Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1026 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain D residue 1066 CYS Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain E residue 747 LEU Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain J residue 118 ASP Chi-restraints excluded: chain O residue 23 ILE Chi-restraints excluded: chain O residue 29 THR Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain P residue 197 PHE Chi-restraints excluded: chain P residue 307 SER Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 320 VAL Chi-restraints excluded: chain Q residue 333 ASN Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 171 GLU Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 189 LYS Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 248 ARG Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 77 ARG Chi-restraints excluded: chain U residue 113 ARG Chi-restraints excluded: chain U residue 122 THR Chi-restraints excluded: chain U residue 174 ARG Chi-restraints excluded: chain U residue 176 LEU Chi-restraints excluded: chain U residue 191 LEU Chi-restraints excluded: chain V residue 142 LYS Chi-restraints excluded: chain V residue 146 ARG Chi-restraints excluded: chain V residue 147 ASP Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain V residue 154 LEU Chi-restraints excluded: chain V residue 163 LEU Chi-restraints excluded: chain V residue 175 LEU Chi-restraints excluded: chain V residue 188 GLN Chi-restraints excluded: chain c residue 106 VAL Chi-restraints excluded: chain d residue 967 MET Chi-restraints excluded: chain e residue 296 THR Chi-restraints excluded: chain e residue 378 LYS Chi-restraints excluded: chain f residue 323 VAL Chi-restraints excluded: chain f residue 356 THR Chi-restraints excluded: chain f residue 421 ASP Chi-restraints excluded: chain l residue 145 THR Chi-restraints excluded: chain o residue 95 PHE Chi-restraints excluded: chain o residue 100 LEU Chi-restraints excluded: chain o residue 141 LEU Chi-restraints excluded: chain o residue 220 ARG Chi-restraints excluded: chain o residue 222 HIS Chi-restraints excluded: chain o residue 260 VAL Chi-restraints excluded: chain o residue 264 VAL Chi-restraints excluded: chain o residue 265 VAL Chi-restraints excluded: chain o residue 434 LYS Chi-restraints excluded: chain o residue 503 LEU Chi-restraints excluded: chain o residue 511 THR Chi-restraints excluded: chain o residue 607 SER Chi-restraints excluded: chain o residue 732 THR Chi-restraints excluded: chain o residue 750 ASP Chi-restraints excluded: chain o residue 860 ILE Chi-restraints excluded: chain o residue 864 LEU Chi-restraints excluded: chain o residue 930 LEU Chi-restraints excluded: chain o residue 1095 LEU Chi-restraints excluded: chain o residue 1127 LEU Chi-restraints excluded: chain o residue 1356 ARG Chi-restraints excluded: chain o residue 1423 ASP Chi-restraints excluded: chain o residue 1455 SER Chi-restraints excluded: chain o residue 1482 TYR Chi-restraints excluded: chain o residue 1486 ILE Chi-restraints excluded: chain p residue 20 ASP Chi-restraints excluded: chain p residue 225 LEU Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 262 TYR Chi-restraints excluded: chain p residue 272 VAL Chi-restraints excluded: chain p residue 289 ILE Chi-restraints excluded: chain p residue 698 ILE Chi-restraints excluded: chain p residue 706 VAL Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 1159 PHE Chi-restraints excluded: chain r residue 87 LEU Chi-restraints excluded: chain s residue 168 ASN Chi-restraints excluded: chain s residue 173 ILE Chi-restraints excluded: chain t residue 58 THR Chi-restraints excluded: chain v residue 41 LEU Chi-restraints excluded: chain w residue 32 ASN Chi-restraints excluded: chain w residue 95 VAL Chi-restraints excluded: chain x residue 7 CYS Chi-restraints excluded: chain y residue 2 ASN Chi-restraints excluded: chain u residue 131 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 509 optimal weight: 7.9990 chunk 284 optimal weight: 5.9990 chunk 763 optimal weight: 20.0000 chunk 624 optimal weight: 8.9990 chunk 253 optimal weight: 40.0000 chunk 918 optimal weight: 10.0000 chunk 992 optimal weight: 2.9990 chunk 818 optimal weight: 5.9990 chunk 911 optimal weight: 7.9990 chunk 313 optimal weight: 4.9990 chunk 737 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 702 ASN B 36 ASN ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1069 ASN E 420 ASN ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 GLN F 79 ASN ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 160 GLN ** J 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 167 ASN P 277 HIS Q 37 GLN Q 60 HIS R 271 GLN c 85 HIS f 220 GLN f 326 HIS i 38 GLN i 98 GLN k 186 HIS l 73 ASN ** o 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 372 ASN ** o 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 673 GLN ** o 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1230 GLN p 197 GLN ** p 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 22 ASN w 118 HIS w 121 HIS ** u 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3381 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 86292 Z= 0.337 Angle : 0.699 15.392 117258 Z= 0.363 Chirality : 0.045 0.318 13082 Planarity : 0.005 0.080 14642 Dihedral : 13.708 117.277 12697 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.95 % Favored : 93.90 % Rotamer: Outliers : 2.91 % Allowed : 14.02 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.08), residues: 10028 helix: -0.39 (0.08), residues: 4010 sheet: -0.86 (0.14), residues: 1325 loop : -1.90 (0.09), residues: 4693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 612 HIS 0.028 0.001 HIS w 118 PHE 0.036 0.002 PHE O 81 TYR 0.031 0.002 TYR F 253 ARG 0.020 0.001 ARG i 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20056 Ramachandran restraints generated. 10028 Oldfield, 0 Emsley, 10028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20056 Ramachandran restraints generated. 10028 Oldfield, 0 Emsley, 10028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 9048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 389 time to evaluate : 7.678 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 511 LEU cc_start: -0.0414 (OUTLIER) cc_final: -0.1866 (mp) REVERT: A 607 MET cc_start: -0.1733 (ptp) cc_final: -0.4714 (mmt) REVERT: A 649 MET cc_start: -0.1363 (ttm) cc_final: -0.1882 (ppp) REVERT: A 717 CYS cc_start: -0.0744 (OUTLIER) cc_final: -0.1269 (m) REVERT: B 757 MET cc_start: 0.5201 (OUTLIER) cc_final: 0.4545 (ttt) REVERT: E 444 MET cc_start: 0.1480 (mmt) cc_final: 0.1213 (ptt) REVERT: E 528 MET cc_start: 0.2415 (tpp) cc_final: 0.1397 (mmm) REVERT: E 747 LEU cc_start: -0.0935 (OUTLIER) cc_final: -0.1276 (mm) REVERT: F 285 MET cc_start: -0.0214 (ptm) cc_final: -0.0451 (ttp) REVERT: F 290 MET cc_start: 0.3083 (mtt) cc_final: 0.2636 (tmm) REVERT: F 361 LYS cc_start: 0.4038 (OUTLIER) cc_final: 0.3241 (tptt) REVERT: G 74 MET cc_start: 0.1040 (mpp) cc_final: -0.0035 (mpp) REVERT: H 59 GLU cc_start: 0.1325 (OUTLIER) cc_final: 0.0848 (mm-30) REVERT: H 166 ARG cc_start: 0.0284 (tpt170) cc_final: -0.0152 (ppt170) REVERT: J 197 MET cc_start: -0.1379 (mmm) cc_final: -0.2164 (mtt) REVERT: U 76 MET cc_start: 0.1645 (mtp) cc_final: 0.0492 (ppp) REVERT: U 110 MET cc_start: 0.1478 (ptt) cc_final: -0.1873 (tpt) REVERT: V 228 MET cc_start: 0.0477 (OUTLIER) cc_final: -0.0916 (tpt) REVERT: c 24 ASP cc_start: 0.2355 (OUTLIER) cc_final: 0.1200 (m-30) REVERT: e 247 MET cc_start: -0.1581 (ttm) cc_final: -0.3256 (mmt) REVERT: m 39 MET cc_start: -0.1410 (tpp) cc_final: -0.2337 (tpt) REVERT: o 565 MET cc_start: 0.7991 (mmm) cc_final: 0.7756 (tpp) REVERT: o 872 MET cc_start: 0.7534 (ppp) cc_final: 0.6999 (ttp) REVERT: p 550 MET cc_start: 0.7475 (tmm) cc_final: 0.7242 (tmm) REVERT: p 594 MET cc_start: 0.8689 (mmp) cc_final: 0.8257 (mmm) REVERT: q 15 THR cc_start: 0.8102 (OUTLIER) cc_final: 0.7456 (p) REVERT: s 94 MET cc_start: 0.8635 (mmp) cc_final: 0.8131 (mmp) REVERT: u 51 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8406 (mp) REVERT: u 131 MET cc_start: 0.2260 (OUTLIER) cc_final: 0.1727 (mmt) outliers start: 260 outliers final: 128 residues processed: 614 average time/residue: 0.7379 time to fit residues: 810.1040 Evaluate side-chains 500 residues out of total 9048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 361 time to evaluate : 7.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 572 TYR Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 970 ASN Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1026 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain D residue 1066 CYS Chi-restraints excluded: chain E residue 519 GLU Chi-restraints excluded: chain E residue 747 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 361 LYS Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain O residue 23 ILE Chi-restraints excluded: chain O residue 29 THR Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain P residue 306 VAL Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain Q residue 320 VAL Chi-restraints excluded: chain Q residue 336 VAL Chi-restraints excluded: chain Q residue 358 MET Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 171 GLU Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 189 LYS Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 249 SER Chi-restraints excluded: chain R residue 283 VAL Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 151 THR Chi-restraints excluded: chain U residue 168 MET Chi-restraints excluded: chain U residue 176 LEU Chi-restraints excluded: chain U residue 190 LEU Chi-restraints excluded: chain U residue 191 LEU Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain V residue 154 LEU Chi-restraints excluded: chain V residue 175 LEU Chi-restraints excluded: chain V residue 213 ASP Chi-restraints excluded: chain V residue 228 MET Chi-restraints excluded: chain c residue 24 ASP Chi-restraints excluded: chain c residue 106 VAL Chi-restraints excluded: chain e residue 296 THR Chi-restraints excluded: chain e residue 378 LYS Chi-restraints excluded: chain e residue 663 ARG Chi-restraints excluded: chain f residue 323 VAL Chi-restraints excluded: chain f residue 356 THR Chi-restraints excluded: chain f residue 411 VAL Chi-restraints excluded: chain f residue 421 ASP Chi-restraints excluded: chain l residue 145 THR Chi-restraints excluded: chain m residue 68 MET Chi-restraints excluded: chain o residue 95 PHE Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 222 HIS Chi-restraints excluded: chain o residue 260 VAL Chi-restraints excluded: chain o residue 264 VAL Chi-restraints excluded: chain o residue 484 LEU Chi-restraints excluded: chain o residue 487 SER Chi-restraints excluded: chain o residue 511 THR Chi-restraints excluded: chain o residue 607 SER Chi-restraints excluded: chain o residue 675 VAL Chi-restraints excluded: chain o residue 732 THR Chi-restraints excluded: chain o residue 750 ASP Chi-restraints excluded: chain o residue 860 ILE Chi-restraints excluded: chain o residue 930 LEU Chi-restraints excluded: chain o residue 1095 LEU Chi-restraints excluded: chain o residue 1127 LEU Chi-restraints excluded: chain o residue 1386 ILE Chi-restraints excluded: chain o residue 1404 THR Chi-restraints excluded: chain o residue 1423 ASP Chi-restraints excluded: chain o residue 1482 TYR Chi-restraints excluded: chain p residue 20 ASP Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 225 LEU Chi-restraints excluded: chain p residue 262 TYR Chi-restraints excluded: chain p residue 272 VAL Chi-restraints excluded: chain p residue 289 ILE Chi-restraints excluded: chain p residue 373 LEU Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 678 THR Chi-restraints excluded: chain p residue 706 VAL Chi-restraints excluded: chain p residue 717 ASN Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 796 MET Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1116 VAL Chi-restraints excluded: chain p residue 1161 GLU Chi-restraints excluded: chain q residue 15 THR Chi-restraints excluded: chain q residue 66 HIS Chi-restraints excluded: chain q residue 80 ASP Chi-restraints excluded: chain q residue 223 ASN Chi-restraints excluded: chain r residue 62 MET Chi-restraints excluded: chain s residue 120 ASP Chi-restraints excluded: chain s residue 168 ASN Chi-restraints excluded: chain s residue 173 ILE Chi-restraints excluded: chain t residue 58 THR Chi-restraints excluded: chain t residue 68 THR Chi-restraints excluded: chain v residue 41 LEU Chi-restraints excluded: chain w residue 32 ASN Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 95 VAL Chi-restraints excluded: chain x residue 7 CYS Chi-restraints excluded: chain x residue 30 THR Chi-restraints excluded: chain x residue 33 ASP Chi-restraints excluded: chain x residue 44 CYS Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain y residue 91 ILE Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 51 ILE Chi-restraints excluded: chain u residue 122 ASN Chi-restraints excluded: chain u residue 131 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 907 optimal weight: 0.7980 chunk 690 optimal weight: 0.5980 chunk 476 optimal weight: 0.2980 chunk 101 optimal weight: 0.2980 chunk 438 optimal weight: 0.2980 chunk 616 optimal weight: 10.0000 chunk 922 optimal weight: 2.9990 chunk 976 optimal weight: 0.9980 chunk 481 optimal weight: 50.0000 chunk 873 optimal weight: 9.9990 chunk 263 optimal weight: 7.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 GLN ** F 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 HIS H 157 HIS H 182 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 210 ASN c 43 GLN c 85 HIS e 254 ASN f 385 HIS i 38 GLN ** o 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 493 ASN ** o 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1005 HIS o1042 ASN o1077 ASN o1248 ASN o1462 GLN ** p 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p1120 ASN ** r 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 87 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3288 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 86292 Z= 0.152 Angle : 0.586 11.961 117258 Z= 0.301 Chirality : 0.042 0.274 13082 Planarity : 0.004 0.060 14642 Dihedral : 13.345 116.093 12650 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.67 % Favored : 95.16 % Rotamer: Outliers : 2.09 % Allowed : 15.40 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.08), residues: 10028 helix: 0.12 (0.08), residues: 4028 sheet: -0.53 (0.14), residues: 1319 loop : -1.66 (0.09), residues: 4681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP e 612 HIS 0.007 0.001 HIS E 246 PHE 0.023 0.001 PHE O 81 TYR 0.017 0.001 TYR j 216 ARG 0.010 0.000 ARG o 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20056 Ramachandran restraints generated. 10028 Oldfield, 0 Emsley, 10028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20056 Ramachandran restraints generated. 10028 Oldfield, 0 Emsley, 10028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 9048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 390 time to evaluate : 9.030 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 511 LEU cc_start: -0.0388 (OUTLIER) cc_final: -0.1883 (mp) REVERT: A 607 MET cc_start: -0.1921 (ptp) cc_final: -0.4758 (mmt) REVERT: A 691 MET cc_start: 0.0596 (mpp) cc_final: 0.0297 (mpp) REVERT: A 757 MET cc_start: -0.2692 (mmm) cc_final: -0.3306 (ttp) REVERT: E 528 MET cc_start: 0.2176 (tpp) cc_final: 0.1305 (mmm) REVERT: E 747 LEU cc_start: -0.1026 (OUTLIER) cc_final: -0.1245 (mm) REVERT: F 290 MET cc_start: 0.3392 (mtt) cc_final: 0.3073 (tmm) REVERT: F 361 LYS cc_start: 0.3934 (OUTLIER) cc_final: 0.3066 (tptt) REVERT: G 74 MET cc_start: 0.0782 (OUTLIER) cc_final: 0.0118 (mpp) REVERT: H 166 ARG cc_start: 0.0564 (tpt170) cc_final: -0.0166 (ppt170) REVERT: H 182 GLN cc_start: 0.2169 (OUTLIER) cc_final: 0.0413 (tm130) REVERT: I 39 MET cc_start: 0.1278 (mtm) cc_final: 0.0723 (mmp) REVERT: J 197 MET cc_start: -0.1433 (mmm) cc_final: -0.2211 (mtt) REVERT: U 76 MET cc_start: 0.1649 (mtp) cc_final: 0.0546 (ppp) REVERT: V 228 MET cc_start: 0.1681 (mtm) cc_final: 0.0138 (tpt) REVERT: c 24 ASP cc_start: 0.1906 (OUTLIER) cc_final: 0.0836 (m-30) REVERT: e 205 TYR cc_start: 0.2580 (OUTLIER) cc_final: 0.0883 (m-10) REVERT: e 291 MET cc_start: 0.0138 (mtt) cc_final: -0.1639 (tpp) REVERT: f 421 ASP cc_start: 0.3321 (OUTLIER) cc_final: 0.2989 (t70) REVERT: m 39 MET cc_start: -0.1361 (tpp) cc_final: -0.2242 (tpt) REVERT: m 68 MET cc_start: 0.3521 (OUTLIER) cc_final: 0.3206 (mmp) REVERT: o 524 MET cc_start: 0.7153 (mmm) cc_final: 0.6665 (mtt) REVERT: o 872 MET cc_start: 0.7484 (ppp) cc_final: 0.6953 (ttp) REVERT: o 1102 MET cc_start: -0.1707 (tpt) cc_final: -0.2598 (mtt) REVERT: p 550 MET cc_start: 0.7588 (tmm) cc_final: 0.7326 (tmm) REVERT: p 594 MET cc_start: 0.8298 (mmp) cc_final: 0.7817 (mmm) REVERT: p 603 MET cc_start: 0.7212 (pmm) cc_final: 0.6752 (ptt) REVERT: q 15 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7546 (p) REVERT: s 94 MET cc_start: 0.8454 (mmp) cc_final: 0.7845 (mmp) REVERT: u 51 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8441 (mp) REVERT: u 104 MET cc_start: 0.3500 (mpp) cc_final: 0.2913 (mtt) REVERT: u 131 MET cc_start: 0.2467 (OUTLIER) cc_final: 0.1429 (mmt) outliers start: 187 outliers final: 101 residues processed: 554 average time/residue: 0.7320 time to fit residues: 726.3991 Evaluate side-chains 478 residues out of total 9048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 365 time to evaluate : 7.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 804 ARG Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 970 ASN Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1026 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain D residue 1066 CYS Chi-restraints excluded: chain E residue 747 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 361 LYS Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 182 GLN Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain O residue 23 ILE Chi-restraints excluded: chain O residue 29 THR Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 320 VAL Chi-restraints excluded: chain Q residue 333 ASN Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 189 LYS Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 248 ARG Chi-restraints excluded: chain S residue 147 THR Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 155 THR Chi-restraints excluded: chain U residue 168 MET Chi-restraints excluded: chain U residue 176 LEU Chi-restraints excluded: chain U residue 191 LEU Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain V residue 175 LEU Chi-restraints excluded: chain c residue 24 ASP Chi-restraints excluded: chain c residue 106 VAL Chi-restraints excluded: chain d residue 967 MET Chi-restraints excluded: chain e residue 205 TYR Chi-restraints excluded: chain e residue 296 THR Chi-restraints excluded: chain e residue 378 LYS Chi-restraints excluded: chain e residue 663 ARG Chi-restraints excluded: chain f residue 323 VAL Chi-restraints excluded: chain f residue 356 THR Chi-restraints excluded: chain f residue 421 ASP Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain l residue 145 THR Chi-restraints excluded: chain m residue 68 MET Chi-restraints excluded: chain o residue 95 PHE Chi-restraints excluded: chain o residue 100 LEU Chi-restraints excluded: chain o residue 220 ARG Chi-restraints excluded: chain o residue 222 HIS Chi-restraints excluded: chain o residue 264 VAL Chi-restraints excluded: chain o residue 265 VAL Chi-restraints excluded: chain o residue 750 ASP Chi-restraints excluded: chain o residue 779 ILE Chi-restraints excluded: chain o residue 793 VAL Chi-restraints excluded: chain o residue 864 LEU Chi-restraints excluded: chain o residue 875 TYR Chi-restraints excluded: chain o residue 930 LEU Chi-restraints excluded: chain o residue 1095 LEU Chi-restraints excluded: chain o residue 1106 THR Chi-restraints excluded: chain o residue 1127 LEU Chi-restraints excluded: chain o residue 1472 ASP Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 205 VAL Chi-restraints excluded: chain p residue 225 LEU Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 262 TYR Chi-restraints excluded: chain p residue 272 VAL Chi-restraints excluded: chain p residue 289 ILE Chi-restraints excluded: chain p residue 373 LEU Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 474 THR Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 677 MET Chi-restraints excluded: chain p residue 698 ILE Chi-restraints excluded: chain p residue 706 VAL Chi-restraints excluded: chain p residue 717 ASN Chi-restraints excluded: chain p residue 752 TYR Chi-restraints excluded: chain p residue 1116 VAL Chi-restraints excluded: chain p residue 1161 GLU Chi-restraints excluded: chain q residue 15 THR Chi-restraints excluded: chain r residue 62 MET Chi-restraints excluded: chain r residue 87 LEU Chi-restraints excluded: chain s residue 168 ASN Chi-restraints excluded: chain s residue 173 ILE Chi-restraints excluded: chain t residue 53 THR Chi-restraints excluded: chain v residue 41 LEU Chi-restraints excluded: chain x residue 47 ARG Chi-restraints excluded: chain u residue 51 ILE Chi-restraints excluded: chain u residue 131 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 813 optimal weight: 1.9990 chunk 554 optimal weight: 0.0770 chunk 14 optimal weight: 9.9990 chunk 726 optimal weight: 10.0000 chunk 402 optimal weight: 50.0000 chunk 833 optimal weight: 8.9990 chunk 674 optimal weight: 3.9990 chunk 1 optimal weight: 40.0000 chunk 498 optimal weight: 20.0000 chunk 876 optimal weight: 0.9990 chunk 246 optimal weight: 40.0000 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 182 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 85 HIS l 148 HIS o 222 HIS ** o 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 711 GLN ** o 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3363 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 86292 Z= 0.226 Angle : 0.598 13.078 117258 Z= 0.306 Chirality : 0.042 0.428 13082 Planarity : 0.004 0.060 14642 Dihedral : 13.258 114.952 12644 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.37 % Favored : 94.46 % Rotamer: Outliers : 2.54 % Allowed : 15.55 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: -0.95 (0.08), residues: 10028 helix: 0.37 (0.08), residues: 4016 sheet: -0.44 (0.14), residues: 1312 loop : -1.57 (0.09), residues: 4700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP E 612 HIS 0.015 0.001 HIS E 616 PHE 0.062 0.001 PHE D 947 TYR 0.019 0.001 TYR j 216 ARG 0.005 0.000 ARG p 385 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20056 Ramachandran restraints generated. 10028 Oldfield, 0 Emsley, 10028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20056 Ramachandran restraints generated. 10028 Oldfield, 0 Emsley, 10028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 9048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 367 time to evaluate : 7.758 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 511 LEU cc_start: -0.0034 (OUTLIER) cc_final: -0.1616 (mp) REVERT: A 607 MET cc_start: -0.1936 (ptp) cc_final: -0.4692 (mmt) REVERT: A 649 MET cc_start: -0.1057 (ppp) cc_final: -0.3254 (ptp) REVERT: A 691 MET cc_start: 0.0449 (mpp) cc_final: 0.0163 (mpp) REVERT: A 696 MET cc_start: 0.4402 (tmm) cc_final: 0.4068 (tmm) REVERT: A 757 MET cc_start: -0.2572 (mmm) cc_final: -0.3347 (ttp) REVERT: E 528 MET cc_start: 0.2283 (tpp) cc_final: 0.1698 (mmm) REVERT: E 747 LEU cc_start: -0.1253 (OUTLIER) cc_final: -0.1464 (mm) REVERT: F 361 LYS cc_start: 0.3807 (OUTLIER) cc_final: 0.2950 (tptt) REVERT: H 166 ARG cc_start: 0.0684 (tpt170) cc_final: -0.0156 (ppt170) REVERT: I 39 MET cc_start: 0.1592 (mtm) cc_final: 0.0788 (mmp) REVERT: J 197 MET cc_start: -0.1403 (mmm) cc_final: -0.2204 (mtt) REVERT: U 76 MET cc_start: 0.1677 (mtp) cc_final: 0.0552 (ppp) REVERT: V 228 MET cc_start: 0.0943 (mtm) cc_final: -0.0566 (tpt) REVERT: c 24 ASP cc_start: 0.2547 (OUTLIER) cc_final: 0.1438 (m-30) REVERT: e 205 TYR cc_start: 0.2430 (OUTLIER) cc_final: 0.0763 (m-10) REVERT: f 421 ASP cc_start: 0.3604 (OUTLIER) cc_final: 0.3088 (t70) REVERT: i 78 ARG cc_start: 0.2380 (OUTLIER) cc_final: 0.1469 (ptm160) REVERT: m 39 MET cc_start: -0.1197 (tpp) cc_final: -0.2479 (tpt) REVERT: m 73 MET cc_start: 0.2520 (OUTLIER) cc_final: 0.2232 (ttm) REVERT: o 496 PHE cc_start: 0.7323 (m-80) cc_final: 0.6914 (m-80) REVERT: o 524 MET cc_start: 0.7204 (mmm) cc_final: 0.6733 (mtt) REVERT: o 1102 MET cc_start: -0.1933 (tpt) cc_final: -0.2293 (ptt) REVERT: o 1296 MET cc_start: 0.5223 (ppp) cc_final: 0.4420 (pmm) REVERT: p 297 MET cc_start: 0.9109 (mmm) cc_final: 0.8832 (mmm) REVERT: p 550 MET cc_start: 0.7588 (tmm) cc_final: 0.7281 (tmm) REVERT: p 594 MET cc_start: 0.8399 (mmp) cc_final: 0.8001 (mmm) REVERT: q 15 THR cc_start: 0.8200 (OUTLIER) cc_final: 0.7637 (p) REVERT: r 110 GLU cc_start: -0.0302 (OUTLIER) cc_final: -0.0855 (mt-10) REVERT: s 94 MET cc_start: 0.8598 (mmp) cc_final: 0.7987 (mmp) REVERT: s 130 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8134 (m-80) REVERT: u 51 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8514 (mp) REVERT: u 104 MET cc_start: 0.3518 (mpp) cc_final: 0.3110 (mtt) outliers start: 227 outliers final: 130 residues processed: 563 average time/residue: 0.7426 time to fit residues: 745.1426 Evaluate side-chains 501 residues out of total 9048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 359 time to evaluate : 7.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 637 GLN Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 804 ARG Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 970 ASN Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1026 ILE Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain D residue 1066 CYS Chi-restraints excluded: chain E residue 519 GLU Chi-restraints excluded: chain E residue 747 LEU Chi-restraints excluded: chain E residue 761 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 361 LYS Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 23 ILE Chi-restraints excluded: chain O residue 29 THR Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 320 VAL Chi-restraints excluded: chain Q residue 336 VAL Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 189 LYS Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 248 ARG Chi-restraints excluded: chain R residue 249 SER Chi-restraints excluded: chain S residue 147 THR Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 168 MET Chi-restraints excluded: chain U residue 176 LEU Chi-restraints excluded: chain U residue 191 LEU Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain V residue 175 LEU Chi-restraints excluded: chain c residue 24 ASP Chi-restraints excluded: chain c residue 106 VAL Chi-restraints excluded: chain d residue 967 MET Chi-restraints excluded: chain e residue 205 TYR Chi-restraints excluded: chain e residue 296 THR Chi-restraints excluded: chain e residue 378 LYS Chi-restraints excluded: chain e residue 663 ARG Chi-restraints excluded: chain f residue 323 VAL Chi-restraints excluded: chain f residue 356 THR Chi-restraints excluded: chain f residue 421 ASP Chi-restraints excluded: chain i residue 78 ARG Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain l residue 145 THR Chi-restraints excluded: chain l residue 148 HIS Chi-restraints excluded: chain m residue 68 MET Chi-restraints excluded: chain m residue 73 MET Chi-restraints excluded: chain o residue 100 LEU Chi-restraints excluded: chain o residue 220 ARG Chi-restraints excluded: chain o residue 222 HIS Chi-restraints excluded: chain o residue 264 VAL Chi-restraints excluded: chain o residue 322 LEU Chi-restraints excluded: chain o residue 434 LYS Chi-restraints excluded: chain o residue 556 GLU Chi-restraints excluded: chain o residue 607 SER Chi-restraints excluded: chain o residue 732 THR Chi-restraints excluded: chain o residue 750 ASP Chi-restraints excluded: chain o residue 793 VAL Chi-restraints excluded: chain o residue 864 LEU Chi-restraints excluded: chain o residue 875 TYR Chi-restraints excluded: chain o residue 1038 THR Chi-restraints excluded: chain o residue 1095 LEU Chi-restraints excluded: chain o residue 1127 LEU Chi-restraints excluded: chain o residue 1472 ASP Chi-restraints excluded: chain p residue 20 ASP Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 168 ASP Chi-restraints excluded: chain p residue 205 VAL Chi-restraints excluded: chain p residue 225 LEU Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 260 LEU Chi-restraints excluded: chain p residue 262 TYR Chi-restraints excluded: chain p residue 272 VAL Chi-restraints excluded: chain p residue 289 ILE Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 373 LEU Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 474 THR Chi-restraints excluded: chain p residue 478 THR Chi-restraints excluded: chain p residue 686 GLU Chi-restraints excluded: chain p residue 698 ILE Chi-restraints excluded: chain p residue 706 VAL Chi-restraints excluded: chain p residue 717 ASN Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 796 MET Chi-restraints excluded: chain p residue 1057 ASP Chi-restraints excluded: chain p residue 1116 VAL Chi-restraints excluded: chain p residue 1161 GLU Chi-restraints excluded: chain q residue 15 THR Chi-restraints excluded: chain q residue 61 ASP Chi-restraints excluded: chain q residue 212 ASP Chi-restraints excluded: chain q residue 223 ASN Chi-restraints excluded: chain r residue 62 MET Chi-restraints excluded: chain r residue 110 GLU Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 120 ASP Chi-restraints excluded: chain s residue 130 PHE Chi-restraints excluded: chain s residue 168 ASN Chi-restraints excluded: chain s residue 173 ILE Chi-restraints excluded: chain t residue 58 THR Chi-restraints excluded: chain t residue 80 MET Chi-restraints excluded: chain v residue 41 LEU Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain w residue 95 VAL Chi-restraints excluded: chain x residue 44 CYS Chi-restraints excluded: chain x residue 47 ARG Chi-restraints excluded: chain u residue 51 ILE Chi-restraints excluded: chain u residue 122 ASN Chi-restraints excluded: chain u residue 131 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 328 optimal weight: 9.9990 chunk 879 optimal weight: 20.0000 chunk 192 optimal weight: 40.0000 chunk 573 optimal weight: 40.0000 chunk 241 optimal weight: 7.9990 chunk 977 optimal weight: 0.9980 chunk 811 optimal weight: 8.9990 chunk 452 optimal weight: 50.0000 chunk 81 optimal weight: 30.0000 chunk 323 optimal weight: 8.9990 chunk 513 optimal weight: 0.9980 overall best weight: 5.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 925 ASN ** D1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 ASN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 ASN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 359 ASN U 65 ASN c 85 HIS ** e 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 343 HIS f 349 ASN j 168 ASN k 205 HIS l 148 HIS o 222 HIS ** o 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 493 ASN ** o 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1332 GLN ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 287 HIS p 631 GLN ** p 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3445 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 86292 Z= 0.325 Angle : 0.667 15.369 117258 Z= 0.340 Chirality : 0.043 0.299 13082 Planarity : 0.004 0.065 14642 Dihedral : 13.372 116.889 12644 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.89 % Favored : 93.95 % Rotamer: Outliers : 2.80 % Allowed : 16.29 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: -0.94 (0.08), residues: 10028 helix: 0.39 (0.08), residues: 4037 sheet: -0.45 (0.14), residues: 1313 loop : -1.58 (0.09), residues: 4678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 612 HIS 0.024 0.001 HIS o 222 PHE 0.033 0.002 PHE D 947 TYR 0.028 0.001 TYR o1482 ARG 0.013 0.001 ARG R 132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20056 Ramachandran restraints generated. 10028 Oldfield, 0 Emsley, 10028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20056 Ramachandran restraints generated. 10028 Oldfield, 0 Emsley, 10028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 9048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 357 time to evaluate : 7.505 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 511 LEU cc_start: -0.0003 (OUTLIER) cc_final: -0.1459 (mp) REVERT: A 607 MET cc_start: -0.1672 (ptp) cc_final: -0.4344 (mmt) REVERT: A 649 MET cc_start: -0.1119 (ppp) cc_final: -0.3258 (ptp) REVERT: A 665 MET cc_start: -0.0197 (ptm) cc_final: -0.0480 (ptt) REVERT: A 691 MET cc_start: 0.0297 (mpp) cc_final: 0.0016 (mpp) REVERT: A 696 MET cc_start: 0.4698 (tmm) cc_final: 0.4381 (tmm) REVERT: A 757 MET cc_start: -0.2280 (mmm) cc_final: -0.3230 (ttp) REVERT: B 322 MET cc_start: 0.2017 (tmm) cc_final: 0.1526 (tmm) REVERT: B 496 MET cc_start: 0.0786 (OUTLIER) cc_final: 0.0361 (ptm) REVERT: B 757 MET cc_start: 0.5340 (mpp) cc_final: 0.3414 (mpp) REVERT: E 519 GLU cc_start: 0.2595 (OUTLIER) cc_final: 0.1533 (mm-30) REVERT: E 528 MET cc_start: 0.2326 (tpp) cc_final: 0.1714 (mmm) REVERT: F 361 LYS cc_start: 0.3851 (OUTLIER) cc_final: 0.2929 (tptt) REVERT: H 166 ARG cc_start: 0.0829 (tpt170) cc_final: -0.0095 (ppt170) REVERT: J 197 MET cc_start: -0.1655 (mmm) cc_final: -0.1982 (mtt) REVERT: U 76 MET cc_start: 0.2129 (mtp) cc_final: 0.0977 (ppp) REVERT: V 85 MET cc_start: 0.0749 (ptm) cc_final: 0.0304 (ptp) REVERT: V 228 MET cc_start: 0.0763 (mtm) cc_final: -0.0968 (tpt) REVERT: e 205 TYR cc_start: 0.2522 (OUTLIER) cc_final: 0.0670 (m-10) REVERT: e 291 MET cc_start: 0.0069 (mtt) cc_final: -0.1762 (tpp) REVERT: e 774 MET cc_start: 0.2056 (tpt) cc_final: 0.1157 (tpt) REVERT: f 421 ASP cc_start: 0.3363 (OUTLIER) cc_final: 0.2879 (t70) REVERT: i 78 ARG cc_start: 0.2384 (OUTLIER) cc_final: 0.1523 (ptm160) REVERT: m 39 MET cc_start: -0.1104 (tpp) cc_final: -0.1965 (tpt) REVERT: m 68 MET cc_start: 0.3563 (OUTLIER) cc_final: 0.3327 (mmp) REVERT: o 524 MET cc_start: 0.7364 (mmm) cc_final: 0.6705 (mtt) REVERT: o 546 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8311 (tmt170) REVERT: o 1102 MET cc_start: -0.1476 (tpt) cc_final: -0.2559 (mtt) REVERT: o 1296 MET cc_start: 0.5555 (ppp) cc_final: 0.4864 (ppp) REVERT: o 1451 MET cc_start: 0.7074 (ppp) cc_final: 0.6638 (ppp) REVERT: p 297 MET cc_start: 0.9166 (mmm) cc_final: 0.8871 (mmm) REVERT: p 594 MET cc_start: 0.8682 (mmp) cc_final: 0.8363 (mmm) REVERT: p 945 CYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7792 (t) REVERT: q 15 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.7771 (p) REVERT: r 110 GLU cc_start: -0.0221 (OUTLIER) cc_final: -0.0775 (mt-10) REVERT: s 94 MET cc_start: 0.8573 (mmp) cc_final: 0.7937 (mmp) REVERT: s 130 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8160 (m-80) REVERT: u 51 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8609 (mp) outliers start: 251 outliers final: 154 residues processed: 584 average time/residue: 0.7108 time to fit residues: 739.1042 Evaluate side-chains 513 residues out of total 9048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 345 time to evaluate : 7.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 565 TRP Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 804 ARG Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 970 ASN Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1026 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 726 MET Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain D residue 1066 CYS Chi-restraints excluded: chain E residue 519 GLU Chi-restraints excluded: chain E residue 761 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 361 LYS Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 23 ILE Chi-restraints excluded: chain O residue 29 THR Chi-restraints excluded: chain P residue 317 VAL Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain Q residue 336 VAL Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 171 GLU Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 189 LYS Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 248 ARG Chi-restraints excluded: chain R residue 249 SER Chi-restraints excluded: chain S residue 147 THR Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 155 THR Chi-restraints excluded: chain U residue 168 MET Chi-restraints excluded: chain U residue 176 LEU Chi-restraints excluded: chain U residue 191 LEU Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain V residue 154 LEU Chi-restraints excluded: chain V residue 175 LEU Chi-restraints excluded: chain c residue 24 ASP Chi-restraints excluded: chain c residue 106 VAL Chi-restraints excluded: chain d residue 967 MET Chi-restraints excluded: chain e residue 205 TYR Chi-restraints excluded: chain e residue 296 THR Chi-restraints excluded: chain e residue 491 ASP Chi-restraints excluded: chain e residue 663 ARG Chi-restraints excluded: chain e residue 696 TRP Chi-restraints excluded: chain f residue 323 VAL Chi-restraints excluded: chain f residue 346 THR Chi-restraints excluded: chain f residue 356 THR Chi-restraints excluded: chain f residue 421 ASP Chi-restraints excluded: chain i residue 78 ARG Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain l residue 145 THR Chi-restraints excluded: chain m residue 68 MET Chi-restraints excluded: chain o residue 95 PHE Chi-restraints excluded: chain o residue 220 ARG Chi-restraints excluded: chain o residue 322 LEU Chi-restraints excluded: chain o residue 434 LYS Chi-restraints excluded: chain o residue 436 SER Chi-restraints excluded: chain o residue 546 ARG Chi-restraints excluded: chain o residue 556 GLU Chi-restraints excluded: chain o residue 607 SER Chi-restraints excluded: chain o residue 732 THR Chi-restraints excluded: chain o residue 793 VAL Chi-restraints excluded: chain o residue 860 ILE Chi-restraints excluded: chain o residue 864 LEU Chi-restraints excluded: chain o residue 875 TYR Chi-restraints excluded: chain o residue 1038 THR Chi-restraints excluded: chain o residue 1095 LEU Chi-restraints excluded: chain o residue 1106 THR Chi-restraints excluded: chain o residue 1127 LEU Chi-restraints excluded: chain o residue 1386 ILE Chi-restraints excluded: chain o residue 1472 ASP Chi-restraints excluded: chain p residue 20 ASP Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 205 VAL Chi-restraints excluded: chain p residue 211 LYS Chi-restraints excluded: chain p residue 225 LEU Chi-restraints excluded: chain p residue 272 VAL Chi-restraints excluded: chain p residue 289 ILE Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 365 LEU Chi-restraints excluded: chain p residue 373 LEU Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 390 ASN Chi-restraints excluded: chain p residue 455 ASP Chi-restraints excluded: chain p residue 474 THR Chi-restraints excluded: chain p residue 478 THR Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 601 VAL Chi-restraints excluded: chain p residue 606 ASP Chi-restraints excluded: chain p residue 655 ASP Chi-restraints excluded: chain p residue 686 GLU Chi-restraints excluded: chain p residue 706 VAL Chi-restraints excluded: chain p residue 717 ASN Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 796 MET Chi-restraints excluded: chain p residue 945 CYS Chi-restraints excluded: chain p residue 964 ASP Chi-restraints excluded: chain p residue 983 GLU Chi-restraints excluded: chain p residue 1057 ASP Chi-restraints excluded: chain p residue 1116 VAL Chi-restraints excluded: chain q residue 15 THR Chi-restraints excluded: chain q residue 61 ASP Chi-restraints excluded: chain q residue 66 HIS Chi-restraints excluded: chain q residue 80 ASP Chi-restraints excluded: chain q residue 212 ASP Chi-restraints excluded: chain q residue 223 ASN Chi-restraints excluded: chain r residue 62 MET Chi-restraints excluded: chain r residue 87 LEU Chi-restraints excluded: chain r residue 107 THR Chi-restraints excluded: chain r residue 110 GLU Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 72 MET Chi-restraints excluded: chain s residue 120 ASP Chi-restraints excluded: chain s residue 130 PHE Chi-restraints excluded: chain s residue 168 ASN Chi-restraints excluded: chain s residue 173 ILE Chi-restraints excluded: chain t residue 53 THR Chi-restraints excluded: chain t residue 58 THR Chi-restraints excluded: chain t residue 68 THR Chi-restraints excluded: chain t residue 80 MET Chi-restraints excluded: chain v residue 41 LEU Chi-restraints excluded: chain w residue 32 ASN Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 95 VAL Chi-restraints excluded: chain x residue 7 CYS Chi-restraints excluded: chain x residue 29 TYR Chi-restraints excluded: chain x residue 44 CYS Chi-restraints excluded: chain x residue 47 ARG Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 51 ILE Chi-restraints excluded: chain u residue 122 ASN Chi-restraints excluded: chain u residue 131 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 942 optimal weight: 1.9990 chunk 110 optimal weight: 40.0000 chunk 556 optimal weight: 20.0000 chunk 713 optimal weight: 1.9990 chunk 552 optimal weight: 40.0000 chunk 822 optimal weight: 2.9990 chunk 545 optimal weight: 50.0000 chunk 973 optimal weight: 0.9980 chunk 609 optimal weight: 0.6980 chunk 593 optimal weight: 50.0000 chunk 449 optimal weight: 10.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 925 ASN ** D1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 ASN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 359 ASN c 85 HIS ** e 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 349 ASN ** i 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 173 HIS o 493 ASN ** o 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 287 HIS ** p 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 135 GLN ** s 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3384 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 86292 Z= 0.174 Angle : 0.579 14.229 117258 Z= 0.294 Chirality : 0.042 0.255 13082 Planarity : 0.004 0.063 14642 Dihedral : 13.265 116.638 12637 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.06 % Favored : 94.78 % Rotamer: Outliers : 2.04 % Allowed : 17.16 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: -0.66 (0.09), residues: 10028 helix: 0.64 (0.08), residues: 4033 sheet: -0.30 (0.15), residues: 1294 loop : -1.43 (0.09), residues: 4701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP e 612 HIS 0.006 0.001 HIS o 84 PHE 0.025 0.001 PHE T 96 TYR 0.023 0.001 TYR o1482 ARG 0.006 0.000 ARG p 385 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20056 Ramachandran restraints generated. 10028 Oldfield, 0 Emsley, 10028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20056 Ramachandran restraints generated. 10028 Oldfield, 0 Emsley, 10028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 9048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 355 time to evaluate : 7.588 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 511 LEU cc_start: 0.0006 (OUTLIER) cc_final: -0.1506 (mp) REVERT: A 607 MET cc_start: -0.1704 (ptp) cc_final: -0.4306 (mmt) REVERT: A 649 MET cc_start: -0.1325 (ppp) cc_final: -0.3376 (ptp) REVERT: A 691 MET cc_start: 0.0504 (mpp) cc_final: 0.0228 (mpp) REVERT: A 696 MET cc_start: 0.4545 (tmm) cc_final: 0.4279 (tmm) REVERT: A 757 MET cc_start: -0.2141 (mmm) cc_final: -0.3170 (ttp) REVERT: A 879 MET cc_start: -0.1807 (mtp) cc_final: -0.2415 (ptp) REVERT: B 322 MET cc_start: 0.2046 (tmm) cc_final: 0.1647 (tmm) REVERT: B 448 MET cc_start: 0.1570 (mmt) cc_final: 0.1306 (mmm) REVERT: E 519 GLU cc_start: 0.2597 (OUTLIER) cc_final: 0.1576 (mm-30) REVERT: E 528 MET cc_start: 0.2192 (tpp) cc_final: 0.1479 (mmm) REVERT: F 361 LYS cc_start: 0.3460 (OUTLIER) cc_final: 0.2610 (tptt) REVERT: H 166 ARG cc_start: 0.0680 (tpt170) cc_final: -0.0180 (ppt170) REVERT: J 197 MET cc_start: -0.1696 (mmm) cc_final: -0.2294 (mtt) REVERT: U 76 MET cc_start: 0.2060 (mtp) cc_final: 0.0890 (ppp) REVERT: U 110 MET cc_start: 0.0766 (ptt) cc_final: -0.1995 (tpt) REVERT: U 192 ARG cc_start: 0.0350 (OUTLIER) cc_final: -0.1180 (tpt170) REVERT: V 85 MET cc_start: 0.0875 (ptm) cc_final: 0.0359 (ptp) REVERT: V 228 MET cc_start: 0.0702 (mtm) cc_final: -0.1036 (tpt) REVERT: c 73 MET cc_start: 0.1370 (mpp) cc_final: 0.0970 (mtm) REVERT: e 205 TYR cc_start: 0.2452 (OUTLIER) cc_final: 0.0706 (m-10) REVERT: e 291 MET cc_start: 0.0009 (mtt) cc_final: -0.1776 (tpp) REVERT: e 774 MET cc_start: 0.2147 (tpt) cc_final: 0.1192 (tpt) REVERT: f 421 ASP cc_start: 0.3349 (OUTLIER) cc_final: 0.2954 (t70) REVERT: i 78 ARG cc_start: 0.2367 (OUTLIER) cc_final: 0.1392 (ptm160) REVERT: k 179 MET cc_start: 0.2374 (mmt) cc_final: -0.0667 (ptt) REVERT: m 39 MET cc_start: -0.1229 (tpp) cc_final: -0.1634 (tpp) REVERT: o 524 MET cc_start: 0.7253 (mmm) cc_final: 0.6746 (mtt) REVERT: o 872 MET cc_start: 0.7352 (ppp) cc_final: 0.6955 (ttp) REVERT: o 1102 MET cc_start: -0.1510 (tpt) cc_final: -0.2606 (ptt) REVERT: o 1296 MET cc_start: 0.5501 (ppp) cc_final: 0.4698 (pmm) REVERT: o 1451 MET cc_start: 0.6872 (ppp) cc_final: 0.6399 (ppp) REVERT: p 297 MET cc_start: 0.9162 (mmm) cc_final: 0.8902 (mmm) REVERT: p 529 MET cc_start: 0.8403 (mmm) cc_final: 0.8113 (mmp) REVERT: p 594 MET cc_start: 0.8400 (mmp) cc_final: 0.8109 (mmm) REVERT: q 15 THR cc_start: 0.8256 (OUTLIER) cc_final: 0.7777 (p) REVERT: r 110 GLU cc_start: -0.0152 (OUTLIER) cc_final: -0.0702 (mt-10) REVERT: r 125 GLU cc_start: 0.8541 (tp30) cc_final: 0.8086 (pp20) REVERT: s 94 MET cc_start: 0.8571 (mmp) cc_final: 0.7937 (mmp) REVERT: s 130 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8206 (m-80) REVERT: u 51 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8662 (mp) outliers start: 183 outliers final: 134 residues processed: 516 average time/residue: 0.7531 time to fit residues: 691.3782 Evaluate side-chains 491 residues out of total 9048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 346 time to evaluate : 7.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 565 TRP Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 804 ARG Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 970 ASN Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1026 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain D residue 925 ASN Chi-restraints excluded: chain D residue 1066 CYS Chi-restraints excluded: chain E residue 519 GLU Chi-restraints excluded: chain E residue 761 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 361 LYS Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 23 ILE Chi-restraints excluded: chain O residue 29 THR Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 336 VAL Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 189 LYS Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 248 ARG Chi-restraints excluded: chain R residue 249 SER Chi-restraints excluded: chain S residue 147 THR Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 151 THR Chi-restraints excluded: chain U residue 168 MET Chi-restraints excluded: chain U residue 176 LEU Chi-restraints excluded: chain U residue 191 LEU Chi-restraints excluded: chain U residue 192 ARG Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain V residue 175 LEU Chi-restraints excluded: chain c residue 24 ASP Chi-restraints excluded: chain c residue 106 VAL Chi-restraints excluded: chain d residue 967 MET Chi-restraints excluded: chain e residue 205 TYR Chi-restraints excluded: chain e residue 296 THR Chi-restraints excluded: chain e residue 574 THR Chi-restraints excluded: chain e residue 663 ARG Chi-restraints excluded: chain e residue 696 TRP Chi-restraints excluded: chain f residue 323 VAL Chi-restraints excluded: chain f residue 346 THR Chi-restraints excluded: chain f residue 356 THR Chi-restraints excluded: chain f residue 421 ASP Chi-restraints excluded: chain i residue 78 ARG Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain l residue 145 THR Chi-restraints excluded: chain l residue 148 HIS Chi-restraints excluded: chain o residue 95 PHE Chi-restraints excluded: chain o residue 100 LEU Chi-restraints excluded: chain o residue 198 LEU Chi-restraints excluded: chain o residue 322 LEU Chi-restraints excluded: chain o residue 434 LYS Chi-restraints excluded: chain o residue 436 SER Chi-restraints excluded: chain o residue 437 ASP Chi-restraints excluded: chain o residue 493 ASN Chi-restraints excluded: chain o residue 607 SER Chi-restraints excluded: chain o residue 691 ASP Chi-restraints excluded: chain o residue 793 VAL Chi-restraints excluded: chain o residue 806 THR Chi-restraints excluded: chain o residue 864 LEU Chi-restraints excluded: chain o residue 875 TYR Chi-restraints excluded: chain o residue 1095 LEU Chi-restraints excluded: chain o residue 1106 THR Chi-restraints excluded: chain o residue 1117 VAL Chi-restraints excluded: chain o residue 1127 LEU Chi-restraints excluded: chain o residue 1158 LEU Chi-restraints excluded: chain o residue 1432 PHE Chi-restraints excluded: chain o residue 1472 ASP Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 168 ASP Chi-restraints excluded: chain p residue 205 VAL Chi-restraints excluded: chain p residue 225 LEU Chi-restraints excluded: chain p residue 272 VAL Chi-restraints excluded: chain p residue 289 ILE Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 365 LEU Chi-restraints excluded: chain p residue 373 LEU Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 390 ASN Chi-restraints excluded: chain p residue 455 ASP Chi-restraints excluded: chain p residue 474 THR Chi-restraints excluded: chain p residue 478 THR Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 514 THR Chi-restraints excluded: chain p residue 518 HIS Chi-restraints excluded: chain p residue 601 VAL Chi-restraints excluded: chain p residue 686 GLU Chi-restraints excluded: chain p residue 698 ILE Chi-restraints excluded: chain p residue 706 VAL Chi-restraints excluded: chain p residue 717 ASN Chi-restraints excluded: chain p residue 752 TYR Chi-restraints excluded: chain p residue 1057 ASP Chi-restraints excluded: chain p residue 1116 VAL Chi-restraints excluded: chain q residue 15 THR Chi-restraints excluded: chain q residue 61 ASP Chi-restraints excluded: chain q residue 66 HIS Chi-restraints excluded: chain q residue 223 ASN Chi-restraints excluded: chain r residue 62 MET Chi-restraints excluded: chain r residue 87 LEU Chi-restraints excluded: chain r residue 107 THR Chi-restraints excluded: chain r residue 110 GLU Chi-restraints excluded: chain s residue 120 ASP Chi-restraints excluded: chain s residue 130 PHE Chi-restraints excluded: chain s residue 168 ASN Chi-restraints excluded: chain t residue 53 THR Chi-restraints excluded: chain t residue 80 MET Chi-restraints excluded: chain v residue 41 LEU Chi-restraints excluded: chain w residue 62 VAL Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain w residue 95 VAL Chi-restraints excluded: chain x residue 7 CYS Chi-restraints excluded: chain x residue 29 TYR Chi-restraints excluded: chain x residue 30 THR Chi-restraints excluded: chain x residue 47 ARG Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 51 ILE Chi-restraints excluded: chain u residue 131 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 602 optimal weight: 40.0000 chunk 388 optimal weight: 6.9990 chunk 581 optimal weight: 0.5980 chunk 293 optimal weight: 6.9990 chunk 191 optimal weight: 30.0000 chunk 188 optimal weight: 5.9990 chunk 618 optimal weight: 1.9990 chunk 663 optimal weight: 0.4980 chunk 481 optimal weight: 30.0000 chunk 90 optimal weight: 7.9990 chunk 765 optimal weight: 0.5980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 925 ASN ** D1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 ASN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 GLN P 279 GLN c 85 HIS e 254 ASN e 320 HIS ** i 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 168 ASN j 172 GLN j 173 HIS ** o 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1462 GLN ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 135 GLN ** s 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3384 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 86292 Z= 0.170 Angle : 0.581 15.208 117258 Z= 0.294 Chirality : 0.042 0.252 13082 Planarity : 0.004 0.075 14642 Dihedral : 13.184 115.307 12635 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.30 % Favored : 94.55 % Rotamer: Outliers : 2.12 % Allowed : 17.12 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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 (0.09), residues: 10028 helix: 0.76 (0.09), residues: 4049 sheet: -0.31 (0.14), residues: 1310 loop : -1.37 (0.09), residues: 4669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP e 612 HIS 0.005 0.001 HIS G 36 PHE 0.022 0.001 PHE D 947 TYR 0.022 0.001 TYR o1482 ARG 0.005 0.000 ARG z 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20056 Ramachandran restraints generated. 10028 Oldfield, 0 Emsley, 10028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20056 Ramachandran restraints generated. 10028 Oldfield, 0 Emsley, 10028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 9048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 358 time to evaluate : 7.764 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: A 511 LEU cc_start: -0.0549 (OUTLIER) cc_final: -0.2058 (mp) REVERT: A 607 MET cc_start: -0.1778 (ptp) cc_final: -0.4294 (mmt) REVERT: A 649 MET cc_start: -0.1360 (ppp) cc_final: -0.3395 (ptp) REVERT: A 691 MET cc_start: 0.0646 (mpp) cc_final: 0.0345 (mpp) REVERT: A 757 MET cc_start: -0.2312 (mmm) cc_final: -0.3241 (ttp) REVERT: A 943 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7267 (pttt) REVERT: B 322 MET cc_start: 0.2094 (tmm) cc_final: 0.1640 (tmm) REVERT: B 448 MET cc_start: 0.1375 (mmt) cc_final: 0.0939 (mmm) REVERT: E 519 GLU cc_start: 0.2689 (OUTLIER) cc_final: 0.1657 (mm-30) REVERT: E 528 MET cc_start: 0.2192 (tpp) cc_final: 0.1499 (mmm) REVERT: H 166 ARG cc_start: 0.0633 (tpt170) cc_final: -0.0198 (ppt170) REVERT: J 197 MET cc_start: -0.1664 (mmm) cc_final: -0.2296 (mtt) REVERT: U 76 MET cc_start: 0.2044 (mtp) cc_final: 0.0937 (ppp) REVERT: U 110 MET cc_start: 0.0828 (ptt) cc_final: -0.2020 (tpt) REVERT: U 192 ARG cc_start: 0.0336 (OUTLIER) cc_final: -0.1323 (tpt170) REVERT: V 85 MET cc_start: 0.0942 (ptm) cc_final: 0.0339 (ptp) REVERT: V 228 MET cc_start: 0.0775 (mtm) cc_final: -0.1045 (tpt) REVERT: c 73 MET cc_start: 0.1106 (mpp) cc_final: 0.0792 (mtm) REVERT: e 205 TYR cc_start: 0.2438 (OUTLIER) cc_final: 0.0692 (m-10) REVERT: e 291 MET cc_start: -0.0057 (mtt) cc_final: -0.1736 (tpp) REVERT: e 703 MET cc_start: -0.0662 (mtm) cc_final: -0.3824 (ptt) REVERT: e 774 MET cc_start: 0.2137 (tpt) cc_final: 0.1194 (tpt) REVERT: f 421 ASP cc_start: 0.3341 (OUTLIER) cc_final: 0.2987 (t70) REVERT: i 78 ARG cc_start: 0.2303 (OUTLIER) cc_final: 0.1350 (ptm160) REVERT: k 179 MET cc_start: 0.2435 (mmt) cc_final: -0.0744 (ptt) REVERT: m 39 MET cc_start: -0.1339 (tpp) cc_final: -0.1735 (tpp) REVERT: o 524 MET cc_start: 0.7253 (mmm) cc_final: 0.6754 (mtt) REVERT: o 872 MET cc_start: 0.7350 (ppp) cc_final: 0.6968 (ttp) REVERT: o 1049 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8715 (mt) REVERT: o 1102 MET cc_start: -0.1665 (tpt) cc_final: -0.2425 (ptt) REVERT: o 1296 MET cc_start: 0.5590 (ppp) cc_final: 0.4790 (pmm) REVERT: o 1451 MET cc_start: 0.7081 (ppp) cc_final: 0.6644 (ppp) REVERT: p 297 MET cc_start: 0.9129 (mmm) cc_final: 0.8916 (mmm) REVERT: p 529 MET cc_start: 0.8397 (mmm) cc_final: 0.8104 (mmp) REVERT: p 594 MET cc_start: 0.8355 (mmp) cc_final: 0.8068 (mmm) REVERT: q 15 THR cc_start: 0.8264 (OUTLIER) cc_final: 0.7797 (p) REVERT: r 110 GLU cc_start: 0.0213 (OUTLIER) cc_final: -0.0043 (tt0) REVERT: r 125 GLU cc_start: 0.8532 (tp30) cc_final: 0.8106 (pp20) REVERT: s 94 MET cc_start: 0.8604 (mmp) cc_final: 0.7964 (mmp) REVERT: s 130 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8203 (m-80) REVERT: u 51 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8694 (mp) outliers start: 190 outliers final: 146 residues processed: 524 average time/residue: 0.7345 time to fit residues: 686.5205 Evaluate side-chains 508 residues out of total 9048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 350 time to evaluate : 7.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 565 TRP Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 804 ARG Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 970 ASN Chi-restraints excluded: chain A residue 1026 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain D residue 925 ASN Chi-restraints excluded: chain D residue 1066 CYS Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 519 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 23 ILE Chi-restraints excluded: chain O residue 29 THR Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain P residue 279 GLN Chi-restraints excluded: chain P residue 317 VAL Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 333 ASN Chi-restraints excluded: chain Q residue 336 VAL Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 189 LYS Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 248 ARG Chi-restraints excluded: chain R residue 249 SER Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 151 THR Chi-restraints excluded: chain U residue 168 MET Chi-restraints excluded: chain U residue 176 LEU Chi-restraints excluded: chain U residue 191 LEU Chi-restraints excluded: chain U residue 192 ARG Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain V residue 154 LEU Chi-restraints excluded: chain V residue 175 LEU Chi-restraints excluded: chain c residue 24 ASP Chi-restraints excluded: chain c residue 106 VAL Chi-restraints excluded: chain d residue 967 MET Chi-restraints excluded: chain e residue 205 TYR Chi-restraints excluded: chain e residue 296 THR Chi-restraints excluded: chain e residue 574 THR Chi-restraints excluded: chain e residue 663 ARG Chi-restraints excluded: chain e residue 696 TRP Chi-restraints excluded: chain e residue 780 VAL Chi-restraints excluded: chain f residue 323 VAL Chi-restraints excluded: chain f residue 346 THR Chi-restraints excluded: chain f residue 356 THR Chi-restraints excluded: chain f residue 421 ASP Chi-restraints excluded: chain i residue 78 ARG Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain j residue 173 HIS Chi-restraints excluded: chain l residue 83 MET Chi-restraints excluded: chain l residue 145 THR Chi-restraints excluded: chain l residue 148 HIS Chi-restraints excluded: chain o residue 95 PHE Chi-restraints excluded: chain o residue 322 LEU Chi-restraints excluded: chain o residue 434 LYS Chi-restraints excluded: chain o residue 436 SER Chi-restraints excluded: chain o residue 607 SER Chi-restraints excluded: chain o residue 793 VAL Chi-restraints excluded: chain o residue 806 THR Chi-restraints excluded: chain o residue 860 ILE Chi-restraints excluded: chain o residue 864 LEU Chi-restraints excluded: chain o residue 875 TYR Chi-restraints excluded: chain o residue 1049 LEU Chi-restraints excluded: chain o residue 1095 LEU Chi-restraints excluded: chain o residue 1106 THR Chi-restraints excluded: chain o residue 1117 VAL Chi-restraints excluded: chain o residue 1127 LEU Chi-restraints excluded: chain o residue 1158 LEU Chi-restraints excluded: chain o residue 1432 PHE Chi-restraints excluded: chain o residue 1472 ASP Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 168 ASP Chi-restraints excluded: chain p residue 205 VAL Chi-restraints excluded: chain p residue 225 LEU Chi-restraints excluded: chain p residue 272 VAL Chi-restraints excluded: chain p residue 289 ILE Chi-restraints excluded: chain p residue 343 LEU Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 365 LEU Chi-restraints excluded: chain p residue 373 LEU Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 390 ASN Chi-restraints excluded: chain p residue 455 ASP Chi-restraints excluded: chain p residue 474 THR Chi-restraints excluded: chain p residue 478 THR Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 514 THR Chi-restraints excluded: chain p residue 518 HIS Chi-restraints excluded: chain p residue 606 ASP Chi-restraints excluded: chain p residue 698 ILE Chi-restraints excluded: chain p residue 706 VAL Chi-restraints excluded: chain p residue 717 ASN Chi-restraints excluded: chain p residue 752 TYR Chi-restraints excluded: chain p residue 964 ASP Chi-restraints excluded: chain p residue 983 GLU Chi-restraints excluded: chain p residue 1057 ASP Chi-restraints excluded: chain p residue 1116 VAL Chi-restraints excluded: chain q residue 15 THR Chi-restraints excluded: chain q residue 61 ASP Chi-restraints excluded: chain q residue 66 HIS Chi-restraints excluded: chain q residue 80 ASP Chi-restraints excluded: chain q residue 212 ASP Chi-restraints excluded: chain q residue 223 ASN Chi-restraints excluded: chain r residue 62 MET Chi-restraints excluded: chain r residue 107 THR Chi-restraints excluded: chain r residue 110 GLU Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 72 MET Chi-restraints excluded: chain s residue 120 ASP Chi-restraints excluded: chain s residue 130 PHE Chi-restraints excluded: chain s residue 168 ASN Chi-restraints excluded: chain s residue 173 ILE Chi-restraints excluded: chain t residue 53 THR Chi-restraints excluded: chain t residue 58 THR Chi-restraints excluded: chain t residue 80 MET Chi-restraints excluded: chain v residue 41 LEU Chi-restraints excluded: chain w residue 62 VAL Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 95 VAL Chi-restraints excluded: chain x residue 7 CYS Chi-restraints excluded: chain x residue 29 TYR Chi-restraints excluded: chain x residue 30 THR Chi-restraints excluded: chain x residue 44 CYS Chi-restraints excluded: chain x residue 47 ARG Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 51 ILE Chi-restraints excluded: chain u residue 131 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 885 optimal weight: 2.9990 chunk 932 optimal weight: 4.9990 chunk 850 optimal weight: 0.0980 chunk 907 optimal weight: 2.9990 chunk 546 optimal weight: 20.0000 chunk 395 optimal weight: 0.9980 chunk 712 optimal weight: 4.9990 chunk 278 optimal weight: 30.0000 chunk 819 optimal weight: 0.9990 chunk 857 optimal weight: 0.0030 chunk 903 optimal weight: 3.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 925 ASN ** D1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 GLN ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1146 GLN ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 135 GLN ** z 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3360 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 86292 Z= 0.146 Angle : 0.578 15.422 117258 Z= 0.291 Chirality : 0.042 0.283 13082 Planarity : 0.004 0.053 14642 Dihedral : 13.107 113.856 12635 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.85 % Favored : 95.00 % Rotamer: Outliers : 1.79 % Allowed : 17.61 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: -0.40 (0.09), residues: 10028 helix: 0.88 (0.09), residues: 4051 sheet: -0.28 (0.15), residues: 1305 loop : -1.28 (0.09), residues: 4672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP e 612 HIS 0.027 0.001 HIS j 173 PHE 0.025 0.001 PHE P 280 TYR 0.021 0.001 TYR o1482 ARG 0.010 0.000 ARG o 334 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20056 Ramachandran restraints generated. 10028 Oldfield, 0 Emsley, 10028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20056 Ramachandran restraints generated. 10028 Oldfield, 0 Emsley, 10028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 9048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 357 time to evaluate : 7.768 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: A 511 LEU cc_start: -0.0706 (OUTLIER) cc_final: -0.2197 (mp) REVERT: A 607 MET cc_start: -0.2204 (ptp) cc_final: -0.3913 (mmt) REVERT: A 649 MET cc_start: -0.1431 (ppp) cc_final: -0.3439 (ptp) REVERT: A 691 MET cc_start: 0.0483 (mpp) cc_final: -0.0053 (mtm) REVERT: A 757 MET cc_start: -0.2624 (mmm) cc_final: -0.3020 (tmm) REVERT: A 943 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7309 (pttt) REVERT: B 229 MET cc_start: 0.2750 (tpp) cc_final: 0.2389 (tpt) REVERT: B 322 MET cc_start: 0.2072 (tmm) cc_final: 0.1566 (tmm) REVERT: B 448 MET cc_start: 0.1257 (mmt) cc_final: 0.0945 (mmm) REVERT: E 519 GLU cc_start: 0.2561 (OUTLIER) cc_final: 0.1547 (mm-30) REVERT: E 528 MET cc_start: 0.2028 (tpp) cc_final: 0.1453 (mmm) REVERT: H 166 ARG cc_start: 0.0638 (tpt170) cc_final: -0.0199 (ppt170) REVERT: I 26 MET cc_start: 0.2985 (ttm) cc_final: 0.2424 (ptm) REVERT: J 197 MET cc_start: -0.1717 (mmm) cc_final: -0.2103 (mtt) REVERT: L 86 GLN cc_start: 0.2635 (OUTLIER) cc_final: 0.1722 (tt0) REVERT: U 76 MET cc_start: 0.2235 (mtp) cc_final: 0.1144 (ppp) REVERT: U 110 MET cc_start: 0.0817 (ptt) cc_final: -0.2027 (tpt) REVERT: U 192 ARG cc_start: 0.0300 (OUTLIER) cc_final: -0.1368 (tpt170) REVERT: V 85 MET cc_start: 0.0924 (ptm) cc_final: 0.0191 (ptp) REVERT: V 175 LEU cc_start: -0.2155 (OUTLIER) cc_final: -0.2811 (tt) REVERT: V 228 MET cc_start: 0.0712 (mtm) cc_final: -0.1032 (tpt) REVERT: c 73 MET cc_start: 0.1100 (mpp) cc_final: 0.0835 (mtm) REVERT: e 205 TYR cc_start: 0.2648 (OUTLIER) cc_final: 0.0390 (m-10) REVERT: e 703 MET cc_start: -0.0887 (mtm) cc_final: -0.3928 (ptt) REVERT: e 774 MET cc_start: 0.2105 (tpt) cc_final: 0.1151 (tpt) REVERT: f 421 ASP cc_start: 0.3342 (OUTLIER) cc_final: 0.2966 (t0) REVERT: i 78 ARG cc_start: 0.2218 (OUTLIER) cc_final: 0.1385 (ptm160) REVERT: j 173 HIS cc_start: -0.0650 (OUTLIER) cc_final: -0.0907 (t70) REVERT: k 179 MET cc_start: 0.2501 (mmt) cc_final: -0.0660 (ptt) REVERT: m 39 MET cc_start: -0.1348 (tpp) cc_final: -0.1711 (tpp) REVERT: o 524 MET cc_start: 0.7132 (mmm) cc_final: 0.6791 (mtt) REVERT: o 872 MET cc_start: 0.7314 (ppp) cc_final: 0.7027 (ttp) REVERT: o 1102 MET cc_start: -0.1915 (tpt) cc_final: -0.2425 (ptt) REVERT: o 1296 MET cc_start: 0.5627 (ppp) cc_final: 0.4743 (pmm) REVERT: o 1451 MET cc_start: 0.6895 (ppp) cc_final: 0.6602 (ppp) REVERT: p 594 MET cc_start: 0.8255 (mmp) cc_final: 0.7944 (mmm) REVERT: q 15 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7651 (p) REVERT: r 110 GLU cc_start: 0.0218 (OUTLIER) cc_final: -0.0048 (tt0) REVERT: r 125 GLU cc_start: 0.8497 (tp30) cc_final: 0.8090 (pp20) REVERT: s 94 MET cc_start: 0.8560 (mmp) cc_final: 0.7979 (mmp) REVERT: s 130 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8203 (m-80) REVERT: u 131 MET cc_start: 0.2500 (OUTLIER) cc_final: 0.1155 (mmt) outliers start: 160 outliers final: 118 residues processed: 494 average time/residue: 0.7578 time to fit residues: 666.8018 Evaluate side-chains 482 residues out of total 9048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 350 time to evaluate : 7.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 565 TRP Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 804 ARG Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 970 ASN Chi-restraints excluded: chain A residue 1026 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain D residue 1066 CYS Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 519 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 29 THR Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain P residue 279 GLN Chi-restraints excluded: chain P residue 295 MET Chi-restraints excluded: chain P residue 317 VAL Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 336 VAL Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 189 LYS Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 248 ARG Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 151 THR Chi-restraints excluded: chain U residue 168 MET Chi-restraints excluded: chain U residue 176 LEU Chi-restraints excluded: chain U residue 191 LEU Chi-restraints excluded: chain U residue 192 ARG Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain V residue 175 LEU Chi-restraints excluded: chain c residue 24 ASP Chi-restraints excluded: chain c residue 106 VAL Chi-restraints excluded: chain d residue 967 MET Chi-restraints excluded: chain e residue 205 TYR Chi-restraints excluded: chain e residue 296 THR Chi-restraints excluded: chain e residue 663 ARG Chi-restraints excluded: chain e residue 696 TRP Chi-restraints excluded: chain e residue 780 VAL Chi-restraints excluded: chain f residue 323 VAL Chi-restraints excluded: chain f residue 346 THR Chi-restraints excluded: chain f residue 421 ASP Chi-restraints excluded: chain i residue 78 ARG Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain j residue 173 HIS Chi-restraints excluded: chain l residue 83 MET Chi-restraints excluded: chain l residue 145 THR Chi-restraints excluded: chain l residue 148 HIS Chi-restraints excluded: chain o residue 322 LEU Chi-restraints excluded: chain o residue 434 LYS Chi-restraints excluded: chain o residue 436 SER Chi-restraints excluded: chain o residue 691 ASP Chi-restraints excluded: chain o residue 793 VAL Chi-restraints excluded: chain o residue 864 LEU Chi-restraints excluded: chain o residue 875 TYR Chi-restraints excluded: chain o residue 1095 LEU Chi-restraints excluded: chain o residue 1117 VAL Chi-restraints excluded: chain o residue 1127 LEU Chi-restraints excluded: chain o residue 1158 LEU Chi-restraints excluded: chain o residue 1432 PHE Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 168 ASP Chi-restraints excluded: chain p residue 205 VAL Chi-restraints excluded: chain p residue 225 LEU Chi-restraints excluded: chain p residue 289 ILE Chi-restraints excluded: chain p residue 343 LEU Chi-restraints excluded: chain p residue 365 LEU Chi-restraints excluded: chain p residue 373 LEU Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 390 ASN Chi-restraints excluded: chain p residue 455 ASP Chi-restraints excluded: chain p residue 474 THR Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 514 THR Chi-restraints excluded: chain p residue 698 ILE Chi-restraints excluded: chain p residue 706 VAL Chi-restraints excluded: chain p residue 717 ASN Chi-restraints excluded: chain p residue 752 TYR Chi-restraints excluded: chain p residue 964 ASP Chi-restraints excluded: chain p residue 1057 ASP Chi-restraints excluded: chain p residue 1116 VAL Chi-restraints excluded: chain q residue 15 THR Chi-restraints excluded: chain q residue 61 ASP Chi-restraints excluded: chain q residue 66 HIS Chi-restraints excluded: chain q residue 212 ASP Chi-restraints excluded: chain r residue 62 MET Chi-restraints excluded: chain r residue 110 GLU Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 72 MET Chi-restraints excluded: chain s residue 120 ASP Chi-restraints excluded: chain s residue 130 PHE Chi-restraints excluded: chain s residue 168 ASN Chi-restraints excluded: chain s residue 173 ILE Chi-restraints excluded: chain t residue 53 THR Chi-restraints excluded: chain t residue 58 THR Chi-restraints excluded: chain t residue 80 MET Chi-restraints excluded: chain v residue 41 LEU Chi-restraints excluded: chain w residue 62 VAL Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain w residue 95 VAL Chi-restraints excluded: chain x residue 44 CYS Chi-restraints excluded: chain x residue 47 ARG Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 131 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 595 optimal weight: 9.9990 chunk 959 optimal weight: 8.9990 chunk 585 optimal weight: 9.9990 chunk 455 optimal weight: 11.9990 chunk 666 optimal weight: 4.9990 chunk 1006 optimal weight: 9.9990 chunk 926 optimal weight: 9.9990 chunk 801 optimal weight: 4.9990 chunk 83 optimal weight: 50.0000 chunk 618 optimal weight: 8.9990 chunk 491 optimal weight: 40.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 ASN B 39 ASN B 279 HIS ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 GLN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 GLN ** B 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 882 HIS D 895 HIS ** D1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 GLN E 420 ASN F 275 ASN ** F 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 242 GLN P 279 GLN ** Q 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 177 ASN d1075 HIS f 349 ASN ** i 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 173 HIS ** l 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 432 HIS o 493 ASN ** o 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 790 GLN ** o1420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 287 HIS p 716 HIS ** p 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p1073 GLN p1129 ASN ** r 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3531 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.137 86292 Z= 0.431 Angle : 0.776 17.003 117258 Z= 0.393 Chirality : 0.045 0.246 13082 Planarity : 0.005 0.070 14642 Dihedral : 13.415 115.991 12632 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.47 % Favored : 93.37 % Rotamer: Outliers : 2.04 % Allowed : 17.59 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.20 % 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: -0.82 (0.08), residues: 10028 helix: 0.49 (0.08), residues: 4054 sheet: -0.45 (0.14), residues: 1288 loop : -1.50 (0.09), residues: 4686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP o1210 HIS 0.012 0.002 HIS p 695 PHE 0.041 0.002 PHE q 184 TYR 0.026 0.002 TYR p 811 ARG 0.011 0.001 ARG s 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20056 Ramachandran restraints generated. 10028 Oldfield, 0 Emsley, 10028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20056 Ramachandran restraints generated. 10028 Oldfield, 0 Emsley, 10028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 9048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 343 time to evaluate : 7.756 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: A 511 LEU cc_start: -0.0178 (OUTLIER) cc_final: -0.1636 (mp) REVERT: A 607 MET cc_start: -0.1953 (ptp) cc_final: -0.3926 (mmt) REVERT: A 649 MET cc_start: -0.1225 (ppp) cc_final: -0.3331 (ptp) REVERT: A 691 MET cc_start: 0.0136 (mpp) cc_final: -0.0145 (mpp) REVERT: A 692 MET cc_start: 0.1639 (tmm) cc_final: 0.1391 (tmm) REVERT: A 804 ARG cc_start: 0.4883 (OUTLIER) cc_final: 0.3345 (mmm160) REVERT: A 943 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7430 (pttm) REVERT: B 322 MET cc_start: 0.1800 (tmm) cc_final: 0.1384 (tmm) REVERT: B 448 MET cc_start: 0.1411 (mmt) cc_final: 0.1055 (mmm) REVERT: B 634 MET cc_start: 0.4675 (ttm) cc_final: 0.4443 (ttm) REVERT: E 442 MET cc_start: -0.0242 (mtt) cc_final: -0.0723 (mtt) REVERT: E 519 GLU cc_start: 0.2700 (OUTLIER) cc_final: 0.1674 (mm-30) REVERT: E 528 MET cc_start: 0.2024 (tpp) cc_final: 0.1514 (mmm) REVERT: F 361 LYS cc_start: 0.3471 (OUTLIER) cc_final: 0.2497 (tptt) REVERT: H 166 ARG cc_start: 0.0865 (tpt170) cc_final: -0.0061 (ppt170) REVERT: J 197 MET cc_start: -0.1565 (mmm) cc_final: -0.2106 (mtt) REVERT: U 76 MET cc_start: 0.2208 (mtp) cc_final: 0.1017 (ppp) REVERT: U 110 MET cc_start: 0.0904 (ptt) cc_final: -0.2039 (tpt) REVERT: U 192 ARG cc_start: 0.0358 (OUTLIER) cc_final: -0.1324 (tpt170) REVERT: V 85 MET cc_start: 0.1146 (ptm) cc_final: 0.0225 (ptp) REVERT: V 175 LEU cc_start: -0.1858 (OUTLIER) cc_final: -0.2560 (tt) REVERT: V 228 MET cc_start: 0.1219 (mtm) cc_final: -0.0637 (tpt) REVERT: e 205 TYR cc_start: 0.2302 (OUTLIER) cc_final: 0.0565 (m-10) REVERT: e 503 LYS cc_start: 0.0335 (OUTLIER) cc_final: -0.0209 (pttt) REVERT: e 774 MET cc_start: 0.2160 (tpt) cc_final: 0.1300 (tpt) REVERT: f 421 ASP cc_start: 0.3275 (OUTLIER) cc_final: 0.2888 (t0) REVERT: i 78 ARG cc_start: 0.1912 (OUTLIER) cc_final: 0.1088 (ptm160) REVERT: k 179 MET cc_start: 0.2228 (mmt) cc_final: -0.0918 (ptt) REVERT: o 329 MET cc_start: 0.6814 (mmp) cc_final: 0.6535 (mmp) REVERT: o 872 MET cc_start: 0.7417 (ppp) cc_final: 0.7030 (ttm) REVERT: o 1049 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8870 (mp) REVERT: o 1102 MET cc_start: -0.1340 (tpt) cc_final: -0.2559 (ptt) REVERT: o 1451 MET cc_start: 0.7362 (ppp) cc_final: 0.6969 (ppp) REVERT: q 15 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.7887 (p) REVERT: r 110 GLU cc_start: 0.0480 (OUTLIER) cc_final: 0.0207 (tt0) REVERT: s 94 MET cc_start: 0.8701 (mmp) cc_final: 0.8251 (mmp) REVERT: s 130 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8299 (m-80) outliers start: 183 outliers final: 141 residues processed: 500 average time/residue: 0.7578 time to fit residues: 676.3551 Evaluate side-chains 491 residues out of total 9048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 335 time to evaluate : 7.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 565 TRP Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 804 ARG Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 970 ASN Chi-restraints excluded: chain A residue 1026 ILE Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain D residue 1066 CYS Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 519 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 361 LYS Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 148 PHE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain H residue 132 LYS Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain P residue 279 GLN Chi-restraints excluded: chain P residue 295 MET Chi-restraints excluded: chain P residue 317 VAL Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 336 VAL Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 189 LYS Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 248 ARG Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 151 THR Chi-restraints excluded: chain U residue 168 MET Chi-restraints excluded: chain U residue 176 LEU Chi-restraints excluded: chain U residue 191 LEU Chi-restraints excluded: chain U residue 192 ARG Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain V residue 175 LEU Chi-restraints excluded: chain c residue 24 ASP Chi-restraints excluded: chain c residue 106 VAL Chi-restraints excluded: chain d residue 967 MET Chi-restraints excluded: chain e residue 205 TYR Chi-restraints excluded: chain e residue 296 THR Chi-restraints excluded: chain e residue 503 LYS Chi-restraints excluded: chain e residue 574 THR Chi-restraints excluded: chain e residue 663 ARG Chi-restraints excluded: chain e residue 696 TRP Chi-restraints excluded: chain e residue 780 VAL Chi-restraints excluded: chain f residue 323 VAL Chi-restraints excluded: chain f residue 346 THR Chi-restraints excluded: chain f residue 421 ASP Chi-restraints excluded: chain i residue 78 ARG Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain j residue 173 HIS Chi-restraints excluded: chain l residue 83 MET Chi-restraints excluded: chain l residue 145 THR Chi-restraints excluded: chain l residue 148 HIS Chi-restraints excluded: chain o residue 95 PHE Chi-restraints excluded: chain o residue 322 LEU Chi-restraints excluded: chain o residue 434 LYS Chi-restraints excluded: chain o residue 436 SER Chi-restraints excluded: chain o residue 487 SER Chi-restraints excluded: chain o residue 545 VAL Chi-restraints excluded: chain o residue 607 SER Chi-restraints excluded: chain o residue 732 THR Chi-restraints excluded: chain o residue 793 VAL Chi-restraints excluded: chain o residue 794 GLU Chi-restraints excluded: chain o residue 806 THR Chi-restraints excluded: chain o residue 860 ILE Chi-restraints excluded: chain o residue 864 LEU Chi-restraints excluded: chain o residue 875 TYR Chi-restraints excluded: chain o residue 1049 LEU Chi-restraints excluded: chain o residue 1095 LEU Chi-restraints excluded: chain o residue 1106 THR Chi-restraints excluded: chain o residue 1117 VAL Chi-restraints excluded: chain o residue 1127 LEU Chi-restraints excluded: chain o residue 1158 LEU Chi-restraints excluded: chain o residue 1432 PHE Chi-restraints excluded: chain p residue 168 ASP Chi-restraints excluded: chain p residue 205 VAL Chi-restraints excluded: chain p residue 225 LEU Chi-restraints excluded: chain p residue 272 VAL Chi-restraints excluded: chain p residue 289 ILE Chi-restraints excluded: chain p residue 343 LEU Chi-restraints excluded: chain p residue 365 LEU Chi-restraints excluded: chain p residue 373 LEU Chi-restraints excluded: chain p residue 390 ASN Chi-restraints excluded: chain p residue 455 ASP Chi-restraints excluded: chain p residue 474 THR Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 514 THR Chi-restraints excluded: chain p residue 518 HIS Chi-restraints excluded: chain p residue 606 ASP Chi-restraints excluded: chain p residue 677 MET Chi-restraints excluded: chain p residue 681 ASP Chi-restraints excluded: chain p residue 686 GLU Chi-restraints excluded: chain p residue 717 ASN Chi-restraints excluded: chain p residue 964 ASP Chi-restraints excluded: chain p residue 983 GLU Chi-restraints excluded: chain p residue 1057 ASP Chi-restraints excluded: chain p residue 1116 VAL Chi-restraints excluded: chain p residue 1159 PHE Chi-restraints excluded: chain p residue 1171 MET Chi-restraints excluded: chain q residue 15 THR Chi-restraints excluded: chain q residue 61 ASP Chi-restraints excluded: chain q residue 66 HIS Chi-restraints excluded: chain q residue 80 ASP Chi-restraints excluded: chain q residue 212 ASP Chi-restraints excluded: chain q residue 223 ASN Chi-restraints excluded: chain r residue 62 MET Chi-restraints excluded: chain r residue 110 GLU Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 72 MET Chi-restraints excluded: chain s residue 120 ASP Chi-restraints excluded: chain s residue 130 PHE Chi-restraints excluded: chain s residue 168 ASN Chi-restraints excluded: chain s residue 173 ILE Chi-restraints excluded: chain t residue 53 THR Chi-restraints excluded: chain t residue 58 THR Chi-restraints excluded: chain t residue 80 MET Chi-restraints excluded: chain v residue 41 LEU Chi-restraints excluded: chain w residue 62 VAL Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 95 VAL Chi-restraints excluded: chain x residue 7 CYS Chi-restraints excluded: chain x residue 29 TYR Chi-restraints excluded: chain x residue 30 THR Chi-restraints excluded: chain x residue 44 CYS Chi-restraints excluded: chain x residue 47 ARG Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 122 ASN Chi-restraints excluded: chain u residue 131 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 636 optimal weight: 7.9990 chunk 853 optimal weight: 0.9980 chunk 245 optimal weight: 40.0000 chunk 738 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 222 optimal weight: 0.9990 chunk 802 optimal weight: 0.9990 chunk 335 optimal weight: 0.7980 chunk 824 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 ASN ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 GLN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 GLN F 275 ASN ** F 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 287 HIS ** p 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p1073 GLN ** r 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.115585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.087615 restraints weight = 557939.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.085493 restraints weight = 403368.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.084938 restraints weight = 248845.984| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.5712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.352 86292 Z= 0.392 Angle : 0.823 59.136 117258 Z= 0.432 Chirality : 0.044 0.356 13082 Planarity : 0.006 0.189 14642 Dihedral : 13.418 116.038 12632 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.43 % Favored : 93.42 % Rotamer: Outliers : 1.96 % Allowed : 17.93 % Favored : 80.11 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.20 % 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: -0.85 (0.08), residues: 10028 helix: 0.47 (0.08), residues: 4054 sheet: -0.49 (0.14), residues: 1294 loop : -1.51 (0.09), residues: 4680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP o1210 HIS 0.302 0.002 HIS j 173 PHE 0.052 0.002 PHE O 67 TYR 0.023 0.002 TYR p 811 ARG 0.011 0.001 ARG s 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16840.13 seconds wall clock time: 304 minutes 23.68 seconds (18263.68 seconds total)