Starting phenix.real_space_refine on Mon Mar 18 10:47:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ega_31110/03_2024/7ega_31110.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ega_31110/03_2024/7ega_31110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ega_31110/03_2024/7ega_31110.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ega_31110/03_2024/7ega_31110.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ega_31110/03_2024/7ega_31110.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ega_31110/03_2024/7ega_31110.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 170 5.49 5 Mg 1 5.21 5 S 471 5.16 5 C 53753 2.51 5 N 14974 2.21 5 O 16318 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 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 997": "NH1" <-> "NH2" Residue "A ARG 1008": "NH1" <-> "NH2" Residue "A ARG 1030": "NH1" <-> "NH2" Residue "A ARG 1052": "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 ARG 933": "NH1" <-> "NH2" Residue "D GLU 935": "OE1" <-> "OE2" Residue "D ARG 941": "NH1" <-> "NH2" Residue "D GLU 948": "OE1" <-> "OE2" Residue "D ARG 957": "NH1" <-> "NH2" Residue "D GLU 962": "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 17": "OE1" <-> "OE2" Residue "F GLU 90": "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 315": "NH1" <-> "NH2" Residue "F ARG 320": "NH1" <-> "NH2" Residue "F ARG 330": "NH1" <-> "NH2" Residue "F ARG 335": "NH1" <-> "NH2" Residue "F ARG 373": "NH1" <-> "NH2" Residue "F GLU 382": "OE1" <-> "OE2" Residue "F ARG 395": "NH1" <-> "NH2" Residue "G GLU 13": "OE1" <-> "OE2" Residue "H ARG 113": "NH1" <-> "NH2" Residue "H ARG 183": "NH1" <-> "NH2" Residue "H ARG 184": "NH1" <-> "NH2" 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 ARG 239": "NH1" <-> "NH2" Residue "Q ARG 344": "NH1" <-> "NH2" 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 "T ARG 126": "NH1" <-> "NH2" Residue "T GLU 133": "OE1" <-> "OE2" Residue "T GLU 134": "OE1" <-> "OE2" Residue "T ARG 177": "NH1" <-> "NH2" Residue "U ARG 77": "NH1" <-> "NH2" Residue "U ARG 174": "NH1" <-> "NH2" Residue "U ARG 179": "NH1" <-> "NH2" Residue "U PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 185": "OE1" <-> "OE2" Residue "U ARG 192": "NH1" <-> "NH2" Residue "V GLU 172": "OE1" <-> "OE2" Residue "V GLU 230": "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 GLU 30": "OE1" <-> "OE2" Residue "o GLU 38": "OE1" <-> "OE2" Residue "o GLU 89": "OE1" <-> "OE2" Residue "o ARG 743": "NH1" <-> "NH2" Residue "o ARG 749": "NH1" <-> "NH2" Residue "o PHE 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 869": "OE1" <-> "OE2" Residue "o GLU 1097": "OE1" <-> "OE2" Residue "o GLU 1349": "OE1" <-> "OE2" 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 GLU 914": "OE1" <-> "OE2" 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 "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: 85697 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: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1366 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 161} 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: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1939 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 13, 'TRANS': 237} Chain breaks: 1 Chain: "S" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 872 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain breaks: 1 Chain: "T" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1788 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} 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: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1404 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 5, 'TRANS': 166} 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: {'PCIS': 1, 'PTRANS': 69, '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: "X" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1751 Classifications: {'DNA': 85} Link IDs: {'rna3p': 84} Chain: "Y" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1734 Classifications: {'DNA': 85} Link IDs: {'rna3p': 84} 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 29836 SG CYS R 15 207.265 192.843 197.377 1.00 0.00 S ATOM 29983 SG CYS R 34 204.811 194.281 199.467 1.00 0.00 S ATOM 35297 SG CYS U 129 223.804 165.737 195.611 1.00 0.00 S ATOM 35317 SG CYS U 132 220.445 166.504 194.234 1.00 0.00 S ATOM 35489 SG CYS U 154 223.373 168.274 192.867 1.00 0.00 S ATOM 35513 SG CYS U 157 222.295 169.105 196.262 1.00 0.00 S ATOM 51596 SG CYS o 71 205.165 172.951 184.908 1.00215.08 S ATOM 51665 SG CYS o 81 203.008 175.499 183.045 1.00201.81 S ATOM 51900 SG CYS o 111 194.906 143.168 146.388 1.00291.01 S ATOM 51928 SG CYS o 114 199.395 143.188 145.980 1.00287.14 S ATOM 52241 SG CYS o 154 196.922 142.997 143.045 1.00287.91 S ATOM 71072 SG CYS p1119 210.677 174.135 165.806 1.00179.27 S ATOM 71094 SG CYS p1122 208.293 171.676 165.527 1.00181.25 S ATOM 71209 SG CYS p1137 211.033 171.932 168.555 1.00194.80 S ATOM 71230 SG CYS p1140 210.917 169.352 165.453 1.00200.53 S ATOM 72209 SG CYS q 90 180.151 228.096 215.766 1.00126.45 S ATOM 72244 SG CYS q 94 178.120 229.861 217.828 1.00113.16 S ATOM 72266 SG CYS q 97 176.941 229.094 214.434 1.00107.06 S ATOM 78154 SG CYS w 17 118.681 140.074 147.866 1.00165.50 S ATOM 78178 SG CYS w 20 121.568 139.117 149.783 1.00166.36 S ATOM 78339 SG CYS w 39 123.048 139.707 146.350 1.00170.94 S ATOM 78364 SG CYS w 42 120.456 137.175 147.071 1.00174.09 S ATOM 78716 SG CYS w 86 102.167 183.160 151.810 1.00138.72 S ATOM 78740 SG CYS w 89 99.628 183.317 154.465 1.00141.27 S ATOM 78944 SG CYS w 114 103.229 183.529 155.751 1.00129.58 S ATOM 78979 SG CYS w 119 101.771 180.434 154.286 1.00136.89 S ATOM 79089 SG CYS x 7 150.200 224.176 196.121 1.00 65.12 S ATOM 79113 SG CYS x 10 149.970 228.768 194.791 1.00 73.64 S ATOM 79377 SG CYS x 44 148.468 226.137 193.399 1.00 74.53 S ATOM 79383 SG CYS x 45 147.394 226.921 196.688 1.00 74.88 S ATOM 80520 SG CYS z 19 157.610 187.027 221.367 1.00111.16 S ATOM 80539 SG CYS z 22 156.279 187.838 224.475 1.00114.66 S ATOM 80656 SG CYS z 36 158.967 185.602 224.477 1.00121.32 S Time building chain proxies: 34.67, per 1000 atoms: 0.40 Number of scatterers: 85697 At special positions: 0 Unit cell: (271.36, 273.48, 260.76, 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 471 16.00 P 170 15.00 Mg 1 11.99 O 16318 8.00 N 14974 7.00 C 53753 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: 26.51 Conformation dependent library (CDL) restraints added in 11.9 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 ZN R 401 " - pdb=" SG CYS R 15 " pdb=" ZN U 501 " pdb="ZN ZN U 501 " - pdb=" SG CYS U 132 " pdb="ZN ZN U 501 " - pdb=" SG CYS U 157 " pdb="ZN ZN U 501 " - pdb=" SG CYS U 129 " pdb="ZN ZN U 501 " - pdb=" SG CYS U 154 " pdb=" ZN o2001 " pdb="ZN ZN o2001 " - pdb=" NE2 HIS o 84 " pdb="ZN ZN o2001 " - pdb=" SG CYS o 71 " pdb="ZN ZN o2001 " - pdb=" SG CYS o 81 " pdb=" ZN o2002 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 114 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 154 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 111 " 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 : 30 20250 Ramachandran restraints generated. 10125 Oldfield, 0 Emsley, 10125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19528 Finding SS restraints... Secondary structure from input PDB file: 368 helices and 90 sheets defined 41.4% alpha, 14.4% beta 63 base pairs and 150 stacking pairs defined. Time for finding SS restraints: 22.92 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 472 through 478 Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 569 through 574 removed outlier: 3.637A 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 640 through 657 Processing helix chain 'A' and resid 667 through 672 removed outlier: 4.032A 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: 3.623A pdb=" N ILE A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU A 848 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 880 removed outlier: 3.855A 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 993 through 998 removed outlier: 3.695A pdb=" N ARG A 997 " --> pdb=" O ALA A 993 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 993 through 998' Processing helix chain 'A' and resid 1000 through 1010 removed outlier: 3.537A pdb=" N GLN A1005 " --> pdb=" O LYS A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1019 removed outlier: 3.527A pdb=" N ILE A1017 " --> pdb=" O PRO A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1035 Processing helix chain 'A' and resid 1055 through 1079 Processing helix chain 'A' and resid 1187 through 1204 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: 3.547A 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: 3.776A 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: 4.082A pdb=" N LEU B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL B 388 " --> pdb=" O LYS B 384 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N ASN B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU B 390 " --> pdb=" O PHE B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 441 removed outlier: 3.559A 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: 3.539A 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: 3.801A 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: 3.544A 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: 4.037A pdb=" N PHE B 700 " --> pdb=" O MET B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 728 removed outlier: 3.719A 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 823 through 843 removed outlier: 4.205A pdb=" N LEU B 828 " --> pdb=" O PRO B 824 " (cutoff:3.500A) removed outlier: 3.509A 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: 3.522A 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: 3.561A 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: 3.684A pdb=" N ARG D 880 " --> pdb=" O ALA D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 898 through 922 removed outlier: 3.636A pdb=" N SER D 903 " --> pdb=" O VAL D 899 " (cutoff:3.500A) removed outlier: 3.547A 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: 3.758A pdb=" N THR D 920 " --> pdb=" O LYS D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 940 through 969 Processing helix chain 'D' and resid 982 through 1011 removed outlier: 3.641A pdb=" N GLN D 994 " --> pdb=" O GLU D 990 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLU D 995 " --> pdb=" O MET D 991 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 1059 through 1066 removed outlier: 3.620A pdb=" N LEU D1063 " --> pdb=" O ASN D1059 " (cutoff:3.500A) removed outlier: 3.521A 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: 3.837A pdb=" N SER E 219 " --> pdb=" O GLU E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 237 removed outlier: 3.815A pdb=" N ALA E 234 " --> pdb=" O ASP E 230 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU E 235 " --> pdb=" O CYS E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 254 removed outlier: 3.696A 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: 3.888A 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: 4.057A pdb=" N VAL E 281 " --> pdb=" O ASP E 277 " (cutoff:3.500A) removed outlier: 3.686A 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: 3.709A 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: 3.535A 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: 3.608A pdb=" N MET E 442 " --> pdb=" O LEU E 438 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS E 445 " --> pdb=" O ILE E 441 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU E 446 " --> pdb=" O MET E 442 " (cutoff:3.500A) removed outlier: 3.887A 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: 3.662A pdb=" N ILE E 516 " --> pdb=" O ASP E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 527 removed outlier: 3.821A pdb=" N ILE E 527 " --> pdb=" O VAL E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 764 through 768 Processing helix chain 'F' and resid 15 through 25 removed outlier: 3.589A pdb=" N MET F 19 " --> pdb=" O PRO F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 60 removed outlier: 3.553A pdb=" N LEU F 39 " --> pdb=" O THR F 35 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR F 40 " --> pdb=" O CYS F 36 " (cutoff:3.500A) removed outlier: 3.869A 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: 3.892A pdb=" N LYS F 56 " --> pdb=" O GLN F 52 " (cutoff:3.500A) removed outlier: 3.990A 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: 3.875A 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: 4.353A 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 314 Proline residue: F 306 - end of helix removed outlier: 3.698A pdb=" N CYS F 311 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE F 312 " --> pdb=" O VAL F 308 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL F 313 " --> pdb=" O MET F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 344 removed outlier: 3.530A pdb=" N VAL F 337 " --> pdb=" O ALA F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 364 Processing helix chain 'F' and resid 369 through 382 Processing helix chain 'F' and resid 384 through 391 removed outlier: 4.249A pdb=" N ILE F 388 " --> pdb=" O GLY F 384 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS F 389 " --> pdb=" O HIS F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 394 No H-bonds generated for 'chain 'F' and resid 392 through 394' 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 removed outlier: 3.548A pdb=" N LEU F 438 " --> pdb=" O VAL F 434 " (cutoff:3.500A) 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 42 removed outlier: 3.680A pdb=" N ASP G 41 " --> pdb=" O VAL G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 176 Processing helix chain 'H' and resid 27 through 45 removed outlier: 4.761A 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: 3.517A pdb=" N LYS H 77 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 3.610A 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: 3.874A 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: 4.045A pdb=" N THR H 225 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 18 Processing helix chain 'I' and resid 18 through 26 Processing helix chain 'I' and resid 32 through 62 removed outlier: 4.131A pdb=" N ILE I 36 " --> pdb=" O GLU I 32 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN I 37 " --> pdb=" O PRO I 33 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP I 52 " --> pdb=" O THR I 48 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP I 53 " --> pdb=" O THR I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 77 removed outlier: 3.552A 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: 3.676A 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: 3.689A pdb=" N TYR J 137 " --> pdb=" O ALA J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 170 removed outlier: 3.625A pdb=" N ILE J 152 " --> pdb=" O ASP J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 176 removed outlier: 3.728A 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: 3.611A pdb=" N MET L 83 " --> pdb=" O ASP L 79 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL L 96 " --> pdb=" O ILE L 92 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA L 98 " --> pdb=" O SER L 94 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN L 101 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU L 102 " --> pdb=" O ALA L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 123 removed outlier: 3.949A pdb=" N VAL L 116 " --> pdb=" O GLU L 112 " (cutoff:3.500A) removed outlier: 3.533A 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: 3.791A pdb=" N ARG O 7 " --> pdb=" O GLN O 4 " (cutoff:3.500A) removed outlier: 4.256A 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 25 Processing helix chain 'O' and resid 31 through 52 removed outlier: 3.721A pdb=" N VAL O 52 " --> pdb=" O LEU O 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 187 removed outlier: 3.518A pdb=" N ILE P 183 " --> pdb=" O ASP P 179 " (cutoff:3.500A) Processing helix chain 'P' and resid 226 through 245 removed outlier: 3.559A pdb=" N VAL P 241 " --> pdb=" O TYR P 237 " (cutoff:3.500A) Processing helix chain 'P' and resid 269 through 277 removed outlier: 3.578A pdb=" N LEU P 273 " --> pdb=" O ARG P 269 " (cutoff:3.500A) Processing helix chain 'P' and resid 317 through 335 removed outlier: 4.034A pdb=" N ILE P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) removed outlier: 3.677A 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: 4.800A pdb=" N ASP Q 27 " --> pdb=" O ASN Q 23 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ILE Q 28 " --> pdb=" O ASP Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 35 through 54 removed outlier: 3.730A pdb=" N LEU Q 39 " --> pdb=" O ASP Q 35 " (cutoff:3.500A) removed outlier: 3.918A 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 112 through 127 Processing helix chain 'R' and resid 131 through 149 removed outlier: 3.528A pdb=" N VAL R 135 " --> pdb=" O PRO R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 171 Processing helix chain 'R' and resid 176 through 183 removed outlier: 3.512A 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: 3.845A pdb=" N SER R 216 " --> pdb=" O GLY R 212 " (cutoff:3.500A) removed outlier: 5.419A 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 279 Processing helix chain 'R' and resid 281 through 293 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 5 through 9 Processing helix chain 'S' and resid 38 through 42 Processing helix chain 'T' and resid 9 through 14 Processing helix chain 'T' and resid 25 through 32 Processing helix chain 'T' and resid 123 through 135 Processing helix chain 'T' and resid 158 through 171 removed outlier: 3.897A pdb=" N GLU T 171 " --> pdb=" O ARG T 167 " (cutoff:3.500A) Processing helix chain 'T' and resid 180 through 194 removed outlier: 4.247A pdb=" N LEU T 184 " --> pdb=" O LYS T 180 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS T 193 " --> pdb=" O SER T 189 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS T 194 " --> pdb=" O ALA T 190 " (cutoff:3.500A) Processing helix chain 'T' and resid 199 through 204 Processing helix chain 'T' and resid 209 through 220 Processing helix chain 'U' and resid 13 through 25 Processing helix chain 'U' and resid 27 through 37 removed outlier: 3.772A pdb=" N ALA U 33 " --> pdb=" O GLU U 29 " (cutoff:3.500A) removed outlier: 3.524A 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: 3.599A pdb=" N HIS U 109 " --> pdb=" O TYR U 105 " (cutoff:3.500A) Processing helix chain 'U' and resid 137 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 169 through 182 Processing helix chain 'U' and resid 185 through 203 removed outlier: 4.394A pdb=" N LEU U 190 " --> pdb=" O PRO U 186 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU U 191 " --> pdb=" O ILE U 187 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP U 196 " --> pdb=" O ARG U 192 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 91 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 151 through 156 Processing helix chain 'V' and resid 177 through 187 removed outlier: 3.687A pdb=" N LYS V 183 " --> pdb=" O GLN V 179 " (cutoff:3.500A) Processing helix chain 'V' and resid 212 through 221 Processing helix chain 'V' and resid 230 through 239 removed outlier: 3.547A 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: 3.518A 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: 3.602A 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: 3.610A 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: 3.935A pdb=" N GLN c 71 " --> pdb=" O GLY c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 76 through 87 removed outlier: 3.608A pdb=" N GLU c 81 " --> pdb=" O LEU c 77 " (cutoff:3.500A) removed outlier: 3.716A 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: 3.501A pdb=" N ILE c 87 " --> pdb=" O TYR c 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 844 through 849 removed outlier: 3.525A pdb=" N GLU d 848 " --> pdb=" O ASN d 844 " (cutoff:3.500A) removed outlier: 3.585A 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: 4.154A 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: 3.575A pdb=" N LEU d 883 " --> pdb=" O GLN d 879 " (cutoff:3.500A) Processing helix chain 'd' and resid 898 through 922 removed outlier: 3.545A 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: 3.505A 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: 3.691A 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: 3.503A pdb=" N LYS d 958 " --> pdb=" O GLU d 954 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU d 962 " --> pdb=" O LYS d 958 " (cutoff:3.500A) Processing helix chain 'd' and resid 1059 through 1069 removed outlier: 3.754A pdb=" N LEU d1063 " --> pdb=" O ASN d1059 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS d1066 " --> pdb=" O ASP d1062 " (cutoff:3.500A) removed outlier: 3.740A 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: 3.643A 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: 3.712A 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: 4.226A 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: 3.907A 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: 4.511A 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: 3.504A 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: 3.501A pdb=" N ARG e 526 " --> pdb=" O ASP e 522 " (cutoff:3.500A) Processing helix chain 'f' and resid 16 through 27 removed outlier: 3.720A pdb=" N LYS f 20 " --> pdb=" O SER f 16 " (cutoff:3.500A) removed outlier: 3.718A 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: 3.533A 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: 3.712A pdb=" N TYR f 45 " --> pdb=" O ASP f 41 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS f 48 " --> pdb=" O SER f 44 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP f 53 " --> pdb=" O GLU f 49 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS f 56 " --> pdb=" O GLN f 52 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE f 57 " --> pdb=" O ASP f 53 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 76 removed outlier: 4.018A 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: 3.541A 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: 3.525A 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: 3.633A 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: 4.058A pdb=" N GLY f 384 " --> pdb=" O LEU f 380 " (cutoff:3.500A) Processing helix chain 'f' and resid 384 through 391 removed outlier: 3.545A pdb=" N ILE f 388 " --> pdb=" O GLY f 384 " (cutoff:3.500A) Processing helix chain 'f' and resid 392 through 396 removed outlier: 3.689A pdb=" N LEU f 396 " --> pdb=" O LEU f 393 " (cutoff:3.500A) Processing helix chain 'f' and resid 397 through 404 removed outlier: 3.695A pdb=" N GLU f 401 " --> pdb=" O GLN f 397 " (cutoff:3.500A) Processing helix chain 'f' and resid 415 through 438 removed outlier: 3.824A pdb=" N GLY f 419 " --> pdb=" O ILE f 415 " (cutoff:3.500A) 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: 4.309A 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: 3.506A pdb=" N ALA i 43 " --> pdb=" O MET i 39 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) removed outlier: 3.750A 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: 3.966A 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: 3.642A 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: 3.763A 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: 3.698A 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: 3.572A pdb=" N SER j 205 " --> pdb=" O THR j 201 " (cutoff:3.500A) Processing helix chain 'k' and resid 116 through 127 removed outlier: 3.502A 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: 3.825A pdb=" N ILE k 141 " --> pdb=" O LEU k 137 " (cutoff:3.500A) Processing helix chain 'k' and resid 147 through 176 removed outlier: 3.606A pdb=" N ALA k 153 " --> pdb=" O ASN k 149 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER k 158 " --> pdb=" O MET k 154 " (cutoff:3.500A) removed outlier: 3.863A 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: 3.669A pdb=" N GLU k 168 " --> pdb=" O GLU k 164 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP k 171 " --> pdb=" O GLU k 167 " (cutoff:3.500A) Processing helix chain 'k' and resid 184 through 197 removed outlier: 3.608A 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: 3.575A pdb=" N MET l 83 " --> pdb=" O ASP l 79 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN l 86 " --> pdb=" O GLU l 82 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLN l 101 " --> pdb=" O THR l 97 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU l 102 " --> pdb=" O ALA l 98 " (cutoff:3.500A) Processing helix chain 'l' and resid 113 through 123 removed outlier: 3.892A pdb=" N LEU l 118 " --> pdb=" O LYS l 114 " (cutoff:3.500A) removed outlier: 3.835A 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: 3.793A pdb=" N ALA l 153 " --> pdb=" O LYS l 149 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU l 154 " --> pdb=" O GLN l 150 " (cutoff:3.500A) removed outlier: 3.540A 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: 4.158A pdb=" N LYS l 157 " --> pdb=" O ALA l 153 " (cutoff:3.500A) Processing helix chain 'm' and resid 34 through 43 removed outlier: 3.734A pdb=" N CYS m 38 " --> pdb=" O LYS m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 67 removed outlier: 3.605A 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: 3.562A 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 Processing helix chain 'o' and resid 99 through 110 Processing helix chain 'o' and resid 123 through 132 removed outlier: 3.749A pdb=" N LYS o 127 " --> pdb=" O ASN o 123 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS o 132 " --> pdb=" O ASP o 128 " (cutoff:3.500A) Processing helix chain 'o' and resid 136 through 145 Processing helix chain 'o' and resid 217 through 226 Processing helix chain 'o' and resid 231 through 236 Processing helix chain 'o' and resid 244 through 249 Processing helix chain 'o' and resid 276 through 294 removed outlier: 3.571A pdb=" N ARG o 292 " --> pdb=" O ASN o 288 " (cutoff:3.500A) Processing helix chain 'o' and resid 301 through 319 removed outlier: 3.866A pdb=" N GLU o 305 " --> pdb=" O HIS o 301 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU o 309 " --> pdb=" O GLU o 305 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL o 318 " --> pdb=" O VAL o 314 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP o 319 " --> pdb=" O ALA o 315 " (cutoff:3.500A) Processing helix chain 'o' and resid 338 through 343 removed outlier: 3.635A pdb=" N LEU o 343 " --> pdb=" O LEU o 339 " (cutoff:3.500A) Processing helix chain 'o' and resid 381 through 386 Processing helix chain 'o' and resid 398 through 408 removed outlier: 3.744A pdb=" N ARG o 408 " --> pdb=" O GLU o 404 " (cutoff:3.500A) Processing helix chain 'o' and resid 434 through 438 removed outlier: 3.730A pdb=" N ASP o 437 " --> pdb=" O LYS o 434 " (cutoff:3.500A) Processing helix chain 'o' and resid 465 through 467 No H-bonds generated for 'chain 'o' and resid 465 through 467' Processing helix chain 'o' and resid 488 through 493 removed outlier: 3.699A pdb=" N TYR o 492 " --> pdb=" O VAL o 488 " (cutoff:3.500A) Processing helix chain 'o' and resid 509 through 519 Processing helix chain 'o' and resid 520 through 524 Processing helix chain 'o' and resid 538 through 549 removed outlier: 4.209A pdb=" N THR o 543 " --> pdb=" O GLN o 539 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA o 544 " --> pdb=" O ASP o 540 " (cutoff:3.500A) Processing helix chain 'o' and resid 556 through 565 removed outlier: 3.529A pdb=" N VAL o 560 " --> pdb=" O GLU o 556 " (cutoff:3.500A) 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 664 through 684 removed outlier: 4.534A pdb=" N ILE o 682 " --> pdb=" O ASN o 678 " (cutoff:3.500A) Processing helix chain 'o' and resid 689 through 693 removed outlier: 4.086A pdb=" N ILE o 693 " --> pdb=" O GLY o 690 " (cutoff:3.500A) Processing helix chain 'o' and resid 695 through 721 removed outlier: 3.816A pdb=" N TYR o 699 " --> pdb=" O ASP o 695 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN o 700 " --> pdb=" O SER o 696 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE o 714 " --> pdb=" O LYS o 710 " (cutoff:3.500A) Processing helix chain 'o' and resid 732 through 758 removed outlier: 3.649A pdb=" N ASP o 750 " --> pdb=" O ASN o 746 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS o 751 " --> pdb=" O ASP o 747 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR o 752 " --> pdb=" O ALA o 748 " (cutoff:3.500A) Processing helix chain 'o' and resid 764 through 772 removed outlier: 3.510A pdb=" N SER o 768 " --> pdb=" O ASN o 764 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET o 769 " --> pdb=" O ASN o 765 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER o 772 " --> pdb=" O SER o 768 " (cutoff:3.500A) Processing helix chain 'o' and resid 777 through 786 removed outlier: 3.907A pdb=" N ILE o 781 " --> pdb=" O SER o 777 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER o 782 " --> pdb=" O LYS o 778 " (cutoff:3.500A) Processing helix chain 'o' and resid 832 through 868 removed outlier: 4.223A pdb=" N THR o 850 " --> pdb=" O GLY o 846 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA o 851 " --> pdb=" O LEU o 847 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR o 854 " --> pdb=" O THR o 850 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA o 855 " --> pdb=" O ALA o 851 " (cutoff:3.500A) Processing helix chain 'o' and resid 890 through 894 Processing helix chain 'o' and resid 912 through 920 removed outlier: 3.756A 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 943 removed outlier: 3.680A pdb=" N LYS o 940 " --> pdb=" O GLU o 936 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP o 941 " --> pdb=" O ASP o 937 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU o 943 " --> pdb=" O VAL o 939 " (cutoff:3.500A) Processing helix chain 'o' and resid 945 through 970 removed outlier: 3.751A pdb=" N GLU o 955 " --> pdb=" O GLU o 951 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE o 956 " --> pdb=" O LEU o 952 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU o 957 " --> pdb=" O GLU o 953 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP o 962 " --> pdb=" O ARG o 958 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL o 968 " --> pdb=" O GLU o 964 " (cutoff:3.500A) Processing helix chain 'o' and resid 983 through 994 removed outlier: 3.634A pdb=" N LYS o 992 " --> pdb=" O TRP o 988 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE o 994 " --> pdb=" O ALA o 990 " (cutoff:3.500A) Processing helix chain 'o' and resid 1005 through 1019 removed outlier: 3.514A pdb=" N LYS o1019 " --> pdb=" O GLU o1015 " (cutoff:3.500A) Processing helix chain 'o' and resid 1032 through 1038 Processing helix chain 'o' and resid 1039 through 1049 Processing helix chain 'o' and resid 1052 through 1057 Processing helix chain 'o' and resid 1062 through 1077 removed outlier: 3.772A pdb=" N ASP o1066 " --> pdb=" O GLY o1062 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TRP o1067 " --> pdb=" O GLU o1063 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU o1068 " --> pdb=" O ALA o1064 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU o1073 " --> pdb=" O LEU o1069 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER o1074 " --> pdb=" O GLY o1070 " (cutoff:3.500A) Processing helix chain 'o' and resid 1086 through 1097 removed outlier: 3.512A pdb=" N SER o1094 " --> pdb=" O LEU o1090 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU o1095 " --> pdb=" O ALA o1091 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY o1096 " --> pdb=" O ALA o1092 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU o1097 " --> pdb=" O GLN o1093 " (cutoff:3.500A) Processing helix chain 'o' and resid 1098 through 1100 No H-bonds generated for 'chain 'o' and resid 1098 through 1100' Processing helix chain 'o' and resid 1120 through 1129 Processing helix chain 'o' and resid 1145 through 1149 Processing helix chain 'o' and resid 1150 through 1162 Processing helix chain 'o' and resid 1165 through 1168 removed outlier: 3.659A pdb=" N LYS o1168 " --> pdb=" O THR o1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 1165 through 1168' Processing helix chain 'o' and resid 1189 through 1198 Processing helix chain 'o' and resid 1217 through 1223 Processing helix chain 'o' and resid 1227 through 1237 removed outlier: 3.944A pdb=" N ILE o1231 " --> pdb=" O THR o1227 " (cutoff:3.500A) Processing helix chain 'o' and resid 1263 through 1266 Processing helix chain 'o' and resid 1280 through 1293 removed outlier: 3.727A pdb=" N LEU o1293 " --> pdb=" O GLU o1289 " (cutoff:3.500A) Processing helix chain 'o' and resid 1342 through 1347 removed outlier: 3.562A pdb=" N VAL o1346 " --> pdb=" O SER o1342 " (cutoff:3.500A) Processing helix chain 'o' and resid 1361 through 1369 removed outlier: 3.643A pdb=" N ILE o1365 " --> pdb=" O ASP o1361 " (cutoff:3.500A) Processing helix chain 'o' and resid 1371 through 1387 Processing helix chain 'o' and resid 1388 through 1390 No H-bonds generated for 'chain 'o' and resid 1388 through 1390' Processing helix chain 'o' and resid 1394 through 1405 removed outlier: 4.194A pdb=" N LEU o1398 " --> pdb=" O ASN o1394 " (cutoff:3.500A) Processing helix chain 'o' and resid 1425 through 1430 removed outlier: 3.961A pdb=" N LYS o1429 " --> pdb=" O GLY o1425 " (cutoff:3.500A) Processing helix chain 'o' and resid 1434 through 1446 removed outlier: 3.588A pdb=" N VAL o1438 " --> pdb=" O GLU o1434 " (cutoff:3.500A) Processing helix chain 'o' and resid 1454 through 1459 Processing helix chain 'p' and resid 21 through 37 removed outlier: 4.343A pdb=" N TRP p 27 " --> pdb=" O GLN p 23 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE p 28 " --> pdb=" O GLU p 24 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL p 29 " --> pdb=" O ALA p 25 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER p 31 " --> pdb=" O TRP p 27 " (cutoff:3.500A) removed outlier: 3.703A 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: 4.081A 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: 3.700A pdb=" N VAL p 59 " --> pdb=" O VAL p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 109 through 116 removed outlier: 3.565A 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 removed outlier: 4.595A pdb=" N ILE p 252 " --> pdb=" O LYS p 248 " (cutoff:3.500A) Processing helix chain 'p' and resid 269 through 275 Processing helix chain 'p' and resid 280 through 285 removed outlier: 3.819A pdb=" N LEU p 285 " --> pdb=" O ASP p 281 " (cutoff:3.500A) Processing helix chain 'p' and resid 294 through 302 removed outlier: 3.529A pdb=" N MET p 298 " --> pdb=" O ASP p 294 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET p 300 " --> pdb=" O GLU p 296 " (cutoff:3.500A) Processing helix chain 'p' and resid 303 through 309 removed outlier: 4.351A 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: 3.842A 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: 3.658A pdb=" N LYS p 340 " --> pdb=" O ILE p 336 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU p 341 " --> pdb=" O LYS p 337 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL p 342 " --> pdb=" O TYR p 338 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU p 343 " --> pdb=" O ALA p 339 " (cutoff:3.500A) Processing helix chain 'p' and resid 359 through 375 removed outlier: 3.512A pdb=" N LEU p 374 " --> pdb=" O HIS p 370 " (cutoff:3.500A) removed outlier: 3.559A 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: 3.956A pdb=" N ASN p 410 " --> pdb=" O GLY p 406 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU p 411 " --> pdb=" O MET p 407 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU p 414 " --> pdb=" O ASN p 410 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL p 415 " --> pdb=" O LEU p 411 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG p 416 " --> pdb=" O LEU p 412 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE p 417 " --> pdb=" O LYS p 413 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR p 418 " --> pdb=" O GLU p 414 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS p 421 " --> pdb=" O ILE p 417 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE p 422 " --> pdb=" O TYR p 418 " (cutoff:3.500A) Processing helix chain 'p' and resid 436 through 439 Processing helix chain 'p' and resid 440 through 451 removed outlier: 3.633A pdb=" N SER p 447 " --> pdb=" O GLY p 443 " (cutoff:3.500A) Processing helix chain 'p' and resid 455 through 459 removed outlier: 3.697A pdb=" N ALA p 459 " --> pdb=" O GLN p 456 " (cutoff:3.500A) Processing helix chain 'p' and resid 474 through 480 removed outlier: 3.513A 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: 3.566A pdb=" N TRP p 506 " --> pdb=" O ASN p 503 " (cutoff:3.500A) Processing helix chain 'p' and resid 538 through 547 removed outlier: 3.541A 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: 3.583A 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: 4.017A pdb=" N LYS p 589 " --> pdb=" O ASN p 585 " (cutoff:3.500A) Processing helix chain 'p' and resid 636 through 641 removed outlier: 3.984A pdb=" N ILE p 640 " --> pdb=" O LYS p 636 " (cutoff:3.500A) Processing helix chain 'p' and resid 645 through 649 removed outlier: 3.840A 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: 3.808A 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: 3.798A pdb=" N ASN p 722 " --> pdb=" O GLN p 718 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR p 723 " --> pdb=" O SER p 719 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER p 726 " --> pdb=" O ASN p 722 " (cutoff:3.500A) Processing helix chain 'p' and resid 761 through 765 removed outlier: 4.043A 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: 3.988A pdb=" N CYS p 984 " --> pdb=" O HIS p 980 " (cutoff:3.500A) removed outlier: 3.896A 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: 3.612A pdb=" N VAL p 989 " --> pdb=" O LEU p 985 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN p 992 " --> pdb=" O LYS p 988 " (cutoff:3.500A) Processing helix chain 'p' and resid 1008 through 1016 removed outlier: 3.589A pdb=" N LEU p1014 " --> pdb=" O LYS p1010 " (cutoff:3.500A) Processing helix chain 'p' and resid 1054 through 1058 removed outlier: 3.671A 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: 3.626A 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: 3.531A pdb=" N LYS p1156 " --> pdb=" O PRO p1152 " (cutoff:3.500A) removed outlier: 3.745A 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: 3.722A pdb=" N HIS q 66 " --> pdb=" O GLU q 62 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY q 69 " --> pdb=" O ALA q 65 " (cutoff:3.500A) removed outlier: 3.843A 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: 3.503A pdb=" N LEU q 246 " --> pdb=" O GLU q 242 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS q 254 " --> pdb=" O SER q 250 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP q 258 " --> pdb=" O LYS q 254 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR q 261 " --> pdb=" O SER q 257 " (cutoff:3.500A) Processing helix chain 'r' and resid 33 through 50 removed outlier: 3.503A pdb=" N LEU r 40 " --> pdb=" O GLU r 36 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU r 42 " --> pdb=" O HIS r 38 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS r 43 " --> pdb=" O MET r 39 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER r 50 " --> pdb=" O GLN r 46 " (cutoff:3.500A) Processing helix chain 'r' and resid 59 through 71 removed outlier: 3.701A pdb=" N ARG r 70 " --> pdb=" O ASN r 66 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE r 71 " --> pdb=" O TYR r 67 " (cutoff:3.500A) Processing helix chain 'r' and resid 76 through 87 removed outlier: 3.791A pdb=" N SER r 85 " --> pdb=" O ALA r 81 " (cutoff:3.500A) Processing helix chain 'r' and resid 93 through 102 removed outlier: 3.775A pdb=" N LEU r 97 " --> pdb=" O HIS r 93 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA r 98 " --> pdb=" O LYS r 94 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU r 100 " --> pdb=" O GLU r 96 " (cutoff:3.500A) removed outlier: 3.518A 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: 4.054A pdb=" N LEU r 127 " --> pdb=" O GLU r 123 " (cutoff:3.500A) Processing helix chain 's' and resid 3 through 24 removed outlier: 3.561A pdb=" N TRP s 11 " --> pdb=" O THR s 7 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN s 19 " --> pdb=" O LYS s 15 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS s 22 " --> pdb=" O MET s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 29 through 34 removed outlier: 3.902A pdb=" N LEU s 33 " --> pdb=" O THR s 29 " (cutoff:3.500A) removed outlier: 4.032A 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: 3.555A pdb=" N LEU s 160 " --> pdb=" O VAL s 156 " (cutoff:3.500A) removed outlier: 3.667A 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: 3.682A pdb=" N ALA t 63 " --> pdb=" O LYS t 59 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY t 67 " --> pdb=" O ALA t 63 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET t 75 " --> pdb=" O LEU t 71 " (cutoff:3.500A) Processing helix chain 't' and resid 88 through 98 removed outlier: 3.822A 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: 3.524A pdb=" N LYS t 95 " --> pdb=" O LEU t 91 " (cutoff:3.500A) removed outlier: 3.803A 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: 3.713A 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 17 through 28 removed outlier: 3.814A pdb=" N ALA x 27 " --> pdb=" O GLY x 23 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU x 28 " --> pdb=" O LEU x 24 " (cutoff:3.500A) Processing helix chain 'x' and resid 30 through 35 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: 4.148A pdb=" N MET x 48 " --> pdb=" O CYS x 44 " (cutoff:3.500A) removed outlier: 4.192A 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 removed outlier: 3.501A pdb=" N SER y 9 " --> pdb=" O ALA y 6 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 51 removed outlier: 4.112A pdb=" N ILE y 45 " --> pdb=" O THR y 41 " (cutoff:3.500A) removed outlier: 3.520A 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: 3.558A 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: 4.255A 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: 6.510A 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) removed outlier: 4.821A pdb=" N VAL G 73 " --> pdb=" O TYR A 683 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU G 43 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR A 771 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLN G 15 " --> pdb=" O GLN G 93 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N LEU G 95 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 7.275A 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: 6.699A pdb=" N ARG G 19 " --> pdb=" O SER G 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 786 through 787 removed outlier: 6.510A 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) removed outlier: 4.821A pdb=" N VAL G 73 " --> pdb=" O TYR A 683 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N LYS G 66 " --> pdb=" O THR G 98 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N THR G 98 " --> pdb=" O LYS G 66 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL G 68 " --> pdb=" O VAL G 96 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL G 96 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU G 70 " --> pdb=" O MET G 94 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N MET G 94 " --> pdb=" O LEU G 70 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N CYS G 72 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N CYS G 92 " --> pdb=" O CYS G 72 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET G 74 " --> pdb=" O ASP G 90 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASP G 90 " --> pdb=" O MET G 74 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER G 76 " --> pdb=" O THR G 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 786 through 787 removed outlier: 4.292A pdb=" N GLN A 741 " --> pdb=" O ILE A 752 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N LEU A 754 " --> pdb=" O LEU A 739 " (cutoff:3.500A) removed outlier: 12.851A 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 removed outlier: 3.676A pdb=" N TRP A 861 " --> pdb=" O LYS A 853 " (cutoff:3.500A) 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: 3.612A pdb=" N LYS A1166 " --> pdb=" O GLU G 182 " (cutoff:3.500A) removed outlier: 3.504A 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: 7.123A 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: 4.208A pdb=" N VAL B 46 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASN B 37 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N PHE B 48 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ILE B 35 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLU B 50 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 5.676A 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: 6.343A pdb=" N GLN B 31 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 8.769A 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: 9.635A 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: 6.529A pdb=" N GLN B 31 " --> pdb=" O LYS B 203 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N GLU B 205 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL B 33 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 7.895A 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: 8.865A 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: 6.311A pdb=" N CYS B 200 " --> pdb=" O ILE B 240 " (cutoff:3.500A) removed outlier: 6.412A 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: 5.560A 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: 4.056A 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: 5.758A 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: 6.357A 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: 5.975A 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: 6.560A 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: 7.407A pdb=" N LYS B 565 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE B 630 " --> pdb=" O LYS B 565 " (cutoff:3.500A) removed outlier: 6.698A 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 'E' and resid 308 through 310 Processing sheet with id=AB7, first strand: chain 'E' and resid 782 through 785 Processing sheet with id=AB8, 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=AB9, 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=AC1, first strand: chain 'E' and resid 546 through 550 removed outlier: 3.506A pdb=" N SER E 562 " --> pdb=" O THR E 566 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR E 566 " --> pdb=" O SER E 562 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL E 579 " --> pdb=" O LEU E 569 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 588 through 593 Processing sheet with id=AC3, first strand: chain 'E' and resid 634 through 635 removed outlier: 3.618A pdb=" N ARG E 663 " --> pdb=" O LEU E 653 " (cutoff:3.500A) removed outlier: 6.438A 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=AC4, first strand: chain 'E' and resid 672 through 677 Processing sheet with id=AC5, first strand: chain 'E' and resid 714 through 719 removed outlier: 6.478A pdb=" N LEU E 737 " --> pdb=" O LEU E 770 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 86 through 88 Processing sheet with id=AC7, first strand: chain 'H' and resid 200 through 201 Processing sheet with id=AC8, first strand: chain 'O' and resid 64 through 68 removed outlier: 7.323A pdb=" N LYS O 92 " --> pdb=" O ASN Q 333 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N VAL Q 335 " --> pdb=" O LYS O 92 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LYS O 94 " --> pdb=" O VAL Q 335 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N CYS Q 337 " --> pdb=" O LYS O 94 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL O 96 " --> pdb=" O CYS Q 337 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR Q 339 " --> pdb=" O VAL O 96 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N CYS O 98 " --> pdb=" O TYR Q 339 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LYS Q 341 " --> pdb=" O CYS O 98 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N VAL Q 334 " --> pdb=" O MET Q 358 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N MET Q 358 " --> pdb=" O VAL Q 334 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL Q 336 " --> pdb=" O GLY Q 356 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY Q 356 " --> pdb=" O VAL Q 336 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N HIS Q 352 " --> pdb=" O ASP Q 340 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE Q 342 " --> pdb=" O LYS Q 350 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS Q 350 " --> pdb=" O ILE Q 342 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG Q 344 " --> pdb=" O LYS Q 348 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS Q 348 " --> pdb=" O ARG Q 344 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LYS Q 348 " --> pdb=" O GLU Q 375 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU Q 375 " --> pdb=" O LYS Q 348 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LYS Q 350 " --> pdb=" O ASP Q 373 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASP Q 373 " --> pdb=" O LYS Q 350 " (cutoff:3.500A) removed outlier: 7.049A 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: 6.226A pdb=" N LYS Q 354 " --> pdb=" O LYS Q 369 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LYS Q 369 " --> pdb=" O LYS Q 354 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 81 through 83 Processing sheet with id=AD1, first strand: chain 'P' and resid 190 through 191 removed outlier: 3.585A pdb=" N ILE P 204 " --> pdb=" O THR P 209 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR P 209 " --> pdb=" O ILE P 204 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU P 165 " --> pdb=" O GLY P 260 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLY P 260 " --> pdb=" O LEU P 165 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASN P 167 " --> pdb=" O MET P 258 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N MET P 258 " --> pdb=" O ASN P 167 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL P 169 " --> pdb=" O GLN P 256 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ASN P 173 " --> pdb=" O ASP P 252 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ASP P 252 " --> pdb=" O ASN P 173 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N MET P 258 " --> pdb=" O GLY P 314 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY P 314 " --> pdb=" O MET P 258 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU P 284 " --> pdb=" O PHE P 288 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLY P 290 " --> pdb=" O SER P 282 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N SER P 282 " --> pdb=" O GLY P 290 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'R' and resid 24 through 26 Processing sheet with id=AD3, first strand: chain 'T' and resid 6 through 7 removed outlier: 4.143A pdb=" N ALA S 45 " --> pdb=" O LEU T 7 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN S 142 " --> pdb=" O TYR S 26 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA S 30 " --> pdb=" O TYR S 144 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE S 146 " --> pdb=" O ALA S 30 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASN S 32 " --> pdb=" O PHE S 146 " (cutoff:3.500A) removed outlier: 11.651A pdb=" N GLN T 91 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N VAL T 111 " --> pdb=" O GLN T 91 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU T 93 " --> pdb=" O ILE T 109 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE T 109 " --> pdb=" O LEU T 93 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL T 95 " --> pdb=" O GLU T 107 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG T 113 " --> pdb=" O GLN T 86 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS T 81 " --> pdb=" O PHE T 56 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL T 54 " --> pdb=" O PHE T 83 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU T 85 " --> pdb=" O THR T 52 " (cutoff:3.500A) removed outlier: 10.943A pdb=" N THR T 52 " --> pdb=" O LEU T 85 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N PHE S 135 " --> pdb=" O GLU S 13 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL S 15 " --> pdb=" O PHE S 135 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ALA S 137 " --> pdb=" O VAL S 15 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ARG S 17 " --> pdb=" O ALA S 137 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLN S 129 " --> pdb=" O GLY T 17 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N GLY T 17 " --> pdb=" O GLN S 129 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL T 18 " --> pdb=" O VAL T 110 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN T 112 " --> pdb=" O VAL T 18 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 143 through 144 removed outlier: 3.644A pdb=" N GLN T 143 " --> pdb=" O ILE p 91 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU p 93 " --> pdb=" O GLN T 143 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP p 127 " --> pdb=" O GLU p 89 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE p 91 " --> pdb=" O TYR p 125 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR p 125 " --> pdb=" O ILE p 91 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU p 93 " --> pdb=" O PRO p 123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'T' and resid 143 through 144 removed outlier: 3.644A pdb=" N GLN T 143 " --> pdb=" O ILE p 91 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU p 93 " --> pdb=" O GLN T 143 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP p 127 " --> pdb=" O GLU p 89 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE p 91 " --> pdb=" O TYR p 125 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR p 125 " --> pdb=" O ILE p 91 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU p 93 " --> pdb=" O PRO p 123 " (cutoff:3.500A) removed outlier: 6.604A 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: 7.466A pdb=" N LEU p 124 " --> pdb=" O PHE p 148 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N PHE p 148 " --> pdb=" O LEU p 124 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N VAL p 126 " --> pdb=" O LYS p 146 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU p 140 " --> pdb=" O VAL p 132 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'T' and resid 196 through 198 removed outlier: 3.502A pdb=" N THR T 232 " --> pdb=" O ASN T 224 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'U' and resid 128 through 129 removed outlier: 3.557A pdb=" N SER U 134 " --> pdb=" O CYS U 129 " (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: 3.851A 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: 4.285A 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: 6.692A pdb=" N SER e 561 " --> pdb=" O TYR e 547 " (cutoff:3.500A) removed outlier: 4.578A 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: 3.834A 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: 3.635A 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: 6.553A 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: 4.345A pdb=" N LEU e 675 " --> pdb=" O ALA e 685 " (cutoff:3.500A) removed outlier: 6.790A 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: 6.261A 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: 4.239A 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: 3.506A 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: 3.533A pdb=" N ARG o 20 " --> pdb=" O MET p1172 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'o' and resid 86 through 94 removed outlier: 3.795A pdb=" N LEU o 90 " --> pdb=" O THR o 251 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N THR o 251 " --> pdb=" O LEU o 90 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'o' and resid 264 through 266 removed outlier: 3.843A pdb=" N MET o 266 " --> pdb=" O ALA o 270 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA o 270 " --> pdb=" O MET o 266 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'o' and resid 357 through 359 removed outlier: 3.756A pdb=" N LYS o 357 " --> pdb=" O PHE p1086 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU p1084 " --> pdb=" O VAL o 359 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'p' and resid 1060 through 1062 removed outlier: 3.765A pdb=" N THR o 365 " --> pdb=" O MET o 501 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL o 456 " --> pdb=" O HIS o 472 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N PHE o 482 " --> pdb=" O ARG o 364 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL o 366 " --> pdb=" O PHE o 482 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU o 484 " --> pdb=" O VAL o 366 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR o 368 " --> pdb=" O LEU o 484 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'o' and resid 389 through 393 removed outlier: 4.152A pdb=" N TYR o 418 " --> pdb=" O GLU o 447 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N HIS o 449 " --> pdb=" O ALA o 416 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ALA o 416 " --> pdb=" O HIS o 449 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'o' and resid 526 through 527 removed outlier: 3.832A pdb=" N ARG o 532 " --> pdb=" O THR o 527 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'o' and resid 554 through 555 Processing sheet with id=AG2, first strand: chain 'o' and resid 579 through 581 removed outlier: 6.165A pdb=" N ILE o 579 " --> pdb=" O TYR v 93 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N TYR v 93 " --> pdb=" O ILE o 579 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS o 581 " --> pdb=" O VAL v 91 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL v 91 " --> pdb=" O LYS o 581 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N HIS v 29 " --> pdb=" O LYS v 13 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LEU v 122 " --> pdb=" O ASP v 42 " (cutoff:3.500A) removed outlier: 3.534A 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: 4.142A 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: 5.722A pdb=" N VAL v 96 " --> pdb=" O SER v 117 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'o' and resid 602 through 603 removed outlier: 6.844A 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 Processing sheet with id=AG5, first strand: chain 'o' and resid 872 through 873 removed outlier: 6.936A pdb=" N VAL o 879 " --> pdb=" O VAL o 887 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'o' and resid 902 through 905 Processing sheet with id=AG7, first strand: chain 'o' and resid 1140 through 1142 Processing sheet with id=AG8, first strand: chain 'o' and resid 1243 through 1247 removed outlier: 4.269A pdb=" N LEU o1255 " --> pdb=" O LEU o1216 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU o1211 " --> pdb=" O ILE o1175 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE o1175 " --> pdb=" O LEU o1211 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG o1213 " --> pdb=" O THR o1173 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR o1173 " --> pdb=" O ARG o1213 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU o1215 " --> pdb=" O ALA o1171 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR w 54 " --> pdb=" O ILE o1175 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'o' and resid 1319 through 1322 Processing sheet with id=AH1, first strand: chain 'r' and resid 30 through 31 removed outlier: 3.996A pdb=" N GLU r 30 " --> pdb=" O HIS u 4 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE u 5 " --> pdb=" O ALA u 74 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL u 66 " --> pdb=" O LEU u 13 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY u 57 " --> pdb=" O LEU o1475 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE u 59 " --> pdb=" O LEU o1473 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU o1473 " --> pdb=" O ILE u 59 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP o1472 " --> pdb=" O ARG t 107 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'r' and resid 30 through 31 removed outlier: 3.996A pdb=" N GLU r 30 " --> pdb=" O HIS u 4 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE u 5 " --> pdb=" O ALA u 74 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL u 66 " --> pdb=" O LEU u 13 " (cutoff:3.500A) removed outlier: 11.236A pdb=" N LEU u 67 " --> pdb=" O ILE u 54 " (cutoff:3.500A) removed outlier: 10.344A 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: 7.415A pdb=" N ILE u 75 " --> pdb=" O ILE u 46 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE u 46 " --> pdb=" O ILE u 75 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'p' and resid 97 through 99 Processing sheet with id=AH4, first strand: chain 'p' and resid 185 through 187 Processing sheet with id=AH5, first strand: chain 'p' and resid 391 through 394 removed outlier: 3.562A pdb=" N LYS p 524 " --> pdb=" O LEU p 485 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'p' and resid 206 through 208 removed outlier: 6.849A pdb=" N MET p 239 " --> pdb=" O ALA p 216 " (cutoff:3.500A) removed outlier: 4.719A 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: 4.381A pdb=" N GLU p 220 " --> pdb=" O ILE p 235 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE p 235 " --> pdb=" O GLU p 220 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG p 222 " --> pdb=" O SER p 233 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER p 233 " --> pdb=" O ARG p 222 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP p 236 " --> pdb=" O THR p 259 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'p' and resid 531 through 532 Processing sheet with id=AH8, 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: 3.551A 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=AH9, first strand: chain 'p' and resid 662 through 664 Processing sheet with id=AI1, first strand: chain 'p' and resid 748 through 751 removed outlier: 3.565A 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: 6.707A 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: 5.241A pdb=" N VAL p 907 " --> pdb=" O LYS z 46 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'p' and resid 759 through 760 removed outlier: 3.517A pdb=" N THR p 760 " --> pdb=" O GLY p 997 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'p' and resid 1025 through 1026 removed outlier: 7.441A pdb=" N VAL p 794 " --> pdb=" O GLY p 946 " (cutoff:3.500A) removed outlier: 6.467A 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: 8.969A pdb=" N ILE p 965 " --> pdb=" O ASN p 777 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE p 779 " --> pdb=" O ILE p 965 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ILE p 967 " --> pdb=" O ILE p 779 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA p 781 " --> pdb=" O ILE p 967 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE p1042 " --> pdb=" O ILE p 782 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'p' and resid 827 through 829 removed outlier: 3.917A pdb=" N ILE p 867 " --> pdb=" O THR p 894 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'p' and resid 1115 through 1119 Processing sheet with id=AI6, first strand: chain 'p' and resid 1127 through 1129 Processing sheet with id=AI7, 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: 4.532A 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: 3.736A pdb=" N PHE q 21 " --> pdb=" O TYR q 231 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'q' and resid 121 through 122 removed outlier: 3.519A pdb=" N ALA q 163 " --> pdb=" O PHE q 101 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLU q 158 " --> pdb=" O ALA q 54 " (cutoff:3.500A) removed outlier: 6.525A 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: 6.865A pdb=" N ARG q 162 " --> pdb=" O VAL q 50 " (cutoff:3.500A) removed outlier: 4.563A 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=AI9, first strand: chain 'q' and resid 113 through 116 removed outlier: 3.645A pdb=" N VAL q 151 " --> pdb=" O VAL q 115 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 's' and resid 60 through 63 removed outlier: 3.750A pdb=" N VAL s 60 " --> pdb=" O VAL s 74 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG s 101 " --> pdb=" O GLN s 71 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 's' and resid 81 through 82 Processing sheet with id=AJ3, first strand: chain 's' and resid 147 through 150 removed outlier: 3.805A pdb=" N GLU s 147 " --> pdb=" O ILE s 194 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 't' and resid 56 through 57 Processing sheet with id=AJ5, first strand: chain 'w' and resid 25 through 28 Processing sheet with id=AJ6, first strand: chain 'w' and resid 80 through 81 Processing sheet with id=AJ7, 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: 4.250A pdb=" N TYR y 61 " --> pdb=" O ILE y 72 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ARG y 74 " --> pdb=" O ALA y 59 " (cutoff:3.500A) removed outlier: 4.031A 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=AJ8, 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: 6.470A 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: 6.582A pdb=" N ASP u 156 " --> pdb=" O VAL u 152 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER u 105 " --> pdb=" O ALA u 159 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N GLY u 161 " --> pdb=" O SER u 105 " (cutoff:3.500A) removed outlier: 6.628A 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=AJ9, first strand: chain 'u' and resid 118 through 120 3176 hydrogen bonds defined for protein. 9027 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 158 hydrogen bonds 316 hydrogen bond angles 0 basepair planarities 63 basepair parallelities 150 stacking parallelities Total time for adding SS restraints: 52.16 Time building geometry restraints manager: 29.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 13956 1.30 - 1.44: 23279 1.44 - 1.58: 49440 1.58 - 1.71: 337 1.71 - 1.85: 743 Bond restraints: 87755 Sorted by residual: bond pdb=" C ASN U 123 " pdb=" N ARG U 124 " ideal model delta sigma weight residual 1.332 1.465 -0.133 1.40e-02 5.10e+03 9.00e+01 bond pdb=" C ARG U 124 " pdb=" N ALA U 125 " ideal model delta sigma weight residual 1.334 1.420 -0.086 1.25e-02 6.40e+03 4.74e+01 bond pdb=" C ILE T 132 " pdb=" O ILE T 132 " ideal model delta sigma weight residual 1.237 1.162 0.075 1.17e-02 7.31e+03 4.09e+01 bond pdb=" C ASN B 61 " pdb=" O ASN B 61 " ideal model delta sigma weight residual 1.239 1.179 0.060 9.60e-03 1.09e+04 3.88e+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 3.24e+01 ... (remaining 87750 not shown) Histogram of bond angle deviations from ideal: 95.80 - 103.55: 1652 103.55 - 111.29: 35653 111.29 - 119.04: 37476 119.04 - 126.79: 43168 126.79 - 134.54: 1401 Bond angle restraints: 119350 Sorted by residual: angle pdb=" N ASN U 101 " pdb=" CA ASN U 101 " pdb=" C ASN U 101 " ideal model delta sigma weight residual 112.30 97.82 14.48 1.36e+00 5.41e-01 1.13e+02 angle pdb=" N HIS B 491 " pdb=" CA HIS B 491 " pdb=" C HIS B 491 " ideal model delta sigma weight residual 111.28 100.95 10.33 1.09e+00 8.42e-01 8.99e+01 angle pdb=" O PRO f 149 " pdb=" C PRO f 149 " pdb=" N PRO f 150 " ideal model delta sigma weight residual 121.31 125.61 -4.30 4.60e-01 4.73e+00 8.75e+01 angle pdb=" C PHE U 127 " pdb=" CA PHE U 127 " pdb=" CB PHE U 127 " ideal model delta sigma weight residual 109.54 126.62 -17.08 1.84e+00 2.95e-01 8.62e+01 angle pdb=" N PHE O 58 " pdb=" CA PHE O 58 " pdb=" C PHE O 58 " ideal model delta sigma weight residual 108.24 120.29 -12.05 1.32e+00 5.74e-01 8.33e+01 ... (remaining 119345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 51045 35.58 - 71.16: 2036 71.16 - 106.74: 70 106.74 - 142.32: 1 142.32 - 177.91: 1 Dihedral angle restraints: 53153 sinusoidal: 23068 harmonic: 30085 Sorted by residual: dihedral pdb=" C VAL Q 320 " pdb=" N VAL Q 320 " pdb=" CA VAL Q 320 " pdb=" CB VAL Q 320 " ideal model delta harmonic sigma weight residual -122.00 -137.83 15.83 0 2.50e+00 1.60e-01 4.01e+01 dihedral pdb=" C ARG D 881 " pdb=" N ARG D 881 " pdb=" CA ARG D 881 " pdb=" CB ARG D 881 " ideal model delta harmonic sigma weight residual -122.60 -107.60 -15.00 0 2.50e+00 1.60e-01 3.60e+01 dihedral pdb=" N VAL Q 320 " pdb=" C VAL Q 320 " pdb=" CA VAL Q 320 " pdb=" CB VAL Q 320 " ideal model delta harmonic sigma weight residual 123.40 138.12 -14.72 0 2.50e+00 1.60e-01 3.47e+01 ... (remaining 53150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 11886 0.109 - 0.217: 1214 0.217 - 0.326: 174 0.326 - 0.434: 29 0.434 - 0.543: 10 Chirality restraints: 13313 Sorted by residual: chirality pdb=" CA SER B 490 " pdb=" N SER B 490 " pdb=" C SER B 490 " pdb=" CB SER B 490 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.36e+00 chirality pdb=" CA ARG F 268 " pdb=" N ARG F 268 " pdb=" C ARG F 268 " pdb=" CB ARG F 268 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.18e+00 chirality pdb=" CA PHE V 203 " pdb=" N PHE V 203 " pdb=" C PHE V 203 " pdb=" CB PHE V 203 " both_signs ideal model delta sigma weight residual False 2.51 3.02 -0.51 2.00e-01 2.50e+01 6.49e+00 ... (remaining 13310 not shown) Planarity restraints: 14809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN U 123 " -0.028 2.00e-02 2.50e+03 6.43e-02 4.13e+01 pdb=" C ASN U 123 " 0.111 2.00e-02 2.50e+03 pdb=" O ASN U 123 " -0.046 2.00e-02 2.50e+03 pdb=" N ARG U 124 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO S 6 " -0.030 2.00e-02 2.50e+03 6.24e-02 3.90e+01 pdb=" C PRO S 6 " 0.108 2.00e-02 2.50e+03 pdb=" O PRO S 6 " -0.042 2.00e-02 2.50e+03 pdb=" N SER S 7 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 323 " 0.028 2.00e-02 2.50e+03 5.73e-02 3.29e+01 pdb=" C VAL F 323 " -0.099 2.00e-02 2.50e+03 pdb=" O VAL F 323 " 0.038 2.00e-02 2.50e+03 pdb=" N ASP F 324 " 0.034 2.00e-02 2.50e+03 ... (remaining 14806 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 72 2.14 - 2.83: 26869 2.83 - 3.52: 110886 3.52 - 4.21: 203505 4.21 - 4.90: 346021 Nonbonded interactions: 687353 Sorted by model distance: nonbonded pdb=" OE2 GLU r 110 " pdb=" CD1 TYR u 167 " model vdw 1.445 3.340 nonbonded pdb=" N PHE B 883 " pdb=" CB PRO H 222 " model vdw 1.666 3.520 nonbonded pdb=" OE2 GLU r 110 " pdb=" CE1 TYR u 167 " model vdw 1.730 3.340 nonbonded pdb=" CD1 ILE O 88 " pdb=" CE1 TYR Q 365 " model vdw 1.734 3.760 nonbonded pdb=" OE2 GLU Q 47 " pdb=" CE1 HIS Q 60 " model vdw 1.746 3.260 ... (remaining 687348 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: 5.270 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: 0.070 Extract box with map and model: 24.260 Check model and map are aligned: 0.970 Set scattering table: 0.610 Process input model: 226.260 Find NCS groups from input model: 2.750 Set up NCS constraints: 0.390 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 263.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2785 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 0.133 87755 Z= 0.506 Angle : 1.077 17.080 119350 Z= 0.720 Chirality : 0.072 0.543 13313 Planarity : 0.006 0.105 14809 Dihedral : 16.943 177.906 33622 Min Nonbonded Distance : 1.445 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.51 % Favored : 93.07 % Rotamer: Outliers : 3.89 % Allowed : 6.98 % Favored : 89.13 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 0.81 % 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: -3.75 (0.07), residues: 10125 helix: -2.69 (0.07), residues: 3991 sheet: -1.55 (0.14), residues: 1282 loop : -2.51 (0.08), residues: 4852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.003 TRP T 19 HIS 0.015 0.001 HIS F 385 PHE 0.051 0.002 PHE O 58 TYR 0.036 0.002 TYR p1048 ARG 0.048 0.001 ARG u 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20250 Ramachandran restraints generated. 10125 Oldfield, 0 Emsley, 10125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20250 Ramachandran restraints generated. 10125 Oldfield, 0 Emsley, 10125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1339 residues out of total 9138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 352 poor density : 987 time to evaluate : 7.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 410 TRP cc_start: -0.0860 (OUTLIER) cc_final: -0.1880 (p-90) REVERT: A 607 MET cc_start: -0.0186 (mtm) cc_final: -0.1932 (mmt) REVERT: A 691 MET cc_start: -0.0410 (tpp) cc_final: -0.1491 (tpt) REVERT: A 711 ASP cc_start: 0.0249 (OUTLIER) cc_final: -0.1193 (t0) REVERT: A 757 MET cc_start: -0.2203 (mmm) cc_final: -0.2673 (mmt) REVERT: A 996 ARG cc_start: -0.4761 (OUTLIER) cc_final: -0.5576 (mtt180) REVERT: A 1203 GLU cc_start: -0.2572 (OUTLIER) cc_final: -0.4621 (pt0) REVERT: B 431 LEU cc_start: -0.3079 (OUTLIER) cc_final: -0.3756 (mt) REVERT: B 469 MET cc_start: -0.6233 (tpp) cc_final: -0.6865 (ttt) REVERT: B 607 MET cc_start: -0.0699 (ttp) cc_final: -0.1971 (ptm) REVERT: B 614 MET cc_start: -0.4106 (mtt) cc_final: -0.4810 (mtt) REVERT: B 619 MET cc_start: -0.1624 (ttp) cc_final: -0.2042 (mmt) REVERT: B 719 MET cc_start: -0.2944 (mtm) cc_final: -0.3349 (mtm) REVERT: D 941 ARG cc_start: -0.4032 (OUTLIER) cc_final: -0.5422 (mmt180) REVERT: D 953 ILE cc_start: 0.4750 (OUTLIER) cc_final: 0.4319 (mm) REVERT: D 957 ARG cc_start: -0.0855 (OUTLIER) cc_final: -0.1586 (mmp-170) REVERT: D 968 ARG cc_start: 0.2383 (OUTLIER) cc_final: -0.0175 (mmt180) REVERT: E 297 MET cc_start: -0.1667 (mmt) cc_final: -0.2051 (mmt) REVERT: E 528 MET cc_start: -0.2071 (mmt) cc_final: -0.2813 (mmt) REVERT: E 747 LEU cc_start: -0.2740 (OUTLIER) cc_final: -0.2966 (mm) REVERT: F 19 MET cc_start: -0.4978 (OUTLIER) cc_final: -0.6371 (mtp) REVERT: F 26 MET cc_start: -0.3823 (ttm) cc_final: -0.4461 (mtt) REVERT: F 62 LYS cc_start: -0.2716 (OUTLIER) cc_final: -0.3864 (tttt) REVERT: F 89 GLN cc_start: 0.0074 (OUTLIER) cc_final: -0.1683 (pm20) REVERT: F 290 MET cc_start: -0.0945 (mtm) cc_final: -0.1322 (mmt) REVERT: H 100 MET cc_start: -0.3769 (mtt) cc_final: -0.5085 (ptp) REVERT: H 132 LYS cc_start: -0.4338 (OUTLIER) cc_final: -0.4689 (tptt) REVERT: H 205 LYS cc_start: 0.0599 (OUTLIER) cc_final: 0.0324 (mmtt) REVERT: I 26 MET cc_start: -0.2816 (mmt) cc_final: -0.3234 (mmt) REVERT: I 34 ARG cc_start: -0.2366 (OUTLIER) cc_final: -0.4140 (tpt170) REVERT: L 87 ILE cc_start: -0.3050 (OUTLIER) cc_final: -0.3312 (mt) REVERT: P 172 VAL cc_start: 0.5012 (OUTLIER) cc_final: 0.4517 (t) REVERT: P 278 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7700 (pm20) REVERT: T 47 LYS cc_start: 0.0662 (OUTLIER) cc_final: -0.0457 (mptt) REVERT: U 48 MET cc_start: -0.3422 (ttt) cc_final: -0.4212 (mtt) REVERT: U 110 MET cc_start: -0.1282 (OUTLIER) cc_final: -0.4286 (ptm) REVERT: V 140 LYS cc_start: 0.1100 (OUTLIER) cc_final: 0.0528 (pttm) REVERT: V 142 LYS cc_start: -0.5042 (OUTLIER) cc_final: -0.5441 (pttt) REVERT: V 151 LEU cc_start: -0.2639 (OUTLIER) cc_final: -0.3358 (pp) REVERT: V 161 ARG cc_start: -0.1762 (OUTLIER) cc_final: -0.3186 (tpm170) REVERT: V 172 GLU cc_start: -0.2060 (OUTLIER) cc_final: -0.2590 (pt0) REVERT: V 194 ARG cc_start: -0.0514 (OUTLIER) cc_final: -0.2559 (mpt-90) REVERT: V 197 LYS cc_start: 0.2401 (OUTLIER) cc_final: 0.2078 (pttm) REVERT: V 206 LYS cc_start: -0.0182 (OUTLIER) cc_final: -0.0797 (mppt) REVERT: V 228 MET cc_start: -0.1291 (mtm) cc_final: -0.3615 (ptt) REVERT: e 247 MET cc_start: -0.1154 (mtp) cc_final: -0.1586 (mtt) REVERT: e 291 MET cc_start: -0.2812 (ttm) cc_final: -0.3333 (tpp) REVERT: e 528 MET cc_start: 0.2226 (mmt) cc_final: -0.0226 (mmt) REVERT: i 12 MET cc_start: -0.0995 (mmm) cc_final: -0.1715 (mtt) REVERT: i 39 MET cc_start: -0.1870 (mmp) cc_final: -0.4071 (mtt) REVERT: k 154 MET cc_start: -0.2239 (tpp) cc_final: -0.3318 (mmm) REVERT: o 202 TRP cc_start: 0.4374 (m-90) cc_final: 0.3350 (m100) REVERT: o 213 LYS cc_start: 0.4001 (OUTLIER) cc_final: 0.3577 (tptt) REVERT: o 214 ILE cc_start: 0.2630 (OUTLIER) cc_final: 0.1814 (pt) REVERT: o 593 SER cc_start: 0.8849 (m) cc_final: 0.8533 (t) REVERT: o 834 THR cc_start: 0.8030 (p) cc_final: 0.7606 (t) REVERT: o 979 LEU cc_start: 0.8289 (mt) cc_final: 0.7888 (mt) REVERT: o 1292 MET cc_start: 0.8744 (mmp) cc_final: 0.8343 (mmp) REVERT: p 287 HIS cc_start: 0.7850 (m90) cc_final: 0.7613 (m-70) REVERT: p 363 TYR cc_start: 0.7101 (m-80) cc_final: 0.6425 (m-80) REVERT: p 390 ASN cc_start: 0.8143 (m-40) cc_final: 0.7821 (m110) REVERT: p 702 MET cc_start: 0.9119 (mmm) cc_final: 0.8706 (mmt) REVERT: p 707 CYS cc_start: 0.8143 (m) cc_final: 0.7829 (t) REVERT: p 733 MET cc_start: 0.8401 (mtp) cc_final: 0.8197 (mtm) REVERT: p 802 ASP cc_start: 0.7305 (m-30) cc_final: 0.6824 (m-30) REVERT: p 952 GLU cc_start: 0.7125 (pt0) cc_final: 0.6770 (pt0) REVERT: p 975 ARG cc_start: 0.6200 (ptp-170) cc_final: 0.5935 (mtt180) REVERT: p 1030 ASN cc_start: 0.7870 (t0) cc_final: 0.7542 (t0) REVERT: q 30 VAL cc_start: 0.7927 (t) cc_final: 0.7716 (t) REVERT: q 59 LEU cc_start: 0.8979 (mt) cc_final: 0.8692 (mm) REVERT: s 194 ILE cc_start: 0.8325 (mt) cc_final: 0.7892 (tp) REVERT: v 80 ASP cc_start: 0.7851 (m-30) cc_final: 0.7616 (p0) REVERT: u 117 MET cc_start: -0.3265 (mtm) cc_final: -0.4016 (ttm) outliers start: 352 outliers final: 71 residues processed: 1317 average time/residue: 0.8372 time to fit residues: 1845.4297 Evaluate side-chains 667 residues out of total 9138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 565 time to evaluate : 7.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1022 random chunks: chunk 862 optimal weight: 1.9990 chunk 774 optimal weight: 0.0070 chunk 429 optimal weight: 9.9990 chunk 264 optimal weight: 40.0000 chunk 522 optimal weight: 8.9990 chunk 413 optimal weight: 2.9990 chunk 801 optimal weight: 3.9990 chunk 309 optimal weight: 0.2980 chunk 487 optimal weight: 20.0000 chunk 596 optimal weight: 40.0000 chunk 928 optimal weight: 8.9990 overall best weight: 1.8604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 GLN A 837 HIS A 860 ASN A1073 GLN B 30 HIS B 137 HIS B 176 HIS B 235 HIS B 348 GLN B 432 HIS B 450 GLN B 509 ASN B 521 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 GLN B 813 ASN B 908 GLN D 936 GLN E 254 ASN E 351 GLN E 585 ASN E 616 HIS E 636 HIS E 640 ASN E 673 HIS E 758 HIS F 52 GLN F 59 HIS F 119 ASN F 270 ASN F 275 ASN F 316 GLN G 48 HIS ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 HIS H 201 GLN I 21 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** ** L 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 HIS L 117 GLN ** O 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 16 GLN ** Q 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 352 HIS ** Q 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 129 ASN R 139 ASN ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN T 123 ASN T 144 GLN T 195 GLN T 208 GLN T 229 HIS ** U 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 95 HIS V 117 GLN V 126 ASN ** V 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 177 ASN ** V 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 105 ASN d 912 ASN d1069 ASN e 223 HIS e 294 ASN e 320 HIS e 336 HIS e 556 ASN k 139 GLN m 107 ASN o 123 ASN o 296 ASN o 301 HIS o 311 GLN o 441 GLN o 485 ASN ** o 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 620 HIS o 678 ASN o 721 HIS o 723 ASN ** o 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 739 ASN o 809 HIS o 913 ASN ** o1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1032 GLN ** o1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1230 GLN ** o1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1332 GLN o1445 HIS ** o1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 56 GLN p 68 GLN p 111 ASN ** p 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 203 ASN ** p 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 287 HIS p 468 GLN p 570 ASN ** p1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p1120 ASN q 51 GLN s 133 GLN y 2 ASN y 29 ASN ** u 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 155 ASN Total number of N/Q/H flips: 93 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2946 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 87755 Z= 0.253 Angle : 0.705 17.447 119350 Z= 0.369 Chirality : 0.045 0.258 13313 Planarity : 0.005 0.105 14809 Dihedral : 14.404 178.646 13047 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.89 % Favored : 95.00 % Rotamer: Outliers : 0.27 % Allowed : 4.68 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % 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: 10125 helix: -1.24 (0.07), residues: 4072 sheet: -0.99 (0.14), residues: 1304 loop : -2.05 (0.08), residues: 4749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 612 HIS 0.020 0.001 HIS L 105 PHE 0.037 0.002 PHE p 273 TYR 0.031 0.002 TYR B 692 ARG 0.030 0.001 ARG V 221 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20250 Ramachandran restraints generated. 10125 Oldfield, 0 Emsley, 10125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20250 Ramachandran restraints generated. 10125 Oldfield, 0 Emsley, 10125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 9138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 642 time to evaluate : 7.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 607 MET cc_start: -0.0529 (mtm) cc_final: -0.2301 (mmt) REVERT: A 691 MET cc_start: -0.0638 (tpp) cc_final: -0.1318 (tpt) REVERT: A 757 MET cc_start: -0.3630 (mmm) cc_final: -0.4000 (mmt) REVERT: A 891 MET cc_start: 0.4613 (ttp) cc_final: 0.4292 (ttt) REVERT: B 469 MET cc_start: -0.6256 (tpp) cc_final: -0.6614 (ttt) REVERT: B 607 MET cc_start: -0.1049 (ttp) cc_final: -0.2125 (ptm) REVERT: B 614 MET cc_start: -0.3723 (mtt) cc_final: -0.4531 (mtt) REVERT: B 719 MET cc_start: -0.2588 (mtm) cc_final: -0.4424 (ttm) REVERT: B 798 MET cc_start: -0.5471 (ttm) cc_final: -0.6385 (ttp) REVERT: B 929 MET cc_start: 0.1703 (ptt) cc_final: 0.0999 (ptt) REVERT: E 528 MET cc_start: -0.2153 (mmt) cc_final: -0.2925 (mmt) REVERT: F 19 MET cc_start: -0.4894 (mmp) cc_final: -0.6713 (mtt) REVERT: F 26 MET cc_start: -0.3799 (ttm) cc_final: -0.4498 (mtt) REVERT: F 290 MET cc_start: -0.0922 (mtm) cc_final: -0.1880 (mmt) REVERT: H 100 MET cc_start: -0.4209 (mtt) cc_final: -0.5437 (ptp) REVERT: H 194 MET cc_start: -0.0158 (mtt) cc_final: -0.0513 (mtm) REVERT: I 26 MET cc_start: -0.2283 (mmt) cc_final: -0.3049 (mmt) REVERT: V 228 MET cc_start: -0.1615 (mtm) cc_final: -0.2770 (ptt) REVERT: e 247 MET cc_start: -0.1496 (mtp) cc_final: -0.1764 (mtt) REVERT: e 291 MET cc_start: -0.2070 (ttm) cc_final: -0.3563 (tpt) REVERT: e 528 MET cc_start: 0.2164 (mmt) cc_final: 0.0024 (mmt) REVERT: f 285 MET cc_start: -0.4863 (ttt) cc_final: -0.5332 (ttt) REVERT: i 12 MET cc_start: -0.0872 (mmm) cc_final: -0.1348 (mtt) REVERT: i 18 MET cc_start: -0.0155 (mmm) cc_final: -0.0383 (tpt) REVERT: i 26 MET cc_start: -0.1041 (tpt) cc_final: -0.1366 (tpt) REVERT: i 39 MET cc_start: -0.1746 (mmp) cc_final: -0.3914 (mtt) REVERT: j 176 MET cc_start: -0.1876 (mtt) cc_final: -0.2213 (mtt) REVERT: k 154 MET cc_start: -0.2266 (tpp) cc_final: -0.3118 (mmm) REVERT: o 202 TRP cc_start: 0.3607 (m-90) cc_final: 0.2308 (m100) REVERT: o 501 MET cc_start: 0.8032 (mtt) cc_final: 0.7588 (mmt) REVERT: o 537 ILE cc_start: 0.8703 (tp) cc_final: 0.8370 (mp) REVERT: o 723 ASN cc_start: 0.7119 (OUTLIER) cc_final: 0.6830 (m-40) REVERT: o 979 LEU cc_start: 0.8287 (mt) cc_final: 0.8084 (mt) REVERT: o 1292 MET cc_start: 0.8776 (mmp) cc_final: 0.8333 (mmm) REVERT: o 1344 MET cc_start: 0.8410 (pmm) cc_final: 0.7972 (tpt) REVERT: p 287 HIS cc_start: 0.7801 (m-70) cc_final: 0.7181 (m-70) REVERT: p 363 TYR cc_start: 0.6827 (m-80) cc_final: 0.6409 (m-80) REVERT: p 403 LEU cc_start: 0.8676 (tp) cc_final: 0.8319 (tt) REVERT: p 675 LEU cc_start: 0.8887 (mp) cc_final: 0.8635 (mp) REVERT: p 896 LEU cc_start: 0.7033 (tp) cc_final: 0.6726 (tp) REVERT: t 80 MET cc_start: 0.5875 (ttt) cc_final: 0.4855 (tpt) REVERT: u 117 MET cc_start: -0.3185 (mtm) cc_final: -0.4249 (ttp) outliers start: 24 outliers final: 1 residues processed: 662 average time/residue: 0.7866 time to fit residues: 911.6116 Evaluate side-chains 488 residues out of total 9138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 486 time to evaluate : 7.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1022 random chunks: chunk 515 optimal weight: 30.0000 chunk 288 optimal weight: 8.9990 chunk 772 optimal weight: 3.9990 chunk 631 optimal weight: 6.9990 chunk 256 optimal weight: 30.0000 chunk 929 optimal weight: 3.9990 chunk 1004 optimal weight: 10.0000 chunk 828 optimal weight: 1.9990 chunk 922 optimal weight: 1.9990 chunk 316 optimal weight: 20.0000 chunk 745 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 741 GLN B 415 HIS ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 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** I 126 ASN J 160 GLN ** L 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 GLN ** O 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 139 ASN ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 158 ASN ** T 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 89 HIS V 127 ASN ** V 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 43 GLN e 238 GLN e 246 HIS e 368 ASN e 673 HIS f 220 GLN f 254 GLN i 81 GLN j 173 HIS o 372 ASN o 539 GLN ** o 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 731 ASN o 740 GLN o 791 GLN ** o1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1129 ASN ** o1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 197 GLN ** p 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 350 HIS p 410 ASN ** p 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 639 HIS ** p1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p1040 GLN ** p1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 135 GLN ** s 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 121 HIS y 2 ASN y 22 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3096 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.177 87755 Z= 0.300 Angle : 0.678 18.167 119350 Z= 0.355 Chirality : 0.044 0.261 13313 Planarity : 0.005 0.119 14809 Dihedral : 14.306 178.890 13047 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.24 % Favored : 94.64 % Rotamer: Outliers : 0.15 % Allowed : 4.50 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % 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: -1.69 (0.08), residues: 10125 helix: -0.45 (0.08), residues: 4078 sheet: -0.67 (0.14), residues: 1296 loop : -1.83 (0.08), residues: 4751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP e 612 HIS 0.015 0.001 HIS j 173 PHE 0.034 0.002 PHE o 822 TYR 0.043 0.002 TYR p1048 ARG 0.032 0.001 ARG s 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20250 Ramachandran restraints generated. 10125 Oldfield, 0 Emsley, 10125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20250 Ramachandran restraints generated. 10125 Oldfield, 0 Emsley, 10125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 9138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 568 time to evaluate : 7.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: -0.0269 (ptt) cc_final: -0.2449 (ptt) REVERT: A 607 MET cc_start: -0.0852 (mtm) cc_final: -0.2154 (mmt) REVERT: A 665 MET cc_start: -0.4642 (ttt) cc_final: -0.4862 (ttt) REVERT: A 691 MET cc_start: -0.0509 (tpp) cc_final: -0.1373 (tpt) REVERT: A 757 MET cc_start: -0.3696 (mmm) cc_final: -0.3938 (mmt) REVERT: A 891 MET cc_start: 0.4754 (ttp) cc_final: 0.4393 (ttt) REVERT: B 212 MET cc_start: -0.4020 (ttt) cc_final: -0.5133 (ttt) REVERT: B 469 MET cc_start: -0.6146 (tpp) cc_final: -0.6472 (ttt) REVERT: B 607 MET cc_start: -0.1101 (ttp) cc_final: -0.2184 (ptm) REVERT: B 614 MET cc_start: -0.3965 (mtt) cc_final: -0.4767 (mtt) REVERT: B 719 MET cc_start: -0.3400 (mtm) cc_final: -0.4413 (ttm) REVERT: B 798 MET cc_start: -0.5371 (ttm) cc_final: -0.6426 (ttp) REVERT: B 929 MET cc_start: 0.1139 (ptt) cc_final: 0.0456 (ptt) REVERT: E 297 MET cc_start: -0.2596 (mtt) cc_final: -0.3311 (mtt) REVERT: E 528 MET cc_start: -0.2295 (mmt) cc_final: -0.2589 (mmt) REVERT: F 19 MET cc_start: -0.4866 (mmp) cc_final: -0.6763 (mtp) REVERT: F 26 MET cc_start: -0.3801 (ttm) cc_final: -0.4456 (mtt) REVERT: F 290 MET cc_start: -0.1152 (mtm) cc_final: -0.1846 (mmt) REVERT: F 309 MET cc_start: -0.3295 (mtt) cc_final: -0.3935 (mtm) REVERT: F 382 GLU cc_start: -0.2513 (OUTLIER) cc_final: -0.3496 (pp20) REVERT: H 100 MET cc_start: -0.4026 (mtt) cc_final: -0.5447 (ptp) REVERT: I 26 MET cc_start: -0.1772 (mmt) cc_final: -0.2777 (mmt) REVERT: R 124 MET cc_start: 0.5997 (ptp) cc_final: 0.5725 (ptp) REVERT: U 110 MET cc_start: -0.1680 (ttt) cc_final: -0.2422 (ttp) REVERT: V 228 MET cc_start: -0.1537 (mtm) cc_final: -0.2994 (ptt) REVERT: e 247 MET cc_start: -0.1584 (mtp) cc_final: -0.1814 (mtt) REVERT: e 291 MET cc_start: -0.2223 (ttm) cc_final: -0.3860 (tpt) REVERT: f 19 MET cc_start: -0.4044 (ttt) cc_final: -0.4846 (ttt) REVERT: f 58 MET cc_start: -0.3323 (tmm) cc_final: -0.4035 (ttt) REVERT: f 285 MET cc_start: -0.4714 (ttt) cc_final: -0.5450 (ttt) REVERT: i 12 MET cc_start: -0.0957 (mmm) cc_final: -0.1593 (mtt) REVERT: i 39 MET cc_start: -0.1954 (mmp) cc_final: -0.4195 (mtt) REVERT: j 176 MET cc_start: -0.2019 (mtt) cc_final: -0.2370 (mtt) REVERT: k 154 MET cc_start: -0.2092 (tpp) cc_final: -0.2617 (mmm) REVERT: o 202 TRP cc_start: 0.3867 (m-90) cc_final: 0.2545 (m100) REVERT: o 561 MET cc_start: 0.8639 (mtt) cc_final: 0.8291 (mtp) REVERT: o 564 LEU cc_start: 0.8237 (mt) cc_final: 0.8017 (mt) REVERT: o 1292 MET cc_start: 0.8869 (mmp) cc_final: 0.8423 (mmm) REVERT: o 1344 MET cc_start: 0.8397 (pmm) cc_final: 0.8002 (tpt) REVERT: p 176 GLU cc_start: 0.7619 (tp30) cc_final: 0.6974 (tp30) REVERT: p 206 TYR cc_start: 0.7787 (m-10) cc_final: 0.7522 (m-10) REVERT: p 287 HIS cc_start: 0.7832 (m-70) cc_final: 0.7527 (m90) REVERT: p 347 MET cc_start: 0.7728 (mmt) cc_final: 0.7407 (mmm) REVERT: p 363 TYR cc_start: 0.7016 (m-80) cc_final: 0.6211 (m-80) REVERT: p 403 LEU cc_start: 0.8825 (tp) cc_final: 0.8500 (tt) REVERT: p 522 LEU cc_start: 0.9384 (mt) cc_final: 0.8742 (tt) REVERT: p 594 MET cc_start: 0.7493 (tpt) cc_final: 0.6878 (tpp) REVERT: p 675 LEU cc_start: 0.8974 (mp) cc_final: 0.8621 (mp) REVERT: p 681 ASP cc_start: 0.8134 (m-30) cc_final: 0.7894 (m-30) REVERT: p 797 ASN cc_start: 0.8945 (t0) cc_final: 0.8710 (t0) REVERT: t 80 MET cc_start: 0.5491 (ttt) cc_final: 0.4896 (tpp) REVERT: w 33 ARG cc_start: 0.2869 (mmp-170) cc_final: 0.1912 (mmt180) REVERT: u 117 MET cc_start: -0.3270 (mtm) cc_final: -0.4124 (ttp) outliers start: 14 outliers final: 4 residues processed: 580 average time/residue: 0.7564 time to fit residues: 773.7229 Evaluate side-chains 461 residues out of total 9138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 456 time to evaluate : 7.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1022 random chunks: chunk 918 optimal weight: 2.9990 chunk 699 optimal weight: 3.9990 chunk 482 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 443 optimal weight: 0.0470 chunk 624 optimal weight: 0.0970 chunk 933 optimal weight: 20.0000 chunk 987 optimal weight: 1.9990 chunk 487 optimal weight: 0.3980 chunk 884 optimal weight: 0.8980 chunk 266 optimal weight: 2.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 ASN ** A 837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 652 GLN D 936 GLN E 268 HIS F 221 GLN F 422 HIS ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 208 GLN ** U 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 143 GLN ** U 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 43 GLN e 238 GLN e 254 ASN j 160 GLN ** o 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 576 GLN ** o 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 700 GLN o 704 ASN o 740 GLN ** o1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1024 ASN o1078 GLN o1244 ASN ** o1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1397 HIS ** o1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p1040 GLN ** p1117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 74 GLN y 2 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3009 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 87755 Z= 0.165 Angle : 0.594 14.104 119350 Z= 0.306 Chirality : 0.042 0.227 13313 Planarity : 0.004 0.064 14809 Dihedral : 14.149 176.107 13047 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.36 % Favored : 95.53 % Rotamer: Outliers : 0.03 % Allowed : 2.63 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.08), residues: 10125 helix: -0.01 (0.08), residues: 4053 sheet: -0.39 (0.14), residues: 1280 loop : -1.59 (0.09), residues: 4792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP e 612 HIS 0.007 0.001 HIS E 268 PHE 0.038 0.001 PHE f 259 TYR 0.025 0.001 TYR o 669 ARG 0.008 0.000 ARG P 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20250 Ramachandran restraints generated. 10125 Oldfield, 0 Emsley, 10125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20250 Ramachandran restraints generated. 10125 Oldfield, 0 Emsley, 10125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 9138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 585 time to evaluate : 7.883 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: A 352 MET cc_start: -0.0503 (ptt) cc_final: -0.1489 (ppp) REVERT: A 491 MET cc_start: -0.2787 (mtt) cc_final: -0.3439 (mmt) REVERT: A 607 MET cc_start: -0.0785 (mtm) cc_final: -0.2226 (mmt) REVERT: A 691 MET cc_start: -0.0752 (tpp) cc_final: -0.1581 (tpt) REVERT: A 757 MET cc_start: -0.3666 (mmm) cc_final: -0.3887 (mmt) REVERT: A 891 MET cc_start: 0.4878 (ttp) cc_final: 0.4490 (ttt) REVERT: B 469 MET cc_start: -0.6185 (tpp) cc_final: -0.6425 (ttt) REVERT: B 607 MET cc_start: -0.1035 (ttp) cc_final: -0.2128 (ptm) REVERT: B 614 MET cc_start: -0.3617 (mtt) cc_final: -0.4459 (mtt) REVERT: B 634 MET cc_start: -0.5687 (mtt) cc_final: -0.6840 (ttt) REVERT: B 719 MET cc_start: -0.3355 (mtm) cc_final: -0.4255 (ttp) REVERT: B 798 MET cc_start: -0.5481 (ttm) cc_final: -0.6630 (ttp) REVERT: B 929 MET cc_start: 0.0954 (ptt) cc_final: 0.0141 (ptt) REVERT: E 291 MET cc_start: -0.0943 (mmt) cc_final: -0.1315 (mmt) REVERT: E 297 MET cc_start: -0.2847 (mtt) cc_final: -0.3378 (mtt) REVERT: E 528 MET cc_start: -0.2263 (mmt) cc_final: -0.2551 (mmt) REVERT: F 19 MET cc_start: -0.4913 (mmp) cc_final: -0.6665 (mtt) REVERT: F 26 MET cc_start: -0.3742 (ttm) cc_final: -0.4570 (mtt) REVERT: F 290 MET cc_start: -0.1633 (mtm) cc_final: -0.2227 (mmt) REVERT: F 309 MET cc_start: -0.3088 (mtt) cc_final: -0.3536 (mtm) REVERT: I 26 MET cc_start: -0.2007 (mmt) cc_final: -0.2948 (mmt) REVERT: L 83 MET cc_start: -0.2253 (ppp) cc_final: -0.2725 (ptt) REVERT: R 124 MET cc_start: 0.5916 (ptp) cc_final: 0.5544 (ptp) REVERT: U 48 MET cc_start: -0.2245 (mtp) cc_final: -0.3780 (mmt) REVERT: U 110 MET cc_start: -0.1520 (ttt) cc_final: -0.2777 (ttp) REVERT: V 228 MET cc_start: -0.1269 (mtm) cc_final: -0.3003 (ptt) REVERT: e 291 MET cc_start: -0.2186 (ttm) cc_final: -0.3838 (tpt) REVERT: e 528 MET cc_start: 0.1347 (mmt) cc_final: -0.1096 (mmt) REVERT: f 19 MET cc_start: -0.3949 (ttt) cc_final: -0.4261 (ttt) REVERT: f 26 MET cc_start: -0.3884 (tpt) cc_final: -0.4604 (tpt) REVERT: f 58 MET cc_start: -0.3091 (tmm) cc_final: -0.3877 (ttt) REVERT: f 285 MET cc_start: -0.4750 (ttt) cc_final: -0.5356 (ttt) REVERT: i 12 MET cc_start: -0.0798 (mmm) cc_final: -0.1449 (mtt) REVERT: i 39 MET cc_start: -0.1599 (mmp) cc_final: -0.4169 (mtt) REVERT: j 176 MET cc_start: -0.1758 (mtt) cc_final: -0.2178 (mtt) REVERT: k 154 MET cc_start: -0.2057 (tpp) cc_final: -0.2662 (mmm) REVERT: o 501 MET cc_start: 0.8492 (mtt) cc_final: 0.7965 (mmt) REVERT: o 841 MET cc_start: 0.9293 (mtt) cc_final: 0.8923 (mtt) REVERT: o 1086 MET cc_start: 0.7965 (tpt) cc_final: 0.7443 (tpp) REVERT: o 1228 MET cc_start: -0.2557 (ttt) cc_final: -0.2843 (ttp) REVERT: o 1292 MET cc_start: 0.8893 (mmp) cc_final: 0.8486 (mmm) REVERT: o 1344 MET cc_start: 0.8300 (pmm) cc_final: 0.7691 (tpt) REVERT: p 176 GLU cc_start: 0.7529 (tp30) cc_final: 0.7004 (tp30) REVERT: p 206 TYR cc_start: 0.7586 (m-10) cc_final: 0.7100 (m-10) REVERT: p 287 HIS cc_start: 0.7739 (m-70) cc_final: 0.7336 (m90) REVERT: p 363 TYR cc_start: 0.6896 (m-80) cc_final: 0.6060 (m-80) REVERT: p 382 LEU cc_start: 0.8014 (tp) cc_final: 0.7732 (tt) REVERT: p 403 LEU cc_start: 0.8855 (tp) cc_final: 0.8516 (tt) REVERT: p 482 LEU cc_start: 0.9250 (mt) cc_final: 0.8687 (tt) REVERT: p 522 LEU cc_start: 0.9284 (mt) cc_final: 0.8735 (tt) REVERT: p 702 MET cc_start: 0.8790 (mmt) cc_final: 0.8492 (mmt) REVERT: p 797 ASN cc_start: 0.8735 (t0) cc_final: 0.8535 (t0) REVERT: t 80 MET cc_start: 0.5260 (ttt) cc_final: 0.4639 (tpp) REVERT: u 117 MET cc_start: -0.3254 (mtm) cc_final: -0.4012 (ttp) outliers start: 3 outliers final: 1 residues processed: 588 average time/residue: 0.7572 time to fit residues: 782.9736 Evaluate side-chains 464 residues out of total 9138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 463 time to evaluate : 7.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1022 random chunks: chunk 822 optimal weight: 6.9990 chunk 560 optimal weight: 10.0000 chunk 14 optimal weight: 50.0000 chunk 735 optimal weight: 20.0000 chunk 407 optimal weight: 40.0000 chunk 842 optimal weight: 0.8980 chunk 682 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 504 optimal weight: 0.9980 chunk 886 optimal weight: 2.9990 chunk 249 optimal weight: 9.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 ASN ** A 837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 ASN B 882 HIS F 275 ASN F 385 HIS I 38 GLN ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 HIS L 64 GLN ** O 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 144 GLN T 208 GLN U 58 GLN ** U 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 238 GLN ** e 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 59 HIS j 160 GLN m 107 ASN ** o 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 539 GLN ** o 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 685 HIS o 740 GLN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1005 HIS o1093 GLN ** o1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 2 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3066 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 87755 Z= 0.190 Angle : 0.587 18.260 119350 Z= 0.302 Chirality : 0.042 0.233 13313 Planarity : 0.004 0.054 14809 Dihedral : 14.093 175.808 13047 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.89 % Favored : 94.98 % Rotamer: Outliers : 0.02 % Allowed : 2.31 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % 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: -0.92 (0.08), residues: 10125 helix: 0.30 (0.08), residues: 4055 sheet: -0.33 (0.14), residues: 1314 loop : -1.48 (0.09), residues: 4756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 612 HIS 0.007 0.001 HIS o 685 PHE 0.026 0.001 PHE o1058 TYR 0.020 0.001 TYR p1048 ARG 0.008 0.000 ARG p 721 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20250 Ramachandran restraints generated. 10125 Oldfield, 0 Emsley, 10125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20250 Ramachandran restraints generated. 10125 Oldfield, 0 Emsley, 10125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 9138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 543 time to evaluate : 7.881 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 352 MET cc_start: -0.0788 (ptt) cc_final: -0.1290 (ppp) REVERT: A 491 MET cc_start: -0.2784 (mtt) cc_final: -0.3568 (mmt) REVERT: A 607 MET cc_start: -0.0921 (mtm) cc_final: -0.2370 (mmt) REVERT: A 691 MET cc_start: -0.0558 (tpp) cc_final: -0.1743 (tpt) REVERT: A 757 MET cc_start: -0.3569 (mmm) cc_final: -0.3829 (mmt) REVERT: B 170 MET cc_start: -0.3390 (tmm) cc_final: -0.3591 (ttt) REVERT: B 607 MET cc_start: -0.1303 (ttp) cc_final: -0.2248 (ptm) REVERT: B 614 MET cc_start: -0.3811 (mtt) cc_final: -0.4665 (mtt) REVERT: B 634 MET cc_start: -0.5689 (mtt) cc_final: -0.6851 (ttt) REVERT: B 719 MET cc_start: -0.3104 (mtm) cc_final: -0.4282 (ttm) REVERT: B 798 MET cc_start: -0.5457 (ttm) cc_final: -0.6152 (ttt) REVERT: B 929 MET cc_start: 0.0954 (ptt) cc_final: 0.0127 (ptt) REVERT: E 291 MET cc_start: -0.0211 (mmt) cc_final: -0.0809 (mmt) REVERT: E 297 MET cc_start: -0.2783 (mtt) cc_final: -0.3292 (mtt) REVERT: E 528 MET cc_start: -0.2100 (mmt) cc_final: -0.2638 (mmt) REVERT: F 19 MET cc_start: -0.4880 (mmp) cc_final: -0.6585 (mtt) REVERT: F 290 MET cc_start: -0.1736 (mtm) cc_final: -0.2033 (mmt) REVERT: F 309 MET cc_start: -0.2904 (mtt) cc_final: -0.3685 (mtm) REVERT: F 382 GLU cc_start: -0.2650 (OUTLIER) cc_final: -0.3570 (pp20) REVERT: I 19 MET cc_start: -0.2789 (mmt) cc_final: -0.3032 (mmt) REVERT: I 26 MET cc_start: -0.2326 (mmt) cc_final: -0.3118 (mmt) REVERT: L 83 MET cc_start: -0.1854 (ppp) cc_final: -0.2456 (ptt) REVERT: R 124 MET cc_start: 0.5988 (ptp) cc_final: 0.5440 (ptp) REVERT: U 48 MET cc_start: -0.2025 (mtp) cc_final: -0.3639 (mmt) REVERT: U 110 MET cc_start: -0.1192 (ttt) cc_final: -0.3161 (ttp) REVERT: V 228 MET cc_start: -0.1257 (mtm) cc_final: -0.2899 (ptt) REVERT: e 291 MET cc_start: -0.2182 (ttm) cc_final: -0.3545 (tpt) REVERT: e 528 MET cc_start: 0.1299 (mmt) cc_final: -0.1068 (mmt) REVERT: f 19 MET cc_start: -0.4036 (ttt) cc_final: -0.4294 (ttt) REVERT: f 26 MET cc_start: -0.3765 (tpt) cc_final: -0.4518 (tpt) REVERT: f 58 MET cc_start: -0.3015 (tmm) cc_final: -0.3769 (ttt) REVERT: f 285 MET cc_start: -0.4761 (ttt) cc_final: -0.5224 (ttt) REVERT: i 12 MET cc_start: -0.0864 (mmm) cc_final: -0.1489 (mtt) REVERT: i 39 MET cc_start: -0.1966 (mmp) cc_final: -0.4353 (mtt) REVERT: j 176 MET cc_start: -0.1597 (mtt) cc_final: -0.2017 (mtt) REVERT: k 154 MET cc_start: -0.2224 (tpp) cc_final: -0.2674 (mmm) REVERT: o 501 MET cc_start: 0.8528 (mtt) cc_final: 0.7738 (mmt) REVERT: o 561 MET cc_start: 0.8812 (mtt) cc_final: 0.8318 (mtp) REVERT: o 835 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8036 (mt-10) REVERT: o 841 MET cc_start: 0.9283 (mtt) cc_final: 0.8965 (mtt) REVERT: o 1292 MET cc_start: 0.8924 (mmp) cc_final: 0.8538 (mmm) REVERT: o 1344 MET cc_start: 0.8306 (pmm) cc_final: 0.7564 (tpt) REVERT: p 176 GLU cc_start: 0.7541 (tp30) cc_final: 0.7076 (tp30) REVERT: p 206 TYR cc_start: 0.7533 (m-10) cc_final: 0.7077 (m-10) REVERT: p 287 HIS cc_start: 0.7638 (m-70) cc_final: 0.7336 (m90) REVERT: p 347 MET cc_start: 0.7862 (mmt) cc_final: 0.7478 (mmm) REVERT: p 363 TYR cc_start: 0.7008 (m-80) cc_final: 0.5991 (m-80) REVERT: p 403 LEU cc_start: 0.8899 (tp) cc_final: 0.8463 (tt) REVERT: p 482 LEU cc_start: 0.9249 (mt) cc_final: 0.8690 (tt) REVERT: p 522 LEU cc_start: 0.9367 (mt) cc_final: 0.8748 (tt) REVERT: p 584 MET cc_start: 0.9077 (ttm) cc_final: 0.8688 (ttm) REVERT: p 594 MET cc_start: 0.7553 (tpt) cc_final: 0.6748 (tpp) REVERT: p 1078 ARG cc_start: 0.6683 (tmm160) cc_final: 0.5652 (mtt-85) REVERT: q 48 ASP cc_start: 0.6473 (t70) cc_final: 0.6174 (t70) REVERT: t 80 MET cc_start: 0.5418 (ttt) cc_final: 0.4774 (tpp) REVERT: u 117 MET cc_start: -0.3157 (mtm) cc_final: -0.3970 (ttp) outliers start: 2 outliers final: 0 residues processed: 545 average time/residue: 0.7561 time to fit residues: 725.9589 Evaluate side-chains 451 residues out of total 9138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 450 time to evaluate : 7.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1022 random chunks: chunk 332 optimal weight: 20.0000 chunk 889 optimal weight: 10.0000 chunk 195 optimal weight: 50.0000 chunk 579 optimal weight: 9.9990 chunk 243 optimal weight: 5.9990 chunk 988 optimal weight: 9.9990 chunk 820 optimal weight: 5.9990 chunk 457 optimal weight: 30.0000 chunk 82 optimal weight: 40.0000 chunk 327 optimal weight: 40.0000 chunk 519 optimal weight: 50.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 837 HIS B 426 ASN B 474 ASN B 521 GLN I 38 GLN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 139 ASN R 140 ASN ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 86 GLN ** T 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 238 GLN e 468 ASN ** e 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 98 GLN k 186 HIS o 62 GLN ** o 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 387 ASN ** o 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 507 GLN ** o 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 678 ASN ** o 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 740 GLN ** o 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 825 ASN ** o1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1163 HIS ** o1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1397 HIS ** o1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p1007 ASN ** p1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 60 HIS ** 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 22 HIS ** s 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 133 GLN v 87 GLN w 60 HIS ** w 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 21 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3344 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.260 87755 Z= 0.576 Angle : 0.914 24.107 119350 Z= 0.471 Chirality : 0.050 0.439 13313 Planarity : 0.007 0.134 14809 Dihedral : 14.553 177.050 13047 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 23.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.63 % Favored : 93.15 % Rotamer: Outliers : 0.14 % Allowed : 2.99 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.32 (0.08), residues: 10125 helix: 0.04 (0.08), residues: 4080 sheet: -0.70 (0.14), residues: 1344 loop : -1.74 (0.09), residues: 4701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP q 176 HIS 0.030 0.002 HIS p 970 PHE 0.069 0.003 PHE o 566 TYR 0.056 0.002 TYR q 230 ARG 0.028 0.001 ARG o 999 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20250 Ramachandran restraints generated. 10125 Oldfield, 0 Emsley, 10125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20250 Ramachandran restraints generated. 10125 Oldfield, 0 Emsley, 10125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 9138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 466 time to evaluate : 7.936 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: A 352 MET cc_start: -0.0006 (ptt) cc_final: -0.0631 (ppp) REVERT: A 491 MET cc_start: -0.2727 (mtt) cc_final: -0.3918 (mmt) REVERT: A 607 MET cc_start: -0.0819 (mtm) cc_final: -0.2173 (mmt) REVERT: A 691 MET cc_start: -0.0696 (tpp) cc_final: -0.1905 (tpt) REVERT: A 757 MET cc_start: -0.3552 (mmm) cc_final: -0.3834 (mmt) REVERT: B 607 MET cc_start: -0.1015 (ttp) cc_final: -0.2158 (ptm) REVERT: B 614 MET cc_start: -0.4149 (mtt) cc_final: -0.4698 (mtt) REVERT: B 634 MET cc_start: -0.5731 (mtt) cc_final: -0.6706 (ttt) REVERT: B 719 MET cc_start: -0.2753 (mtm) cc_final: -0.3997 (ttm) REVERT: B 798 MET cc_start: -0.5351 (ttm) cc_final: -0.6165 (ttp) REVERT: B 929 MET cc_start: 0.1461 (ptt) cc_final: 0.0512 (ptt) REVERT: E 297 MET cc_start: -0.2710 (mtt) cc_final: -0.3116 (mtt) REVERT: E 528 MET cc_start: -0.1855 (mmt) cc_final: -0.2389 (mmt) REVERT: F 19 MET cc_start: -0.4790 (mmp) cc_final: -0.6568 (mtt) REVERT: F 290 MET cc_start: -0.1566 (mtm) cc_final: -0.2254 (mmt) REVERT: F 309 MET cc_start: -0.3270 (mtt) cc_final: -0.3814 (mtm) REVERT: I 19 MET cc_start: -0.3151 (mmt) cc_final: -0.3468 (mmt) REVERT: I 26 MET cc_start: -0.1948 (mmt) cc_final: -0.2863 (mmt) REVERT: L 83 MET cc_start: -0.2008 (ppp) cc_final: -0.2278 (ptt) REVERT: R 124 MET cc_start: 0.6013 (ptp) cc_final: 0.5777 (ptp) REVERT: U 48 MET cc_start: -0.1991 (mtp) cc_final: -0.3266 (mmt) REVERT: U 110 MET cc_start: -0.1275 (ttt) cc_final: -0.2819 (ttp) REVERT: V 228 MET cc_start: -0.1044 (mtm) cc_final: -0.2618 (ptt) REVERT: e 291 MET cc_start: -0.2369 (ttm) cc_final: -0.3568 (tpt) REVERT: e 528 MET cc_start: 0.1169 (mmt) cc_final: -0.1135 (mmt) REVERT: f 19 MET cc_start: -0.4080 (ttt) cc_final: -0.4287 (ttt) REVERT: f 26 MET cc_start: -0.3771 (tpt) cc_final: -0.4616 (tpt) REVERT: f 58 MET cc_start: -0.3000 (tmm) cc_final: -0.3741 (ttt) REVERT: f 285 MET cc_start: -0.5005 (ttt) cc_final: -0.5435 (ttt) REVERT: i 12 MET cc_start: -0.0876 (mmm) cc_final: -0.1511 (mtt) REVERT: i 39 MET cc_start: -0.2394 (mmp) cc_final: -0.4607 (mtt) REVERT: j 176 MET cc_start: -0.1629 (mtt) cc_final: -0.1990 (mtt) REVERT: k 154 MET cc_start: -0.2410 (tpp) cc_final: -0.2706 (mmm) REVERT: o 355 MET cc_start: 0.5892 (pmm) cc_final: 0.4984 (mpp) REVERT: o 1279 MET cc_start: 0.5691 (tpt) cc_final: 0.5485 (tpt) REVERT: o 1292 MET cc_start: 0.9060 (mmp) cc_final: 0.8692 (mmm) REVERT: p 206 TYR cc_start: 0.7496 (m-10) cc_final: 0.7130 (m-10) REVERT: p 395 LEU cc_start: 0.8311 (mt) cc_final: 0.8066 (mt) REVERT: p 625 LEU cc_start: 0.8832 (mt) cc_final: 0.8621 (mt) REVERT: p 670 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8486 (mt-10) REVERT: p 752 TYR cc_start: 0.8746 (m-10) cc_final: 0.8363 (m-10) REVERT: p 1153 TYR cc_start: 0.7789 (t80) cc_final: 0.7294 (t80) REVERT: s 94 MET cc_start: 0.8421 (mmp) cc_final: 0.8219 (mmp) REVERT: u 117 MET cc_start: -0.2768 (mtm) cc_final: -0.3601 (ttp) outliers start: 13 outliers final: 6 residues processed: 479 average time/residue: 0.7825 time to fit residues: 663.9617 Evaluate side-chains 403 residues out of total 9138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 397 time to evaluate : 7.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1022 random chunks: chunk 953 optimal weight: 5.9990 chunk 111 optimal weight: 40.0000 chunk 563 optimal weight: 5.9990 chunk 722 optimal weight: 4.9990 chunk 559 optimal weight: 20.0000 chunk 832 optimal weight: 1.9990 chunk 552 optimal weight: 0.0980 chunk 985 optimal weight: 3.9990 chunk 616 optimal weight: 50.0000 chunk 600 optimal weight: 0.8980 chunk 454 optimal weight: 0.0040 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 ASN I 38 GLN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 256 GLN ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 234 HIS T 208 GLN ** T 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 238 GLN ** e 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 430 HIS ** o 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 387 ASN ** o 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 740 GLN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 825 ASN ** o1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1078 GLN ** o1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p1040 GLN ** p1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 60 HIS ** r 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 64 HIS s 148 HIS ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 89 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3165 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 87755 Z= 0.187 Angle : 0.616 16.533 119350 Z= 0.315 Chirality : 0.043 0.217 13313 Planarity : 0.004 0.061 14809 Dihedral : 14.309 171.847 13047 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.04 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.90 (0.08), residues: 10125 helix: 0.36 (0.08), residues: 4098 sheet: -0.43 (0.14), residues: 1280 loop : -1.49 (0.09), residues: 4747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP q 176 HIS 0.016 0.001 HIS o 685 PHE 0.045 0.001 PHE c 70 TYR 0.026 0.001 TYR R 27 ARG 0.019 0.000 ARG O 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20250 Ramachandran restraints generated. 10125 Oldfield, 0 Emsley, 10125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20250 Ramachandran restraints generated. 10125 Oldfield, 0 Emsley, 10125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 9138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 514 time to evaluate : 7.779 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: A 352 MET cc_start: 0.0419 (ptt) cc_final: -0.0352 (ppp) REVERT: A 491 MET cc_start: -0.2864 (mtt) cc_final: -0.3787 (mmt) REVERT: A 607 MET cc_start: -0.0898 (mtm) cc_final: -0.2271 (mmt) REVERT: A 691 MET cc_start: -0.0793 (tpp) cc_final: -0.1965 (tpt) REVERT: A 757 MET cc_start: -0.3472 (mmm) cc_final: -0.3778 (mmt) REVERT: A 891 MET cc_start: 0.5077 (ttp) cc_final: 0.4785 (ttt) REVERT: B 170 MET cc_start: -0.3270 (tmm) cc_final: -0.3605 (ttt) REVERT: B 607 MET cc_start: -0.1147 (ttp) cc_final: -0.2163 (ptm) REVERT: B 614 MET cc_start: -0.4104 (mtt) cc_final: -0.4601 (mtt) REVERT: B 634 MET cc_start: -0.5712 (mtt) cc_final: -0.6710 (ttt) REVERT: B 719 MET cc_start: -0.2692 (mtm) cc_final: -0.3964 (ttm) REVERT: B 798 MET cc_start: -0.5243 (ttm) cc_final: -0.5562 (ttm) REVERT: B 929 MET cc_start: 0.1249 (ptt) cc_final: 0.0328 (ptt) REVERT: E 291 MET cc_start: 0.0274 (mpp) cc_final: 0.0047 (mmt) REVERT: E 297 MET cc_start: -0.2349 (mtt) cc_final: -0.2999 (mtt) REVERT: E 528 MET cc_start: -0.1807 (mmt) cc_final: -0.2370 (mmt) REVERT: F 19 MET cc_start: -0.4794 (mmp) cc_final: -0.6506 (mtt) REVERT: F 290 MET cc_start: -0.1710 (mtm) cc_final: -0.2297 (mmt) REVERT: F 309 MET cc_start: -0.3099 (mtt) cc_final: -0.3719 (mtm) REVERT: L 83 MET cc_start: -0.1989 (ppp) cc_final: -0.2604 (ptt) REVERT: U 48 MET cc_start: -0.1847 (mtp) cc_final: -0.3216 (mmt) REVERT: U 110 MET cc_start: -0.1257 (ttt) cc_final: -0.2757 (ttp) REVERT: V 228 MET cc_start: -0.0895 (mtm) cc_final: -0.2555 (ptt) REVERT: e 291 MET cc_start: -0.2342 (ttm) cc_final: -0.3561 (tpt) REVERT: e 528 MET cc_start: 0.1112 (mmt) cc_final: -0.1272 (mmt) REVERT: f 26 MET cc_start: -0.3590 (tpt) cc_final: -0.4343 (tpt) REVERT: f 58 MET cc_start: -0.3046 (tmm) cc_final: -0.3532 (ttt) REVERT: f 285 MET cc_start: -0.5070 (ttt) cc_final: -0.5406 (ttt) REVERT: i 12 MET cc_start: -0.0923 (mmm) cc_final: -0.1504 (mtt) REVERT: i 39 MET cc_start: -0.2353 (mmp) cc_final: -0.4512 (mtt) REVERT: j 176 MET cc_start: -0.1519 (mtt) cc_final: -0.1876 (mtt) REVERT: k 154 MET cc_start: -0.2413 (tpp) cc_final: -0.2678 (mmm) REVERT: o 355 MET cc_start: 0.5670 (pmm) cc_final: 0.4889 (mpp) REVERT: o 476 ILE cc_start: 0.7974 (mt) cc_final: 0.7605 (mm) REVERT: o 535 MET cc_start: 0.6201 (pmm) cc_final: 0.5973 (pmm) REVERT: o 561 MET cc_start: 0.8967 (mtt) cc_final: 0.8071 (mtt) REVERT: o 677 ASN cc_start: 0.8759 (m110) cc_final: 0.8418 (m110) REVERT: o 841 MET cc_start: 0.9292 (mtt) cc_final: 0.9057 (mtt) REVERT: o 1292 MET cc_start: 0.9019 (mmp) cc_final: 0.8647 (mmm) REVERT: o 1344 MET cc_start: 0.8419 (pmm) cc_final: 0.7430 (tpt) REVERT: p 382 LEU cc_start: 0.8260 (tp) cc_final: 0.7967 (tt) REVERT: p 390 ASN cc_start: 0.8154 (m-40) cc_final: 0.7654 (m110) REVERT: p 482 LEU cc_start: 0.9368 (mt) cc_final: 0.8797 (tt) REVERT: p 508 MET cc_start: 0.7957 (mpp) cc_final: 0.7693 (mpp) REVERT: p 594 MET cc_start: 0.7551 (tpt) cc_final: 0.7164 (tpp) REVERT: p 670 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8451 (mt-10) REVERT: p 797 ASN cc_start: 0.8972 (t0) cc_final: 0.8735 (t0) REVERT: p 1057 ASP cc_start: 0.8457 (t0) cc_final: 0.8073 (t0) REVERT: s 94 MET cc_start: 0.8328 (mmp) cc_final: 0.8063 (mmp) REVERT: s 151 MET cc_start: 0.6359 (ppp) cc_final: 0.5594 (ppp) REVERT: u 117 MET cc_start: -0.2792 (mtm) cc_final: -0.3889 (ttp) outliers start: 0 outliers final: 0 residues processed: 514 average time/residue: 0.8219 time to fit residues: 750.0365 Evaluate side-chains 419 residues out of total 9138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 419 time to evaluate : 7.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1022 random chunks: chunk 609 optimal weight: 50.0000 chunk 393 optimal weight: 20.0000 chunk 588 optimal weight: 50.0000 chunk 296 optimal weight: 8.9990 chunk 193 optimal weight: 7.9990 chunk 190 optimal weight: 10.0000 chunk 626 optimal weight: 6.9990 chunk 671 optimal weight: 0.8980 chunk 487 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 774 optimal weight: 0.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 ASN F 142 GLN I 38 GLN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 238 GLN ** e 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 387 ASN ** o 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 740 GLN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 825 ASN o 885 GLN ** o1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1078 GLN o1108 HIS ** o1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 43 GLN ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3287 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.209 87755 Z= 0.367 Angle : 0.715 22.745 119350 Z= 0.367 Chirality : 0.045 0.376 13313 Planarity : 0.005 0.101 14809 Dihedral : 14.358 174.260 13047 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.41 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.03 % 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: -0.93 (0.08), residues: 10125 helix: 0.39 (0.08), residues: 4094 sheet: -0.60 (0.14), residues: 1316 loop : -1.52 (0.09), residues: 4715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP q 176 HIS 0.024 0.001 HIS o 685 PHE 0.047 0.002 PHE o 566 TYR 0.061 0.002 TYR p 752 ARG 0.012 0.001 ARG O 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20250 Ramachandran restraints generated. 10125 Oldfield, 0 Emsley, 10125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20250 Ramachandran restraints generated. 10125 Oldfield, 0 Emsley, 10125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 9138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 463 time to evaluate : 7.657 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: A 352 MET cc_start: 0.0322 (ptt) cc_final: -0.0343 (ppp) REVERT: A 491 MET cc_start: -0.2754 (mtt) cc_final: -0.3660 (mmt) REVERT: A 607 MET cc_start: -0.0713 (mtm) cc_final: -0.2233 (mmt) REVERT: A 691 MET cc_start: -0.0730 (tpp) cc_final: -0.1522 (tpt) REVERT: A 757 MET cc_start: -0.3389 (mmm) cc_final: -0.3746 (mmt) REVERT: A 891 MET cc_start: 0.4977 (ttp) cc_final: 0.4675 (ttt) REVERT: B 607 MET cc_start: -0.0992 (ttp) cc_final: -0.2080 (ptm) REVERT: B 614 MET cc_start: -0.3863 (mtt) cc_final: -0.4389 (mtt) REVERT: B 719 MET cc_start: -0.2544 (mtm) cc_final: -0.3847 (ttm) REVERT: B 798 MET cc_start: -0.5368 (ttm) cc_final: -0.5722 (ttm) REVERT: B 929 MET cc_start: 0.1449 (ptt) cc_final: 0.0522 (ptt) REVERT: E 297 MET cc_start: -0.2438 (mtt) cc_final: -0.3083 (mtt) REVERT: E 528 MET cc_start: -0.1975 (mmt) cc_final: -0.2513 (mmt) REVERT: F 19 MET cc_start: -0.4796 (mmp) cc_final: -0.6524 (mtt) REVERT: F 290 MET cc_start: -0.1156 (mtm) cc_final: -0.1842 (mmt) REVERT: F 309 MET cc_start: -0.3163 (mtt) cc_final: -0.3856 (mtm) REVERT: L 83 MET cc_start: -0.2086 (ppp) cc_final: -0.2711 (ptt) REVERT: U 48 MET cc_start: -0.1775 (mtp) cc_final: -0.2984 (mmt) REVERT: U 110 MET cc_start: -0.1234 (ttt) cc_final: -0.2764 (ttp) REVERT: V 228 MET cc_start: -0.1017 (mtm) cc_final: -0.2583 (ptt) REVERT: e 291 MET cc_start: -0.2315 (ttm) cc_final: -0.3557 (tpt) REVERT: e 528 MET cc_start: 0.0948 (mmt) cc_final: -0.1565 (mmt) REVERT: f 26 MET cc_start: -0.3433 (tpt) cc_final: -0.4113 (tpt) REVERT: f 58 MET cc_start: -0.3015 (tmm) cc_final: -0.3500 (ttt) REVERT: f 285 MET cc_start: -0.5326 (ttt) cc_final: -0.5557 (ttt) REVERT: i 12 MET cc_start: -0.0604 (mmm) cc_final: -0.1348 (mtt) REVERT: i 39 MET cc_start: -0.2268 (mmp) cc_final: -0.4592 (mtt) REVERT: j 176 MET cc_start: -0.1641 (mtt) cc_final: -0.2012 (mtt) REVERT: l 83 MET cc_start: -0.5001 (tpt) cc_final: -0.6237 (ttt) REVERT: o 535 MET cc_start: 0.6704 (pmm) cc_final: 0.6440 (pmm) REVERT: o 1292 MET cc_start: 0.9041 (mmp) cc_final: 0.8781 (mmm) REVERT: p 390 ASN cc_start: 0.8536 (m-40) cc_final: 0.8144 (m110) REVERT: p 670 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8590 (mt-10) REVERT: p 967 ILE cc_start: 0.9068 (pt) cc_final: 0.8801 (mt) REVERT: p 1057 ASP cc_start: 0.8527 (t0) cc_final: 0.8073 (t0) REVERT: p 1153 TYR cc_start: 0.7751 (t80) cc_final: 0.7267 (t80) REVERT: p 1165 MET cc_start: 0.8827 (ptp) cc_final: 0.8063 (tmm) REVERT: s 94 MET cc_start: 0.8433 (mmp) cc_final: 0.8132 (mmp) REVERT: s 151 MET cc_start: 0.6786 (ppp) cc_final: 0.5975 (ppp) REVERT: v 41 LEU cc_start: 0.8579 (tp) cc_final: 0.8276 (tt) REVERT: u 117 MET cc_start: -0.3124 (mtm) cc_final: -0.3519 (ttp) outliers start: 0 outliers final: 0 residues processed: 463 average time/residue: 0.7933 time to fit residues: 654.3088 Evaluate side-chains 394 residues out of total 9138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 394 time to evaluate : 7.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1022 random chunks: chunk 896 optimal weight: 1.9990 chunk 943 optimal weight: 5.9990 chunk 860 optimal weight: 0.7980 chunk 917 optimal weight: 6.9990 chunk 552 optimal weight: 5.9990 chunk 399 optimal weight: 40.0000 chunk 720 optimal weight: 1.9990 chunk 281 optimal weight: 30.0000 chunk 829 optimal weight: 2.9990 chunk 868 optimal weight: 0.9990 chunk 914 optimal weight: 50.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 ASN F 79 ASN I 38 GLN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 63 ASN ** Q 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 208 GLN ** T 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 238 GLN ** e 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 387 ASN ** o 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 677 ASN ** o 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 740 GLN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 885 GLN o1078 GLN ** o1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 631 GLN ** p 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 89 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3195 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 87755 Z= 0.193 Angle : 0.608 16.491 119350 Z= 0.310 Chirality : 0.043 0.243 13313 Planarity : 0.004 0.085 14809 Dihedral : 14.237 172.591 13047 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.18 % Favored : 94.71 % Rotamer: Outliers : 0.01 % Allowed : 0.59 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % 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: -0.69 (0.08), residues: 10125 helix: 0.58 (0.08), residues: 4086 sheet: -0.47 (0.14), residues: 1290 loop : -1.37 (0.09), residues: 4749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP q 176 HIS 0.008 0.001 HIS q 66 PHE 0.030 0.001 PHE o 668 TYR 0.022 0.001 TYR p 752 ARG 0.011 0.000 ARG p 610 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20250 Ramachandran restraints generated. 10125 Oldfield, 0 Emsley, 10125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20250 Ramachandran restraints generated. 10125 Oldfield, 0 Emsley, 10125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 9138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 473 time to evaluate : 7.810 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: A 352 MET cc_start: 0.2572 (ptm) cc_final: 0.1588 (ppp) REVERT: A 491 MET cc_start: -0.2773 (mtt) cc_final: -0.3639 (mmt) REVERT: A 607 MET cc_start: -0.0952 (mtm) cc_final: -0.2417 (mmt) REVERT: A 691 MET cc_start: -0.0731 (tpp) cc_final: -0.1586 (tpt) REVERT: A 891 MET cc_start: 0.5050 (ttp) cc_final: 0.4572 (ttt) REVERT: B 607 MET cc_start: -0.1090 (ttp) cc_final: -0.1711 (ptm) REVERT: B 614 MET cc_start: -0.3835 (mtt) cc_final: -0.4377 (mtt) REVERT: B 719 MET cc_start: -0.2515 (mtm) cc_final: -0.3806 (ttm) REVERT: B 798 MET cc_start: -0.5259 (ttm) cc_final: -0.5651 (ttm) REVERT: B 929 MET cc_start: 0.1383 (ptt) cc_final: 0.0460 (ptt) REVERT: E 297 MET cc_start: -0.2680 (mtt) cc_final: -0.3338 (mtt) REVERT: E 528 MET cc_start: -0.2233 (mmt) cc_final: -0.2769 (mmt) REVERT: F 19 MET cc_start: -0.4795 (mmp) cc_final: -0.6502 (mtt) REVERT: F 290 MET cc_start: -0.1128 (mtm) cc_final: -0.1992 (mmt) REVERT: F 309 MET cc_start: -0.3186 (mtt) cc_final: -0.3894 (mtm) REVERT: J 176 MET cc_start: 0.1490 (pmm) cc_final: 0.1256 (pmm) REVERT: L 83 MET cc_start: -0.1977 (ppp) cc_final: -0.2365 (ptt) REVERT: U 48 MET cc_start: -0.1828 (mtp) cc_final: -0.2994 (mmt) REVERT: U 110 MET cc_start: -0.1315 (ttt) cc_final: -0.3426 (ttp) REVERT: V 228 MET cc_start: -0.0839 (mtm) cc_final: -0.2526 (ptt) REVERT: e 291 MET cc_start: -0.2309 (ttm) cc_final: -0.3955 (tpt) REVERT: f 19 MET cc_start: -0.3842 (ptm) cc_final: -0.4112 (ptm) REVERT: f 26 MET cc_start: -0.3516 (tpt) cc_final: -0.4146 (tpt) REVERT: f 58 MET cc_start: -0.3009 (tmm) cc_final: -0.3479 (ttt) REVERT: i 12 MET cc_start: -0.0486 (mmm) cc_final: -0.1336 (mtt) REVERT: i 39 MET cc_start: -0.2353 (mmp) cc_final: -0.4415 (mtt) REVERT: j 176 MET cc_start: -0.1649 (mtt) cc_final: -0.2067 (mtt) REVERT: k 154 MET cc_start: -0.2048 (mmm) cc_final: -0.2298 (mmt) REVERT: l 83 MET cc_start: -0.4942 (tpt) cc_final: -0.6188 (ttt) REVERT: o 476 ILE cc_start: 0.8000 (mt) cc_final: 0.7776 (mm) REVERT: o 535 MET cc_start: 0.6591 (pmm) cc_final: 0.6333 (pmm) REVERT: o 841 MET cc_start: 0.9324 (mtt) cc_final: 0.9107 (mtt) REVERT: o 1292 MET cc_start: 0.8995 (mmp) cc_final: 0.8746 (mmm) REVERT: o 1344 MET cc_start: 0.8400 (pmm) cc_final: 0.7636 (tpt) REVERT: p 176 GLU cc_start: 0.7546 (tp30) cc_final: 0.6981 (mm-30) REVERT: p 347 MET cc_start: 0.8879 (mmm) cc_final: 0.7985 (mmm) REVERT: p 390 ASN cc_start: 0.8408 (m-40) cc_final: 0.8208 (m110) REVERT: p 482 LEU cc_start: 0.9361 (mt) cc_final: 0.8809 (tt) REVERT: p 553 LEU cc_start: 0.8677 (mt) cc_final: 0.8353 (tp) REVERT: p 670 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8588 (mt-10) REVERT: p 840 MET cc_start: 0.5889 (ptt) cc_final: 0.5383 (pmm) REVERT: p 970 HIS cc_start: 0.7093 (m90) cc_final: 0.6764 (m170) REVERT: p 1057 ASP cc_start: 0.8399 (t0) cc_final: 0.8009 (t0) REVERT: p 1153 TYR cc_start: 0.7729 (t80) cc_final: 0.7269 (t80) REVERT: p 1165 MET cc_start: 0.8695 (ptp) cc_final: 0.8027 (tmm) REVERT: q 48 ASP cc_start: 0.7643 (p0) cc_final: 0.6778 (p0) REVERT: q 223 ASN cc_start: 0.8598 (p0) cc_final: 0.8162 (p0) REVERT: s 94 MET cc_start: 0.8389 (mmp) cc_final: 0.8089 (mmp) REVERT: t 80 MET cc_start: 0.5520 (tpt) cc_final: 0.5312 (tpt) REVERT: v 41 LEU cc_start: 0.8508 (tp) cc_final: 0.8049 (tt) REVERT: u 117 MET cc_start: -0.3069 (mtm) cc_final: -0.3540 (ttp) outliers start: 1 outliers final: 0 residues processed: 473 average time/residue: 0.7574 time to fit residues: 641.1265 Evaluate side-chains 404 residues out of total 9138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 404 time to evaluate : 7.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1022 random chunks: chunk 602 optimal weight: 8.9990 chunk 970 optimal weight: 0.7980 chunk 592 optimal weight: 20.0000 chunk 460 optimal weight: 30.0000 chunk 674 optimal weight: 0.8980 chunk 1018 optimal weight: 0.9980 chunk 937 optimal weight: 0.7980 chunk 810 optimal weight: 0.6980 chunk 84 optimal weight: 9.9990 chunk 626 optimal weight: 0.0050 chunk 497 optimal weight: 5.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 ASN I 38 GLN I 126 ASN ** O 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 343 HIS ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 208 GLN ** T 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 127 ASN ** V 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 32 HIS e 238 GLN ** e 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 387 ASN ** o 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 740 GLN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 825 ASN ** o1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 986 GLN ** p1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3144 moved from start: 0.5642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 87755 Z= 0.155 Angle : 0.582 14.146 119350 Z= 0.297 Chirality : 0.042 0.275 13313 Planarity : 0.004 0.071 14809 Dihedral : 14.090 174.310 13047 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.86 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.47 (0.09), residues: 10125 helix: 0.75 (0.08), residues: 4083 sheet: -0.34 (0.14), residues: 1281 loop : -1.24 (0.09), residues: 4761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP q 176 HIS 0.010 0.001 HIS p 287 PHE 0.028 0.001 PHE o 668 TYR 0.023 0.001 TYR p 724 ARG 0.025 0.000 ARG p 975 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20250 Ramachandran restraints generated. 10125 Oldfield, 0 Emsley, 10125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20250 Ramachandran restraints generated. 10125 Oldfield, 0 Emsley, 10125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 9138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 494 time to evaluate : 7.972 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: A 352 MET cc_start: 0.2973 (ptm) cc_final: 0.1549 (ppp) REVERT: A 491 MET cc_start: -0.2801 (mtt) cc_final: -0.3619 (mmt) REVERT: A 607 MET cc_start: -0.0904 (mtm) cc_final: -0.2461 (mmt) REVERT: A 691 MET cc_start: -0.0906 (tpp) cc_final: -0.1636 (tpt) REVERT: B 607 MET cc_start: -0.1228 (ttp) cc_final: -0.2274 (ptm) REVERT: B 614 MET cc_start: -0.3803 (mtt) cc_final: -0.4325 (mtt) REVERT: B 634 MET cc_start: -0.5882 (mtt) cc_final: -0.6771 (ttt) REVERT: B 719 MET cc_start: -0.2590 (mtm) cc_final: -0.3835 (ttm) REVERT: B 798 MET cc_start: -0.5275 (ttm) cc_final: -0.6324 (tmm) REVERT: B 929 MET cc_start: 0.1272 (ptt) cc_final: 0.0257 (ptt) REVERT: E 297 MET cc_start: -0.2581 (mtt) cc_final: -0.3166 (mtt) REVERT: E 528 MET cc_start: -0.2239 (mmt) cc_final: -0.2809 (mmt) REVERT: F 19 MET cc_start: -0.4795 (mmp) cc_final: -0.6493 (mtt) REVERT: F 290 MET cc_start: -0.1213 (mtm) cc_final: -0.1842 (mmt) REVERT: F 309 MET cc_start: -0.3097 (mtt) cc_final: -0.3852 (mtm) REVERT: J 176 MET cc_start: 0.2041 (pmm) cc_final: 0.1803 (pmm) REVERT: L 83 MET cc_start: -0.2348 (ppp) cc_final: -0.3041 (ptt) REVERT: U 48 MET cc_start: -0.1799 (mtp) cc_final: -0.3003 (mmt) REVERT: U 110 MET cc_start: -0.1044 (ttt) cc_final: -0.2626 (ttp) REVERT: V 228 MET cc_start: -0.0917 (mtm) cc_final: -0.2600 (ptt) REVERT: e 291 MET cc_start: -0.2296 (ttm) cc_final: -0.3935 (tpt) REVERT: f 19 MET cc_start: -0.3337 (ptm) cc_final: -0.3653 (ptm) REVERT: f 26 MET cc_start: -0.3504 (tpt) cc_final: -0.3986 (tpt) REVERT: f 58 MET cc_start: -0.2977 (tmm) cc_final: -0.3450 (ttt) REVERT: f 290 MET cc_start: 0.1554 (mpp) cc_final: 0.1148 (mmp) REVERT: i 12 MET cc_start: -0.0415 (mmm) cc_final: -0.1264 (mtt) REVERT: i 39 MET cc_start: -0.2564 (mmp) cc_final: -0.2835 (mmt) REVERT: j 176 MET cc_start: -0.1734 (mtt) cc_final: -0.2141 (mtt) REVERT: k 154 MET cc_start: -0.2177 (mmm) cc_final: -0.2418 (mmt) REVERT: l 83 MET cc_start: -0.4986 (tpt) cc_final: -0.6162 (ttt) REVERT: o 476 ILE cc_start: 0.7819 (mt) cc_final: 0.7599 (mm) REVERT: o 535 MET cc_start: 0.6547 (pmm) cc_final: 0.6187 (pmm) REVERT: o 1292 MET cc_start: 0.8948 (mmp) cc_final: 0.8746 (mmm) REVERT: o 1344 MET cc_start: 0.8383 (pmm) cc_final: 0.7688 (tpt) REVERT: p 176 GLU cc_start: 0.7343 (tp30) cc_final: 0.7020 (mm-30) REVERT: p 347 MET cc_start: 0.8830 (mmm) cc_final: 0.8024 (mmm) REVERT: p 382 LEU cc_start: 0.8193 (tt) cc_final: 0.7893 (tt) REVERT: p 384 ASP cc_start: 0.6763 (t0) cc_final: 0.6300 (m-30) REVERT: p 482 LEU cc_start: 0.9370 (mt) cc_final: 0.8785 (tt) REVERT: p 976 MET cc_start: 0.7117 (mpp) cc_final: 0.6803 (mpp) REVERT: p 1057 ASP cc_start: 0.8317 (t0) cc_final: 0.7966 (t0) REVERT: p 1153 TYR cc_start: 0.7667 (t80) cc_final: 0.7169 (t80) REVERT: p 1165 MET cc_start: 0.8681 (ptp) cc_final: 0.7981 (tmm) REVERT: q 48 ASP cc_start: 0.7523 (p0) cc_final: 0.6716 (p0) REVERT: q 223 ASN cc_start: 0.8404 (p0) cc_final: 0.7977 (p0) REVERT: s 94 MET cc_start: 0.8347 (mmp) cc_final: 0.8078 (mmp) REVERT: s 151 MET cc_start: 0.6194 (ppp) cc_final: 0.5412 (ppp) REVERT: x 1 MET cc_start: 0.7812 (ppp) cc_final: 0.7212 (ppp) REVERT: u 117 MET cc_start: -0.2955 (mtm) cc_final: -0.3735 (ttp) outliers start: 0 outliers final: 0 residues processed: 494 average time/residue: 0.7548 time to fit residues: 664.9980 Evaluate side-chains 418 residues out of total 9138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 418 time to evaluate : 7.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1022 random chunks: chunk 644 optimal weight: 3.9990 chunk 863 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 747 optimal weight: 30.0000 chunk 119 optimal weight: 1.9990 chunk 225 optimal weight: 50.0000 chunk 812 optimal weight: 0.0170 chunk 339 optimal weight: 9.9990 chunk 833 optimal weight: 1.9990 chunk 102 optimal weight: 50.0000 chunk 149 optimal weight: 10.0000 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 ASN I 38 GLN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 208 GLN ** T 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 238 GLN ** e 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 387 ASN ** o 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 704 ASN o 740 GLN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 89 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.138705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.123849 restraints weight = 637118.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.122585 restraints weight = 741345.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.121351 restraints weight = 475916.065| |-----------------------------------------------------------------------------| r_work (final): 0.4322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5337 moved from start: 0.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.132 87755 Z= 0.217 Angle : 0.602 17.493 119350 Z= 0.307 Chirality : 0.043 0.343 13313 Planarity : 0.004 0.075 14809 Dihedral : 14.095 175.530 13047 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.48 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.43 (0.09), residues: 10125 helix: 0.80 (0.08), residues: 4080 sheet: -0.34 (0.14), residues: 1309 loop : -1.23 (0.09), residues: 4736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP q 176 HIS 0.008 0.001 HIS p1021 PHE 0.030 0.001 PHE o 668 TYR 0.033 0.001 TYR p 752 ARG 0.009 0.000 ARG P 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15468.12 seconds wall clock time: 282 minutes 47.99 seconds (16967.99 seconds total)