Starting phenix.real_space_refine on Thu Feb 15 07:40:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml2_23906/02_2024/7ml2_23906_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml2_23906/02_2024/7ml2_23906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml2_23906/02_2024/7ml2_23906.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml2_23906/02_2024/7ml2_23906.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml2_23906/02_2024/7ml2_23906_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml2_23906/02_2024/7ml2_23906_updated.pdb" } resolution = 3.4 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 ------------------------------------------------------------------------------- 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= 0.003 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: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 17 6.06 5 P 112 5.49 5 Mg 1 5.21 5 S 359 5.16 5 C 40344 2.51 5 N 11343 2.21 5 O 12370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 123": "NH1" <-> "NH2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 812": "OE1" <-> "OE2" Residue "A PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1062": "OE1" <-> "OE2" Residue "A GLU 1167": "OE1" <-> "OE2" Residue "A ASP 1206": "OD1" <-> "OD2" Residue "A GLU 1234": "OE1" <-> "OE2" Residue "A GLU 1256": "OE1" <-> "OE2" Residue "A GLU 1297": "OE1" <-> "OE2" Residue "A TYR 1365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1407": "OE1" <-> "OE2" Residue "B PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 884": "NH1" <-> "NH2" Residue "B GLU 923": "OE1" <-> "OE2" Residue "B ASP 1125": "OD1" <-> "OD2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 233": "OE1" <-> "OE2" Residue "E PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 159": "OD1" <-> "OD2" Residue "F TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 114": "OE1" <-> "OE2" Residue "F GLU 127": "OE1" <-> "OE2" Residue "F PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 149": "OE1" <-> "OE2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 34": "OD1" <-> "OD2" Residue "H ARG 80": "NH1" <-> "NH2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "I ARG 30": "NH1" <-> "NH2" Residue "I PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 19": "OE1" <-> "OE2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 64": "OE1" <-> "OE2" Residue "K PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 85": "OD1" <-> "OD2" Residue "K PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 33": "OE1" <-> "OE2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ASP 50": "OD1" <-> "OD2" Residue "L ARG 63": "NH1" <-> "NH2" Residue "M PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 215": "NH1" <-> "NH2" Residue "M TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 320": "NH1" <-> "NH2" Residue "Q ARG 343": "NH1" <-> "NH2" Residue "Q ARG 398": "NH1" <-> "NH2" Residue "R ARG 63": "NH1" <-> "NH2" Residue "R ARG 251": "NH1" <-> "NH2" Residue "R ARG 271": "NH1" <-> "NH2" Residue "V GLU 88": "OE1" <-> "OE2" Residue "W ARG 18": "NH1" <-> "NH2" Residue "W PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 60": "NH1" <-> "NH2" Residue "W ARG 62": "NH1" <-> "NH2" Residue "W ARG 65": "NH1" <-> "NH2" Residue "W TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 108": "NH1" <-> "NH2" Residue "W GLU 118": "OE1" <-> "OE2" Residue "W ARG 144": "NH1" <-> "NH2" Residue "W GLU 146": "OE1" <-> "OE2" Residue "W ASP 160": "OD1" <-> "OD2" Residue "W ARG 174": "NH1" <-> "NH2" Residue "W ARG 193": "NH1" <-> "NH2" Residue "X ARG 197": "NH1" <-> "NH2" Residue "X ARG 276": "NH1" <-> "NH2" Residue "O PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 280": "OE1" <-> "OE2" Residue "1 ARG 286": "NH1" <-> "NH2" Residue "1 TYR 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 175": "NH1" <-> "NH2" Residue "4 PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 211": "OD1" <-> "OD2" Residue "4 ARG 273": "NH1" <-> "NH2" Residue "4 PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 85": "OE1" <-> "OE2" Residue "0 TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 246": "OE1" <-> "OE2" Residue "0 ASP 315": "OD1" <-> "OD2" Residue "0 GLU 319": "OE1" <-> "OE2" Residue "0 TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 370": "OE1" <-> "OE2" Residue "0 ARG 375": "NH1" <-> "NH2" Residue "0 GLU 421": "OE1" <-> "OE2" Residue "0 ASP 729": "OD1" <-> "OD2" Residue "0 TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 378": "NH1" <-> "NH2" Residue "2 TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 450": "NH1" <-> "NH2" Residue "2 TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 53": "OE1" <-> "OE2" Residue "5 ARG 56": "NH1" <-> "NH2" Residue "7 PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 37": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 64550 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 10997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1398, 10997 Classifications: {'peptide': 1398} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 1333} Chain breaks: 5 Chain: "B" Number of atoms: 9178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1152, 9178 Classifications: {'peptide': 1152} Link IDs: {'PTRANS': 51, 'TRANS': 1100} Chain breaks: 7 Chain: "C" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2061 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 11, 'TRANS': 250} Chain: "D" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1253 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain breaks: 1 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1089 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain breaks: 1 Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 2175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2175 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 10, 'TRANS': 268} Chain breaks: 2 Chain: "Q" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1144 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 141} Chain breaks: 3 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1303 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 371 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 158 Chain: "U" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 383 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "V" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'TRANS': 48} Chain breaks: 1 Chain: "W" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1469 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 8, 'TRANS': 182} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "X" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 984 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 7, 'TRANS': 148} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 277 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 148 Chain: "T" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1140 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain: "N" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1156 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain: "O" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 171} Chain: "1" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2411 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 180} Link IDs: {'PTRANS': 12, 'TRANS': 354} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 462 Unresolved non-hydrogen angles: 633 Unresolved non-hydrogen dihedrals: 311 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'UNK:plan-1': 106, 'TYR:plan': 3, 'ASN:plan1': 9, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 241 Chain: "4" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2041 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 11, 'TRANS': 272} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'UNK:plan-1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 84 Chain: "0" Number of atoms: 6108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 6108 Classifications: {'peptide': 754} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 721} Chain: "6" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2527 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 20, 'TRANS': 330} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TYR:plan': 2, 'UNK:plan-1': 13, 'ASP:plan': 6, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 140 Chain: "2" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3011 Classifications: {'peptide': 460} Incomplete info: {'backbone_only': 154, 'truncation_to_alanine': 14} Link IDs: {'CIS': 2, 'PTRANS': 17, 'TRANS': 440} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 727 Unresolved non-hydrogen angles: 1042 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 210 Planarities with less than four sites: {'GLN:plan1': 11, 'ARG:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 8, 'GLU:plan': 16, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 352 Chain: "5" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 498 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 62} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "7" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 4447 Classifications: {'peptide': 634} Incomplete info: {'backbone_only': 162} Link IDs: {'CIS': 3, 'PTRANS': 26, 'TRANS': 604} Chain breaks: 1 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 688 Unresolved non-hydrogen angles: 1003 Unresolved non-hydrogen dihedrals: 436 Unresolved non-hydrogen chiralities: 214 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 14, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 312 Chain: "3" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 860 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 5, 'TRANS': 132} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 178 Chain: "A" 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: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" 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: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "3" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 813 SG CYS A 107 122.059 124.501 105.380 1.00 0.00 S ATOM 837 SG CYS A 110 121.289 123.939 108.874 1.00 0.00 S ATOM 1142 SG CYS A 148 124.431 126.095 107.706 1.00 0.00 S ATOM 1211 SG CYS A 167 124.302 122.277 107.247 1.00 0.00 S ATOM 508 SG CYS A 67 75.978 115.902 117.892 1.00 0.00 S ATOM 530 SG CYS A 70 77.231 117.154 120.968 1.00 0.00 S ATOM 583 SG CYS A 77 76.123 119.327 118.298 1.00 0.00 S ATOM 19693 SG CYS B1163 90.890 119.885 128.378 1.00 0.00 S ATOM 19711 SG CYS B1166 91.714 120.783 124.826 1.00 0.00 S ATOM 19836 SG CYS B1182 89.687 117.752 125.757 1.00 0.00 S ATOM 19855 SG CYS B1185 93.692 118.144 126.316 1.00 0.00 S ATOM 20822 SG CYS C 86 18.150 152.828 118.268 1.00 0.00 S ATOM 20839 SG CYS C 88 18.654 149.388 117.129 1.00 0.00 S ATOM 20872 SG CYS C 92 15.538 150.822 115.979 1.00 0.00 S ATOM 20895 SG CYS C 95 18.637 152.335 114.584 1.00 0.00 S ATOM 28385 SG CYS I 7 123.466 165.267 52.323 1.00 0.00 S ATOM 28410 SG CYS I 10 123.232 161.242 51.918 1.00 0.00 S ATOM 28576 SG CYS I 29 123.730 163.268 55.403 1.00 0.00 S ATOM 28600 SG CYS I 32 126.120 162.788 52.749 1.00 0.00 S ATOM 28927 SG CYS I 75 97.367 200.660 61.064 1.00 0.00 S ATOM 28949 SG CYS I 78 96.268 200.993 57.524 1.00 0.00 S ATOM 29165 SG CYS I 103 93.949 198.720 60.513 1.00 0.00 S ATOM 29185 SG CYS I 106 96.776 198.175 58.277 1.00 0.00 S ATOM 29330 SG CYS J 7 36.792 173.563 99.743 1.00 0.00 S ATOM 29353 SG CYS J 10 34.115 175.323 100.761 1.00 0.00 S ATOM 29633 SG CYS J 45 36.772 177.259 101.193 1.00 0.00 S ATOM 29639 SG CYS J 46 33.952 176.214 98.606 1.00 0.00 S ATOM 30762 SG CYS L 31 35.704 135.431 78.824 1.00 30.00 S ATOM 30886 SG CYS L 48 37.819 133.570 76.699 1.00 0.00 S ATOM 30909 SG CYS L 51 36.766 135.872 74.386 1.00 0.00 S ATOM 31137 SG CYS M 24 52.433 118.673 127.968 1.00 0.00 S ATOM 31159 SG CYS M 27 48.686 118.747 128.239 1.00 0.00 S ATOM 31303 SG CYS M 45 50.592 120.959 125.807 1.00 0.00 S ATOM 31322 SG CYS M 48 50.660 122.306 128.546 1.00 0.00 S ATOM 37357 SG CYS W 124 74.395 97.478 121.256 1.00 0.00 S ATOM 37378 SG CYS W 127 75.138 100.841 119.576 1.00 0.00 S ATOM 37563 SG CYS W 149 75.179 100.680 123.477 1.00 0.00 S ATOM 37583 SG CYS W 152 72.048 99.976 121.742 1.00 0.00 S ATOM 46868 SG CYS 4 289 190.753 18.603 55.216 1.00 0.00 S ATOM 46887 SG CYS 4 292 193.909 18.618 57.249 1.00 0.00 S ATOM 46972 SG CYS 4 305 192.390 15.613 55.246 1.00 0.00 S ATOM 46988 SG CYS 4 308 191.662 16.602 58.915 1.00 0.00 S ATOM 48011 SG CYS 0 115 134.292 25.463 94.916 1.00117.61 S ATOM 48011 SG CYS 0 115 134.292 25.463 94.916 1.00117.61 S ATOM 48338 SG CYS 0 156 131.006 21.972 96.575 1.00 90.79 S ATOM 48153 SG CYS 0 133 131.777 23.222 99.607 1.00 46.59 S ATOM 55394 SG CYS 6 403 212.756 38.460 73.366 1.00 0.00 S ATOM 55416 SG CYS 6 406 213.662 41.837 71.720 1.00 0.00 S ATOM 55584 SG CYS 6 437 210.835 41.671 74.087 1.00 0.00 S ATOM 55600 SG CYS 6 440 210.622 40.149 70.598 1.00 0.00 S ATOM 55542 SG CYS 6 429 205.361 29.008 73.374 1.00 0.00 S ATOM 55558 SG CYS 6 432 209.142 29.059 73.047 1.00 0.00 S ATOM 55678 SG CYS 6 451 206.915 30.536 70.480 1.00 0.00 S ATOM 55693 SG CYS 6 454 206.890 26.777 70.639 1.00 0.00 S ATOM 55039 SG CYS 6 349 186.649 30.670 38.115 1.00 0.00 S ATOM 55060 SG CYS 6 352 185.847 32.236 34.464 1.00 0.00 S ATOM 55129 SG CYS 6 363 184.438 32.779 36.887 1.00 0.00 S ATOM 55147 SG CYS 6 366 183.827 29.064 36.605 1.00 0.00 S ATOM 54956 SG CYS 6 336 186.173 42.867 34.447 1.00 30.00 S ATOM 54967 SG CYS 6 338 185.515 41.644 37.609 1.00 30.00 S ATOM 55094 SG CYS 6 357 188.568 44.052 36.919 1.00 30.00 S ATOM 63695 SG CYS 3 13 103.586 65.744 116.387 1.00 0.00 S ATOM 63889 SG CYS 3 39 105.093 67.890 116.656 1.00 0.00 S ATOM 63842 SG CYS 3 34 103.134 57.944 123.080 1.00 0.00 S Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" P DT T 109 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 109 " occ=0.00 residue: pdb=" P DT T 111 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 111 " occ=0.00 residue: pdb=" P DT T 113 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 113 " occ=0.00 residue: pdb=" P DT T 115 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 115 " occ=0.00 residue: pdb=" P DA N 51 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 51 " occ=0.00 residue: pdb=" P DA N 53 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 53 " occ=0.00 residue: pdb=" P DA N 55 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 55 " occ=0.00 residue: pdb=" P DA N 57 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 57 " occ=0.00 Time building chain proxies: 25.28, per 1000 atoms: 0.39 Number of scatterers: 64550 At special positions: 0 Unit cell: (254.4, 230.02, 184.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 17 29.99 Fe 4 26.01 S 359 16.00 P 112 15.00 Mg 1 11.99 O 12370 8.00 N 11343 7.00 C 40344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 22.64 Conformation dependent library (CDL) restraints added in 8.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 801 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 133 " pdb="FE2 SF4 0 801 " - pdb=" SG CYS 0 156 " pdb="FE1 SF4 0 801 " - pdb=" SG CYS 0 115 " Number of angles added : 9 Zn2+ tetrahedral coordination pdb=" ZN 3 401 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 39 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 13 " pdb=" ZN 3 402 " pdb="ZN ZN 3 402 " - pdb=" ND1 HIS 3 36 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 34 " pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 292 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 305 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 289 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 308 " pdb=" ZN 6 501 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 406 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 437 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 440 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 403 " pdb=" ZN 6 502 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 451 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 429 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 432 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 454 " pdb=" ZN 6 503 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 349 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 363 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 352 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 366 " pdb=" ZN 6 504 " pdb="ZN ZN 6 504 " - pdb=" ND1 HIS 6 339 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 336 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 357 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 338 " pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 45 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 24 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 27 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 48 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 152 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 124 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 149 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 127 " Number of angles added : 78 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14958 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 313 helices and 64 sheets defined 38.9% alpha, 9.3% beta 46 base pairs and 84 stacking pairs defined. Time for finding SS restraints: 21.91 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 93 through 105 removed outlier: 5.462A pdb=" N ALA A 97 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N CYS A 103 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU A 104 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 131 through 143 removed outlier: 3.527A pdb=" N PHE A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.548A pdb=" N HIS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 261 through 281 removed outlier: 3.709A pdb=" N ILE A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 304 removed outlier: 3.951A pdb=" N GLU A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'A' and resid 335 through 339 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 385 through 394 removed outlier: 3.584A pdb=" N ARG A 393 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 526 through 535 removed outlier: 3.734A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 removed outlier: 3.584A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 581 removed outlier: 4.081A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 622 No H-bonds generated for 'chain 'A' and resid 619 through 622' Processing helix chain 'A' and resid 629 through 660 Proline residue: A 639 - end of helix removed outlier: 3.840A pdb=" N CYS A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 669 Processing helix chain 'A' and resid 673 through 698 removed outlier: 3.753A pdb=" N VAL A 693 " --> pdb=" O LYS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 736 removed outlier: 3.640A pdb=" N PHE A 721 " --> pdb=" O ASN A 717 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 732 " --> pdb=" O LYS A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 748 Processing helix chain 'A' and resid 755 through 761 Processing helix chain 'A' and resid 804 through 806 No H-bonds generated for 'chain 'A' and resid 804 through 806' Processing helix chain 'A' and resid 810 through 844 removed outlier: 3.505A pdb=" N GLY A 819 " --> pdb=" O PHE A 815 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 890 through 897 Processing helix chain 'A' and resid 910 through 912 No H-bonds generated for 'chain 'A' and resid 910 through 912' Processing helix chain 'A' and resid 915 through 919 Processing helix chain 'A' and resid 926 through 946 removed outlier: 3.594A pdb=" N PHE A 942 " --> pdb=" O LYS A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 971 Processing helix chain 'A' and resid 983 through 996 removed outlier: 3.594A pdb=" N LEU A 988 " --> pdb=" O LYS A 984 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 989 " --> pdb=" O ASP A 985 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN A 996 " --> pdb=" O ASP A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1014 Processing helix chain 'A' and resid 1016 through 1025 Processing helix chain 'A' and resid 1028 through 1033 Processing helix chain 'A' and resid 1039 through 1056 Processing helix chain 'A' and resid 1064 through 1073 removed outlier: 3.777A pdb=" N ILE A1072 " --> pdb=" O ALA A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1105 Processing helix chain 'A' and resid 1128 through 1138 removed outlier: 3.756A pdb=" N ALA A1137 " --> pdb=" O LEU A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1174 removed outlier: 3.512A pdb=" N GLU A1168 " --> pdb=" O GLU A1165 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN A1171 " --> pdb=" O GLU A1168 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU A1172 " --> pdb=" O ILE A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1204 Processing helix chain 'A' and resid 1209 through 1220 Processing helix chain 'A' and resid 1256 through 1270 Processing helix chain 'A' and resid 1313 through 1318 removed outlier: 3.678A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1326 No H-bonds generated for 'chain 'A' and resid 1324 through 1326' Processing helix chain 'A' and resid 1332 through 1359 removed outlier: 7.455A pdb=" N ILE A1341 " --> pdb=" O GLU A1337 " (cutoff:3.500A) removed outlier: 9.425A pdb=" N GLU A1342 " --> pdb=" O VAL A1338 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A1355 " --> pdb=" O GLU A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1377 removed outlier: 3.722A pdb=" N THR A1376 " --> pdb=" O VAL A1372 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A1377 " --> pdb=" O ASP A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1386 through 1389 No H-bonds generated for 'chain 'A' and resid 1386 through 1389' Processing helix chain 'A' and resid 1396 through 1402 removed outlier: 3.555A pdb=" N PHE A1402 " --> pdb=" O MET A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1405 through 1415 Processing helix chain 'A' and resid 1424 through 1430 Processing helix chain 'A' and resid 1437 through 1439 No H-bonds generated for 'chain 'A' and resid 1437 through 1439' Processing helix chain 'A' and resid 1448 through 1451 removed outlier: 3.654A pdb=" N VAL A1451 " --> pdb=" O GLU A1448 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1448 through 1451' Processing helix chain 'B' and resid 27 through 40 removed outlier: 4.300A pdb=" N TRP B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 56 removed outlier: 3.686A pdb=" N PHE B 54 " --> pdb=" O SER B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 65 Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 283 through 289 Processing helix chain 'B' and resid 294 through 301 removed outlier: 3.515A pdb=" N HIS B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 301 " --> pdb=" O ILE B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 322 Proline residue: B 316 - end of helix removed outlier: 3.562A pdb=" N GLU B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY B 321 " --> pdb=" O CYS B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 345 through 358 removed outlier: 4.418A pdb=" N GLN B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 389 removed outlier: 4.567A pdb=" N LEU B 378 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE B 382 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS B 388 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 409 through 437 removed outlier: 3.565A pdb=" N ASP B 427 " --> pdb=" O LYS B 423 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 429 " --> pdb=" O THR B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 447 No H-bonds generated for 'chain 'B' and resid 444 through 447' Processing helix chain 'B' and resid 450 through 462 removed outlier: 4.885A pdb=" N SER B 455 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 457 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS B 458 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 459 " --> pdb=" O GLY B 456 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 461 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 495 removed outlier: 3.542A pdb=" N LEU B 495 " --> pdb=" O THR B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 552 through 561 Processing helix chain 'B' and resid 571 through 573 No H-bonds generated for 'chain 'B' and resid 571 through 573' Processing helix chain 'B' and resid 593 through 605 Processing helix chain 'B' and resid 619 through 621 No H-bonds generated for 'chain 'B' and resid 619 through 621' Processing helix chain 'B' and resid 655 through 667 Processing helix chain 'B' and resid 681 through 686 Processing helix chain 'B' and resid 695 through 700 removed outlier: 3.583A pdb=" N GLU B 699 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 695 through 700' Processing helix chain 'B' and resid 707 through 710 No H-bonds generated for 'chain 'B' and resid 707 through 710' Processing helix chain 'B' and resid 745 through 747 No H-bonds generated for 'chain 'B' and resid 745 through 747' Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 764 through 776 removed outlier: 4.317A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 787 removed outlier: 4.504A pdb=" N ASN B 786 " --> pdb=" O THR B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 816 No H-bonds generated for 'chain 'B' and resid 814 through 816' Processing helix chain 'B' and resid 843 through 848 removed outlier: 3.643A pdb=" N ASP B 847 " --> pdb=" O GLN B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 923 No H-bonds generated for 'chain 'B' and resid 920 through 923' Processing helix chain 'B' and resid 927 through 931 removed outlier: 3.768A pdb=" N ALA B 930 " --> pdb=" O GLN B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 996 through 998 No H-bonds generated for 'chain 'B' and resid 996 through 998' Processing helix chain 'B' and resid 1014 through 1016 No H-bonds generated for 'chain 'B' and resid 1014 through 1016' Processing helix chain 'B' and resid 1018 through 1020 No H-bonds generated for 'chain 'B' and resid 1018 through 1020' Processing helix chain 'B' and resid 1023 through 1038 Processing helix chain 'B' and resid 1052 through 1062 removed outlier: 3.549A pdb=" N LEU B1058 " --> pdb=" O GLY B1054 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1101 No H-bonds generated for 'chain 'B' and resid 1099 through 1101' Processing helix chain 'B' and resid 1132 through 1140 removed outlier: 3.637A pdb=" N ASP B1136 " --> pdb=" O GLU B1132 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1152 removed outlier: 3.512A pdb=" N GLU B1149 " --> pdb=" O SER B1145 " (cutoff:3.500A) Processing helix chain 'B' and resid 1198 through 1209 Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 60 through 69 removed outlier: 3.741A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 205 through 208 removed outlier: 3.733A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 205 through 208' Processing helix chain 'C' and resid 240 through 264 removed outlier: 3.864A pdb=" N SER C 257 " --> pdb=" O LYS C 253 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 258 " --> pdb=" O LYS C 254 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 54 through 75 removed outlier: 3.898A pdb=" N ILE D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS D 60 " --> pdb=" O ARG D 56 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS D 75 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 133 removed outlier: 3.893A pdb=" N GLU D 131 " --> pdb=" O ASP D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 151 removed outlier: 3.612A pdb=" N ASN D 150 " --> pdb=" O GLN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 168 Processing helix chain 'D' and resid 174 through 181 Processing helix chain 'D' and resid 188 through 194 Processing helix chain 'D' and resid 196 through 198 No H-bonds generated for 'chain 'D' and resid 196 through 198' Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'E' and resid 4 through 26 removed outlier: 3.517A pdb=" N SER E 10 " --> pdb=" O GLU E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 36 Processing helix chain 'E' and resid 39 through 46 Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 90 through 103 removed outlier: 3.503A pdb=" N PHE E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 removed outlier: 3.508A pdb=" N LYS E 122 " --> pdb=" O PRO E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 158 through 168 removed outlier: 3.589A pdb=" N LEU E 165 " --> pdb=" O LYS E 161 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS E 166 " --> pdb=" O ARG E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'F' and resid 87 through 102 removed outlier: 4.107A pdb=" N ALA F 98 " --> pdb=" O LEU F 94 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU F 99 " --> pdb=" O GLY F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 126 Processing helix chain 'F' and resid 148 through 150 No H-bonds generated for 'chain 'F' and resid 148 through 150' Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 20 through 33 removed outlier: 3.617A pdb=" N LYS G 23 " --> pdb=" O PRO G 20 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU G 30 " --> pdb=" O LYS G 27 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU G 32 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 47 Processing helix chain 'H' and resid 129 through 132 No H-bonds generated for 'chain 'H' and resid 129 through 132' Processing helix chain 'J' and resid 17 through 28 removed outlier: 3.502A pdb=" N LEU J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 38 Processing helix chain 'J' and resid 45 through 52 removed outlier: 3.530A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU J 51 " --> pdb=" O ARG J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 62 No H-bonds generated for 'chain 'J' and resid 60 through 62' Processing helix chain 'K' and resid 7 through 9 No H-bonds generated for 'chain 'K' and resid 7 through 9' Processing helix chain 'K' and resid 40 through 51 removed outlier: 3.669A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 101 removed outlier: 3.560A pdb=" N LYS K 88 " --> pdb=" O LYS K 84 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASN K 89 " --> pdb=" O ASP K 85 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER K 93 " --> pdb=" O ASN K 89 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE K 95 " --> pdb=" O CYS K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 109 removed outlier: 4.527A pdb=" N GLU K 108 " --> pdb=" O ASN K 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 40 No H-bonds generated for 'chain 'M' and resid 38 through 40' Processing helix chain 'M' and resid 104 through 115 removed outlier: 3.783A pdb=" N GLN M 114 " --> pdb=" O LEU M 110 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY M 115 " --> pdb=" O ASN M 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 139 removed outlier: 3.529A pdb=" N GLN M 127 " --> pdb=" O ASN M 124 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA M 128 " --> pdb=" O GLU M 125 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA M 129 " --> pdb=" O VAL M 126 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS M 137 " --> pdb=" O THR M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 156 removed outlier: 4.052A pdb=" N TYR M 154 " --> pdb=" O ALA M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 170 through 182 removed outlier: 4.010A pdb=" N GLY M 179 " --> pdb=" O SER M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 193 Processing helix chain 'M' and resid 201 through 217 Processing helix chain 'M' and resid 237 through 245 removed outlier: 4.456A pdb=" N ARG M 241 " --> pdb=" O THR M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 250 through 266 removed outlier: 3.610A pdb=" N LYS M 264 " --> pdb=" O ALA M 260 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU M 265 " --> pdb=" O LYS M 261 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE M 266 " --> pdb=" O LYS M 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 275 through 287 Processing helix chain 'M' and resid 295 through 302 Processing helix chain 'M' and resid 306 through 319 Processing helix chain 'Q' and resid 26 through 34 removed outlier: 4.134A pdb=" N LEU Q 32 " --> pdb=" O ARG Q 29 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET Q 34 " --> pdb=" O PHE Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 113 Processing helix chain 'Q' and resid 130 through 133 No H-bonds generated for 'chain 'Q' and resid 130 through 133' Processing helix chain 'Q' and resid 338 through 345 Processing helix chain 'Q' and resid 410 through 413 No H-bonds generated for 'chain 'Q' and resid 410 through 413' Processing helix chain 'R' and resid 75 through 81 Processing helix chain 'R' and resid 234 through 245 Processing helix chain 'R' and resid 259 through 266 removed outlier: 4.034A pdb=" N HIS R 265 " --> pdb=" O VAL R 261 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR R 266 " --> pdb=" O THR R 262 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 309 Processing helix chain 'R' and resid 315 through 322 Processing helix chain 'R' and resid 326 through 336 removed outlier: 3.683A pdb=" N LYS R 335 " --> pdb=" O GLU R 331 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 19 Processing helix chain 'W' and resid 23 through 34 Processing helix chain 'W' and resid 40 through 47 Processing helix chain 'W' and resid 51 through 53 No H-bonds generated for 'chain 'W' and resid 51 through 53' Processing helix chain 'W' and resid 55 through 64 Processing helix chain 'W' and resid 91 through 115 removed outlier: 3.528A pdb=" N ASP W 114 " --> pdb=" O LYS W 110 " (cutoff:3.500A) Processing helix chain 'W' and resid 134 through 137 No H-bonds generated for 'chain 'W' and resid 134 through 137' Processing helix chain 'W' and resid 162 through 191 removed outlier: 3.581A pdb=" N ASP W 170 " --> pdb=" O GLU W 167 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU W 172 " --> pdb=" O GLN W 169 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET W 176 " --> pdb=" O ASN W 173 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN W 180 " --> pdb=" O ASP W 177 " (cutoff:3.500A) Proline residue: W 181 - end of helix removed outlier: 3.861A pdb=" N LEU W 186 " --> pdb=" O ILE W 183 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS W 187 " --> pdb=" O ASP W 184 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP W 191 " --> pdb=" O LYS W 188 " (cutoff:3.500A) Processing helix chain 'X' and resid 124 through 138 removed outlier: 3.851A pdb=" N LEU X 128 " --> pdb=" O ASP X 124 " (cutoff:3.500A) Processing helix chain 'X' and resid 144 through 151 removed outlier: 3.799A pdb=" N LEU X 151 " --> pdb=" O LEU X 147 " (cutoff:3.500A) Processing helix chain 'X' and resid 157 through 165 Processing helix chain 'X' and resid 189 through 199 Processing helix chain 'X' and resid 208 through 211 No H-bonds generated for 'chain 'X' and resid 208 through 211' Processing helix chain 'X' and resid 217 through 223 Processing helix chain 'X' and resid 257 through 264 Processing helix chain 'X' and resid 273 through 281 Processing helix chain 'O' and resid 82 through 88 Processing helix chain 'O' and resid 129 through 146 removed outlier: 3.522A pdb=" N ILE O 146 " --> pdb=" O ILE O 142 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 178 Processing helix chain 'O' and resid 180 through 182 No H-bonds generated for 'chain 'O' and resid 180 through 182' Processing helix chain 'O' and resid 220 through 237 Proline residue: O 232 - end of helix Processing helix chain '1' and resid 171 through 175 Processing helix chain '1' and resid 178 through 187 removed outlier: 3.698A pdb=" N LEU 1 184 " --> pdb=" O LEU 1 180 " (cutoff:3.500A) Processing helix chain '1' and resid 189 through 196 Processing helix chain '1' and resid 206 through 212 Processing helix chain '1' and resid 214 through 224 Processing helix chain '1' and resid 231 through 236 Processing helix chain '1' and resid 252 through 262 removed outlier: 3.605A pdb=" N GLU 1 261 " --> pdb=" O LEU 1 257 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN 1 262 " --> pdb=" O ASN 1 258 " (cutoff:3.500A) Processing helix chain '1' and resid 264 through 272 Processing helix chain '1' and resid 280 through 291 removed outlier: 3.790A pdb=" N SER 1 289 " --> pdb=" O ALA 1 285 " (cutoff:3.500A) Processing helix chain '1' and resid 309 through 327 removed outlier: 4.028A pdb=" N UNK 1 320 " --> pdb=" O UNK 1 316 " (cutoff:3.500A) Processing helix chain '1' and resid 372 through 389 removed outlier: 4.349A pdb=" N LEU 1 389 " --> pdb=" O MET 1 385 " (cutoff:3.500A) Processing helix chain '1' and resid 467 through 482 removed outlier: 3.517A pdb=" N UNK 1 477 " --> pdb=" O UNK 1 473 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N UNK 1 478 " --> pdb=" O UNK 1 474 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N UNK 1 480 " --> pdb=" O UNK 1 476 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N UNK 1 481 " --> pdb=" O UNK 1 477 " (cutoff:3.500A) Processing helix chain '1' and resid 497 through 515 Processing helix chain '1' and resid 541 through 564 removed outlier: 3.639A pdb=" N LEU 1 561 " --> pdb=" O CYS 1 557 " (cutoff:3.500A) Processing helix chain '1' and resid 576 through 603 Processing helix chain '1' and resid 607 through 615 Processing helix chain '1' and resid 617 through 638 Processing helix chain '4' and resid 36 through 42 Processing helix chain '4' and resid 50 through 67 Processing helix chain '4' and resid 117 through 134 Processing helix chain '4' and resid 138 through 142 Processing helix chain '4' and resid 149 through 166 Processing helix chain '4' and resid 193 through 205 Processing helix chain '4' and resid 222 through 230 Processing helix chain '4' and resid 245 through 251 Processing helix chain '4' and resid 314 through 320 Processing helix chain '0' and resid 19 through 33 Processing helix chain '0' and resid 48 through 62 removed outlier: 3.773A pdb=" N LEU 0 55 " --> pdb=" O SER 0 51 " (cutoff:3.500A) Processing helix chain '0' and resid 76 through 97 Processing helix chain '0' and resid 118 through 122 Processing helix chain '0' and resid 126 through 136 Processing helix chain '0' and resid 141 through 146 Processing helix chain '0' and resid 158 through 168 removed outlier: 4.159A pdb=" N VAL 0 167 " --> pdb=" O TYR 0 163 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLU 0 168 " --> pdb=" O ASN 0 164 " (cutoff:3.500A) Processing helix chain '0' and resid 178 through 187 removed outlier: 3.706A pdb=" N LYS 0 183 " --> pdb=" O GLU 0 179 " (cutoff:3.500A) Processing helix chain '0' and resid 192 through 198 removed outlier: 3.687A pdb=" N ARG 0 198 " --> pdb=" O PHE 0 194 " (cutoff:3.500A) Processing helix chain '0' and resid 210 through 214 Processing helix chain '0' and resid 224 through 227 No H-bonds generated for 'chain '0' and resid 224 through 227' Processing helix chain '0' and resid 240 through 248 Processing helix chain '0' and resid 254 through 278 removed outlier: 3.699A pdb=" N SER 0 272 " --> pdb=" O ASP 0 268 " (cutoff:3.500A) Processing helix chain '0' and resid 280 through 290 Processing helix chain '0' and resid 295 through 298 No H-bonds generated for 'chain '0' and resid 295 through 298' Processing helix chain '0' and resid 323 through 326 removed outlier: 3.853A pdb=" N ARG 0 326 " --> pdb=" O GLY 0 323 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 323 through 326' Processing helix chain '0' and resid 328 through 346 removed outlier: 4.502A pdb=" N GLU 0 340 " --> pdb=" O LYS 0 336 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR 0 341 " --> pdb=" O ARG 0 337 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU 0 342 " --> pdb=" O LEU 0 338 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS 0 343 " --> pdb=" O ILE 0 339 " (cutoff:3.500A) Processing helix chain '0' and resid 356 through 366 Processing helix chain '0' and resid 371 through 387 removed outlier: 3.697A pdb=" N PHE 0 376 " --> pdb=" O LYS 0 372 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N CYS 0 377 " --> pdb=" O PRO 0 373 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N SER 0 378 " --> pdb=" O LEU 0 374 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLU 0 379 " --> pdb=" O ARG 0 375 " (cutoff:3.500A) Processing helix chain '0' and resid 394 through 411 removed outlier: 4.864A pdb=" N ALA 0 398 " --> pdb=" O ASP 0 395 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP 0 401 " --> pdb=" O ALA 0 398 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA 0 406 " --> pdb=" O ALA 0 403 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR 0 407 " --> pdb=" O THR 0 404 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE 0 409 " --> pdb=" O ALA 0 406 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER 0 410 " --> pdb=" O THR 0 407 " (cutoff:3.500A) Processing helix chain '0' and resid 425 through 427 No H-bonds generated for 'chain '0' and resid 425 through 427' Processing helix chain '0' and resid 443 through 452 Proline residue: 0 448 - end of helix Processing helix chain '0' and resid 468 through 473 Processing helix chain '0' and resid 516 through 532 Processing helix chain '0' and resid 544 through 556 Processing helix chain '0' and resid 559 through 566 removed outlier: 3.710A pdb=" N VAL 0 563 " --> pdb=" O ILE 0 559 " (cutoff:3.500A) Processing helix chain '0' and resid 576 through 591 removed outlier: 3.680A pdb=" N THR 0 585 " --> pdb=" O LEU 0 581 " (cutoff:3.500A) Processing helix chain '0' and resid 606 through 609 No H-bonds generated for 'chain '0' and resid 606 through 609' Processing helix chain '0' and resid 634 through 644 Processing helix chain '0' and resid 650 through 669 removed outlier: 3.717A pdb=" N GLY 0 667 " --> pdb=" O ALA 0 663 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ARG 0 668 " --> pdb=" O GLN 0 664 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL 0 669 " --> pdb=" O CYS 0 665 " (cutoff:3.500A) Processing helix chain '0' and resid 684 through 687 Processing helix chain '0' and resid 695 through 700 removed outlier: 3.733A pdb=" N GLY 0 700 " --> pdb=" O TRP 0 696 " (cutoff:3.500A) Processing helix chain '0' and resid 703 through 705 No H-bonds generated for 'chain '0' and resid 703 through 705' Processing helix chain '0' and resid 710 through 725 removed outlier: 3.572A pdb=" N SER 0 715 " --> pdb=" O ASP 0 711 " (cutoff:3.500A) Processing helix chain '0' and resid 734 through 737 No H-bonds generated for 'chain '0' and resid 734 through 737' Processing helix chain '0' and resid 748 through 751 No H-bonds generated for 'chain '0' and resid 748 through 751' Processing helix chain '6' and resid 134 through 137 Processing helix chain '6' and resid 145 through 163 Processing helix chain '6' and resid 189 through 201 removed outlier: 3.501A pdb=" N ILE 6 199 " --> pdb=" O ALA 6 195 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG 6 200 " --> pdb=" O LEU 6 196 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS 6 201 " --> pdb=" O LYS 6 197 " (cutoff:3.500A) Processing helix chain '6' and resid 210 through 220 removed outlier: 3.613A pdb=" N GLY 6 219 " --> pdb=" O GLU 6 215 " (cutoff:3.500A) Processing helix chain '6' and resid 248 through 257 Processing helix chain '6' and resid 271 through 280 Processing helix chain '6' and resid 294 through 304 removed outlier: 3.950A pdb=" N ALA 6 304 " --> pdb=" O LEU 6 300 " (cutoff:3.500A) Processing helix chain '6' and resid 374 through 383 removed outlier: 3.978A pdb=" N ARG 6 378 " --> pdb=" O THR 6 374 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER 6 379 " --> pdb=" O HIS 6 375 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS 6 381 " --> pdb=" O ALA 6 377 " (cutoff:3.500A) Processing helix chain '6' and resid 419 through 422 No H-bonds generated for 'chain '6' and resid 419 through 422' Processing helix chain '6' and resid 438 through 444 Processing helix chain '6' and resid 452 through 455 No H-bonds generated for 'chain '6' and resid 452 through 455' Processing helix chain '2' and resid 10 through 16 removed outlier: 3.826A pdb=" N GLU 2 15 " --> pdb=" O GLN 2 12 " (cutoff:3.500A) Processing helix chain '2' and resid 19 through 27 Processing helix chain '2' and resid 29 through 38 removed outlier: 3.635A pdb=" N TYR 2 36 " --> pdb=" O CYS 2 32 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG 2 37 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE 2 38 " --> pdb=" O ALA 2 34 " (cutoff:3.500A) Processing helix chain '2' and resid 41 through 52 removed outlier: 3.740A pdb=" N ALA 2 49 " --> pdb=" O PHE 2 45 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET 2 50 " --> pdb=" O PHE 2 46 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE 2 52 " --> pdb=" O MET 2 48 " (cutoff:3.500A) Processing helix chain '2' and resid 59 through 65 Processing helix chain '2' and resid 71 through 83 Processing helix chain '2' and resid 102 through 112 Processing helix chain '2' and resid 120 through 122 No H-bonds generated for 'chain '2' and resid 120 through 122' Processing helix chain '2' and resid 136 through 151 Processing helix chain '2' and resid 161 through 169 Processing helix chain '2' and resid 186 through 191 Processing helix chain '2' and resid 197 through 210 removed outlier: 3.582A pdb=" N LEU 2 204 " --> pdb=" O LEU 2 200 " (cutoff:3.500A) Processing helix chain '2' and resid 218 through 230 Processing helix chain '2' and resid 244 through 255 Processing helix chain '2' and resid 273 through 280 removed outlier: 4.694A pdb=" N THR 2 279 " --> pdb=" O ALA 2 275 " (cutoff:3.500A) Processing helix chain '2' and resid 354 through 362 Processing helix chain '2' and resid 380 through 387 removed outlier: 4.207A pdb=" N ALA 2 386 " --> pdb=" O SER 2 382 " (cutoff:3.500A) Processing helix chain '2' and resid 395 through 402 Processing helix chain '2' and resid 405 through 416 removed outlier: 6.678A pdb=" N ARG 2 410 " --> pdb=" O PRO 2 406 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU 2 411 " --> pdb=" O GLN 2 407 " (cutoff:3.500A) Processing helix chain '2' and resid 421 through 425 removed outlier: 3.841A pdb=" N ASN 2 425 " --> pdb=" O GLU 2 421 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 421 through 425' Processing helix chain '2' and resid 435 through 448 removed outlier: 3.653A pdb=" N GLN 2 440 " --> pdb=" O THR 2 436 " (cutoff:3.500A) Processing helix chain '2' and resid 465 through 478 Processing helix chain '2' and resid 496 through 506 removed outlier: 3.541A pdb=" N GLN 2 500 " --> pdb=" O GLU 2 496 " (cutoff:3.500A) Processing helix chain '5' and resid 14 through 27 Processing helix chain '5' and resid 44 through 61 removed outlier: 4.589A pdb=" N GLU 5 48 " --> pdb=" O PRO 5 44 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N PHE 5 49 " --> pdb=" O SER 5 45 " (cutoff:3.500A) Processing helix chain '7' and resid 105 through 108 No H-bonds generated for 'chain '7' and resid 105 through 108' Processing helix chain '7' and resid 125 through 127 No H-bonds generated for 'chain '7' and resid 125 through 127' Processing helix chain '7' and resid 150 through 160 Processing helix chain '7' and resid 177 through 184 Processing helix chain '7' and resid 190 through 200 Processing helix chain '7' and resid 207 through 218 Processing helix chain '7' and resid 239 through 246 Processing helix chain '7' and resid 262 through 267 Processing helix chain '7' and resid 323 through 332 Processing helix chain '7' and resid 364 through 374 Processing helix chain '7' and resid 392 through 403 removed outlier: 4.160A pdb=" N GLY 7 396 " --> pdb=" O LYS 7 392 " (cutoff:3.500A) Processing helix chain '7' and resid 414 through 423 Processing helix chain '7' and resid 457 through 460 No H-bonds generated for 'chain '7' and resid 457 through 460' Processing helix chain '7' and resid 468 through 479 Processing helix chain '7' and resid 495 through 501 Processing helix chain '7' and resid 527 through 531 removed outlier: 3.557A pdb=" N LEU 7 530 " --> pdb=" O LEU 7 527 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE 7 531 " --> pdb=" O ASN 7 528 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 527 through 531' Processing helix chain '7' and resid 544 through 546 No H-bonds generated for 'chain '7' and resid 544 through 546' Processing helix chain '7' and resid 563 through 571 Processing helix chain '7' and resid 575 through 582 removed outlier: 4.090A pdb=" N LEU 7 579 " --> pdb=" O LYS 7 576 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR 7 581 " --> pdb=" O MET 7 578 " (cutoff:3.500A) Processing helix chain '7' and resid 585 through 600 Processing helix chain '7' and resid 613 through 622 Processing helix chain '7' and resid 633 through 644 Processing helix chain '7' and resid 680 through 690 Processing helix chain '7' and resid 714 through 729 removed outlier: 3.843A pdb=" N TYR 7 717 " --> pdb=" O GLN 7 714 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER 7 719 " --> pdb=" O MET 7 716 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN 7 723 " --> pdb=" O THR 7 720 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA 7 724 " --> pdb=" O LYS 7 721 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL 7 727 " --> pdb=" O ALA 7 724 " (cutoff:3.500A) Processing helix chain '7' and resid 753 through 764 Processing helix chain '3' and resid 40 through 49 Processing helix chain '3' and resid 77 through 91 removed outlier: 3.596A pdb=" N ARG 3 87 " --> pdb=" O ASP 3 83 " (cutoff:3.500A) Processing helix chain '3' and resid 104 through 122 removed outlier: 3.684A pdb=" N ASP 3 115 " --> pdb=" O GLU 3 111 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE 3 117 " --> pdb=" O VAL 3 113 " (cutoff:3.500A) Processing helix chain '3' and resid 128 through 144 Processing sheet with id= A, first strand: chain 'A' and resid 82 through 85 Processing sheet with id= B, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.684A pdb=" N VAL A 182 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 249 through 252 Processing sheet with id= D, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.599A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.472A pdb=" N PHE A 468 " --> pdb=" O SER A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.647A pdb=" N ARG A 434 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 587 through 590 removed outlier: 3.631A pdb=" N PHE A 614 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE A 608 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 849 through 851 removed outlier: 3.589A pdb=" N MET A 849 " --> pdb=" O ARG A 857 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR A 855 " --> pdb=" O HIS A 851 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 879 through 882 Processing sheet with id= J, first strand: chain 'A' and resid 1116 through 1118 Processing sheet with id= K, first strand: chain 'A' and resid 1193 through 1197 removed outlier: 3.521A pdb=" N LEU A1195 " --> pdb=" O ILE A1238 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1283 through 1292 Processing sheet with id= M, first strand: chain 'B' and resid 69 through 71 removed outlier: 3.651A pdb=" N GLU B 89 " --> pdb=" O ARG B 135 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 95 through 97 removed outlier: 4.291A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= P, first strand: chain 'B' and resid 210 through 212 Processing sheet with id= Q, first strand: chain 'B' and resid 223 through 226 removed outlier: 7.142A pdb=" N LEU B 258 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N VAL B 237 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL B 256 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B 270 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 614 through 618 removed outlier: 3.553A pdb=" N SER B 614 " --> pdb=" O PHE B 627 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 623 " --> pdb=" O ASP B 618 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 690 through 694 Processing sheet with id= T, first strand: chain 'B' and resid 793 through 796 removed outlier: 3.559A pdb=" N LYS B 965 " --> pdb=" O LEU B 953 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 1088 through 1092 removed outlier: 6.740A pdb=" N LEU B1010 " --> pdb=" O ALA B 826 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 915 through 917 Processing sheet with id= W, first strand: chain 'B' and resid 979 through 981 removed outlier: 7.294A pdb=" N MET B 841 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR B 993 " --> pdb=" O MET B 841 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id= Y, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id= Z, first strand: chain 'B' and resid 543 through 547 removed outlier: 3.698A pdb=" N ARG B 632 " --> pdb=" O SER B 546 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 578 through 582 removed outlier: 6.728A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 7 through 10 removed outlier: 3.642A pdb=" N ASN C 231 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 118 through 120 removed outlier: 6.036A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 60 through 62 removed outlier: 3.649A pdb=" N PHE E 60 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N THR E 131 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N PHE E 110 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLU E 133 " --> pdb=" O PHE E 110 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 195 through 200 Processing sheet with id= AF, first strand: chain 'F' and resid 133 through 137 Processing sheet with id= AG, first strand: chain 'G' and resid 2 through 13 Processing sheet with id= AH, first strand: chain 'G' and resid 106 through 111 removed outlier: 3.727A pdb=" N GLY G 98 " --> pdb=" O SER G 95 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLN G 102 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL G 91 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS G 146 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER G 152 " --> pdb=" O SER G 156 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER G 156 " --> pdb=" O SER G 152 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.677A pdb=" N THR G 120 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN G 122 " --> pdb=" O SER G 129 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 100 through 105 removed outlier: 6.506A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL H 114 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU H 125 " --> pdb=" O VAL H 114 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE H 42 " --> pdb=" O CYS H 24 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'I' and resid 14 through 19 Processing sheet with id= AL, first strand: chain 'I' and resid 83 through 87 Processing sheet with id= AM, first strand: chain 'K' and resid 30 through 35 removed outlier: 3.691A pdb=" N PHE K 71 " --> pdb=" O PHE K 35 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'M' and resid 35 through 37 Processing sheet with id= AO, first strand: chain 'Q' and resid 117 through 121 removed outlier: 6.746A pdb=" N LYS Q 391 " --> pdb=" O LEU Q 118 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LYS Q 120 " --> pdb=" O LYS Q 391 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N TYR Q 393 " --> pdb=" O LYS Q 120 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'Q' and resid 374 through 378 removed outlier: 3.565A pdb=" N THR Q 385 " --> pdb=" O SER Q 377 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'R' and resid 93 through 96 Processing sheet with id= AR, first strand: chain 'R' and resid 133 through 135 Processing sheet with id= AS, first strand: chain 'U' and resid 278 through 281 removed outlier: 4.047A pdb=" N LYS U 250 " --> pdb=" O SER U 261 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LYS U 263 " --> pdb=" O TYR U 248 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N TYR U 248 " --> pdb=" O LYS U 263 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'U' and resid 265 through 269 removed outlier: 3.890A pdb=" N GLY U 265 " --> pdb=" O PHE U 276 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE U 276 " --> pdb=" O GLY U 265 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'V' and resid 60 through 63 removed outlier: 3.666A pdb=" N GLN V 84 " --> pdb=" O LYS V 63 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'V' and resid 110 through 116 removed outlier: 3.642A pdb=" N THR V 68 " --> pdb=" O ILE V 79 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LYS V 81 " --> pdb=" O LEU V 66 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU V 66 " --> pdb=" O LYS V 81 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'W' and resid 68 through 72 removed outlier: 4.081A pdb=" N TYR W 86 " --> pdb=" O HIS W 70 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN W 72 " --> pdb=" O ARG W 84 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG W 84 " --> pdb=" O GLN W 72 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'O' and resid 72 through 75 removed outlier: 4.087A pdb=" N LYS O 120 " --> pdb=" O PHE O 116 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR O 111 " --> pdb=" O ILE O 106 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'O' and resid 193 through 196 removed outlier: 5.929A pdb=" N SER O 163 " --> pdb=" O LEU O 67 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEU O 67 " --> pdb=" O SER O 163 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain '4' and resid 210 through 216 removed outlier: 6.782A pdb=" N LEU 4 176 " --> pdb=" O ASP 4 211 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N VAL 4 213 " --> pdb=" O LEU 4 176 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL 4 178 " --> pdb=" O VAL 4 213 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE 4 215 " --> pdb=" O VAL 4 178 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N THR 4 180 " --> pdb=" O ILE 4 215 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU 4 177 " --> pdb=" O THR 4 27 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE 4 29 " --> pdb=" O LEU 4 177 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU 4 179 " --> pdb=" O ILE 4 29 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU 4 31 " --> pdb=" O LEU 4 179 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N CYS 4 181 " --> pdb=" O GLU 4 31 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA 4 78 " --> pdb=" O ILE 4 30 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain '0' and resid 2 through 4 removed outlier: 3.743A pdb=" N PHE 0 3 " --> pdb=" O VAL 0 10 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain '0' and resid 456 through 459 removed outlier: 7.037A pdb=" N VAL 0 232 " --> pdb=" O ILE 0 457 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N THR 0 459 " --> pdb=" O VAL 0 232 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N PHE 0 234 " --> pdb=" O THR 0 459 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER 0 73 " --> pdb=" O TYR 0 208 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU 0 106 " --> pdb=" O ILE 0 205 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE 0 207 " --> pdb=" O LEU 0 106 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain '0' and resid 416 through 421 Processing sheet with id= BD, first strand: chain '0' and resid 492 through 496 removed outlier: 7.423A pdb=" N GLY 0 677 " --> pdb=" O LEU 0 493 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N MET 0 495 " --> pdb=" O GLY 0 677 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N MET 0 679 " --> pdb=" O MET 0 495 " (cutoff:3.500A) No H-bonds generated for sheet with id= BD Processing sheet with id= BE, first strand: chain '0' and resid 537 through 541 removed outlier: 3.650A pdb=" N LEU 0 599 " --> pdb=" O LEU 0 570 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain '6' and resid 125 through 129 removed outlier: 3.585A pdb=" N LEU 6 233 " --> pdb=" O ILE 6 127 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG 6 260 " --> pdb=" O VAL 6 232 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ILE 6 234 " --> pdb=" O ARG 6 260 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS 6 262 " --> pdb=" O ILE 6 234 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain '6' and resid 171 through 175 removed outlier: 6.007A pdb=" N ILE 6 173 " --> pdb=" O LEU 6 181 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU 6 181 " --> pdb=" O ILE 6 173 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG 6 175 " --> pdb=" O ALA 6 179 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA 6 179 " --> pdb=" O ARG 6 175 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain '5' and resid 8 through 11 Processing sheet with id= BI, first strand: chain '7' and resid 453 through 456 removed outlier: 6.361A pdb=" N PHE 7 484 " --> pdb=" O ILE 7 408 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU 7 410 " --> pdb=" O PHE 7 484 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE 7 486 " --> pdb=" O LEU 7 410 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU 7 511 " --> pdb=" O LEU 7 487 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain '7' and resid 553 through 555 removed outlier: 6.734A pdb=" N ALA 7 732 " --> pdb=" O CYS 7 554 " (cutoff:3.500A) No H-bonds generated for sheet with id= BJ Processing sheet with id= BK, first strand: chain '7' and resid 557 through 559 Processing sheet with id= BL, first strand: chain '7' and resid 652 through 654 removed outlier: 6.124A pdb=" N PHE 7 704 " --> pdb=" O LEU 7 670 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N GLN 7 672 " --> pdb=" O PHE 7 704 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR 7 706 " --> pdb=" O GLN 7 672 " (cutoff:3.500A) 2122 hydrogen bonds defined for protein. 5916 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 192 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 84 stacking parallelities Total time for adding SS restraints: 24.67 Time building geometry restraints manager: 24.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.37: 22340 1.37 - 1.60: 42813 1.60 - 1.83: 691 1.83 - 2.06: 6 2.06 - 2.29: 12 Bond restraints: 65862 Sorted by residual: bond pdb=" CE LYS 3 61 " pdb=" NZ LYS 3 61 " ideal model delta sigma weight residual 1.489 1.286 0.203 3.00e-02 1.11e+03 4.56e+01 bond pdb=" CD GLU A1074 " pdb=" OE2 GLU A1074 " ideal model delta sigma weight residual 1.249 1.138 0.111 1.90e-02 2.77e+03 3.43e+01 bond pdb=" CA ARG F 135 " pdb=" CB ARG F 135 " ideal model delta sigma weight residual 1.527 1.390 0.137 2.48e-02 1.63e+03 3.07e+01 bond pdb=" CA GLU C 166 " pdb=" CB GLU C 166 " ideal model delta sigma weight residual 1.528 1.440 0.088 1.66e-02 3.63e+03 2.82e+01 bond pdb=" C LEU B 112 " pdb=" N TYR B 113 " ideal model delta sigma weight residual 1.331 1.225 0.106 2.07e-02 2.33e+03 2.65e+01 ... (remaining 65857 not shown) Histogram of bond angle deviations from ideal: 73.48 - 85.79: 12 85.79 - 98.11: 35 98.11 - 110.42: 18445 110.42 - 122.74: 64112 122.74 - 135.05: 6788 Bond angle restraints: 89392 Sorted by residual: angle pdb=" N VAL 7 501 " pdb=" CA VAL 7 501 " pdb=" C VAL 7 501 " ideal model delta sigma weight residual 112.83 101.38 11.45 9.90e-01 1.02e+00 1.34e+02 angle pdb=" N GLY 2 70 " pdb=" CA GLY 2 70 " pdb=" C GLY 2 70 " ideal model delta sigma weight residual 114.48 103.97 10.51 1.19e+00 7.06e-01 7.80e+01 angle pdb=" C TYR J 63 " pdb=" N ASN J 64 " pdb=" CA ASN J 64 " ideal model delta sigma weight residual 120.49 108.93 11.56 1.42e+00 4.96e-01 6.63e+01 angle pdb=" N ARG J 6 " pdb=" CA ARG J 6 " pdb=" C ARG J 6 " ideal model delta sigma weight residual 110.35 121.11 -10.76 1.40e+00 5.10e-01 5.91e+01 angle pdb=" NE ARG K 6 " pdb=" CZ ARG K 6 " pdb=" NH1 ARG K 6 " ideal model delta sigma weight residual 121.50 114.12 7.38 1.00e+00 1.00e+00 5.45e+01 ... (remaining 89387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 38624 35.35 - 70.70: 909 70.70 - 106.04: 44 106.04 - 141.39: 0 141.39 - 176.74: 2 Dihedral angle restraints: 39579 sinusoidal: 16253 harmonic: 23326 Sorted by residual: dihedral pdb=" CA HIS B 363 " pdb=" C HIS B 363 " pdb=" N ILE B 364 " pdb=" CA ILE B 364 " ideal model delta harmonic sigma weight residual -180.00 -130.01 -49.99 0 5.00e+00 4.00e-02 1.00e+02 dihedral pdb=" CA LYS M 272 " pdb=" C LYS M 272 " pdb=" N SER M 273 " pdb=" CA SER M 273 " ideal model delta harmonic sigma weight residual -180.00 -131.03 -48.97 0 5.00e+00 4.00e-02 9.59e+01 dihedral pdb=" CA ASP 3 125 " pdb=" C ASP 3 125 " pdb=" N VAL 3 126 " pdb=" CA VAL 3 126 " ideal model delta harmonic sigma weight residual -180.00 -131.66 -48.34 0 5.00e+00 4.00e-02 9.35e+01 ... (remaining 39576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 9958 0.160 - 0.319: 105 0.319 - 0.479: 5 0.479 - 0.639: 0 0.639 - 0.798: 1 Chirality restraints: 10069 Sorted by residual: chirality pdb=" CG LEU 0 162 " pdb=" CB LEU 0 162 " pdb=" CD1 LEU 0 162 " pdb=" CD2 LEU 0 162 " both_signs ideal model delta sigma weight residual False -2.59 -1.79 -0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" CA ARG J 6 " pdb=" N ARG J 6 " pdb=" C ARG J 6 " pdb=" CB ARG J 6 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CG LEU A 450 " pdb=" CB LEU A 450 " pdb=" CD1 LEU A 450 " pdb=" CD2 LEU A 450 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 10066 not shown) Planarity restraints: 11234 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 451 " 0.049 2.00e-02 2.50e+03 4.49e-02 3.03e+01 pdb=" CG HIS A 451 " -0.090 2.00e-02 2.50e+03 pdb=" ND1 HIS A 451 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS A 451 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS A 451 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS A 451 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 797 " -0.045 2.00e-02 2.50e+03 3.19e-02 2.04e+01 pdb=" CG TYR B 797 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR B 797 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 797 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 797 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR B 797 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR B 797 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 797 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS 3 61 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.48e+01 pdb=" C LYS 3 61 " -0.067 2.00e-02 2.50e+03 pdb=" O LYS 3 61 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE 3 62 " 0.022 2.00e-02 2.50e+03 ... (remaining 11231 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 778 2.44 - 3.06: 50532 3.06 - 3.67: 105842 3.67 - 4.29: 157083 4.29 - 4.90: 238357 Nonbonded interactions: 552592 Sorted by model distance: nonbonded pdb=" NZ LYS B 649 " pdb=" O THR B 736 " model vdw 1.825 2.520 nonbonded pdb=" O GLY L 52 " pdb=" NH1 ARG L 54 " model vdw 1.897 2.520 nonbonded pdb=" N CYS 3 16 " pdb="ZN ZN 3 401 " model vdw 1.899 2.310 nonbonded pdb=" OE1 GLU A 870 " pdb=" OG SER E 202 " model vdw 1.944 2.440 nonbonded pdb=" OG SER A1189 " pdb=" OE1 GLU A1256 " model vdw 1.977 2.440 ... (remaining 552587 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.020 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: 0.080 Extract box with map and model: 20.190 Check model and map are aligned: 0.730 Set scattering table: 0.500 Process input model: 164.610 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 194.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4591 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 0.203 65862 Z= 0.541 Angle : 1.137 17.690 89392 Z= 0.617 Chirality : 0.057 0.798 10069 Planarity : 0.007 0.080 11234 Dihedral : 15.232 176.741 24621 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 40.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.10 % Favored : 86.72 % Rotamer: Outliers : 0.09 % Allowed : 0.72 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 1.77 % Twisted General : 0.39 % 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: -4.05 (0.08), residues: 7932 helix: -2.19 (0.08), residues: 2897 sheet: -2.59 (0.16), residues: 894 loop : -3.14 (0.09), residues: 4141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.004 TRP C 192 HIS 0.041 0.003 HIS A 451 PHE 0.054 0.004 PHE A 252 TYR 0.051 0.004 TYR B 797 ARG 0.050 0.002 ARG K 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 7227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 282 time to evaluate : 5.856 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: U 244 MET cc_start: -0.0985 (ptt) cc_final: -0.1629 (ptp) REVERT: 1 385 MET cc_start: -0.0901 (ttm) cc_final: -0.1216 (ttp) REVERT: 0 61 MET cc_start: 0.2715 (mtm) cc_final: 0.1842 (ptp) REVERT: 0 485 MET cc_start: 0.0028 (mmm) cc_final: -0.0254 (mmm) REVERT: 6 322 MET cc_start: 0.1656 (pmm) cc_final: 0.1431 (pmm) REVERT: 3 61 LYS cc_start: 0.0291 (tmtt) cc_final: -0.0183 (tmtt) outliers start: 6 outliers final: 4 residues processed: 288 average time/residue: 0.5934 time to fit residues: 298.8967 Evaluate side-chains 239 residues out of total 7227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 235 time to evaluate : 5.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 660 optimal weight: 20.0000 chunk 592 optimal weight: 50.0000 chunk 328 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 399 optimal weight: 10.0000 chunk 316 optimal weight: 3.9990 chunk 612 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 chunk 372 optimal weight: 0.8980 chunk 456 optimal weight: 50.0000 chunk 710 optimal weight: 50.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN A 626 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS A 717 ASN ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 HIS A1171 GLN A1354 ASN ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 HIS B1025 HIS B1062 HIS C 7 GLN C 167 HIS ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN I 79 HIS ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN ** M 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 300 GLN ** O 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 258 ASN ** 4 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 159 HIS ** 0 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 163 GLN ** 6 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 212 ASN ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 389 ASN 2 469 ASN ** 7 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 702 ASN ** 7 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 761 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4445 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 65862 Z= 0.269 Angle : 0.759 12.112 89392 Z= 0.399 Chirality : 0.047 0.349 10069 Planarity : 0.005 0.075 11234 Dihedral : 13.470 173.883 10063 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 24.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.23 % Favored : 90.70 % Rotamer: Outliers : 0.64 % Allowed : 6.73 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.88 % Twisted General : 0.26 % 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: -2.86 (0.09), residues: 7932 helix: -0.96 (0.09), residues: 3080 sheet: -2.15 (0.16), residues: 926 loop : -2.65 (0.09), residues: 3926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 192 HIS 0.028 0.002 HIS A 451 PHE 0.033 0.002 PHE A 252 TYR 0.038 0.002 TYR 7 365 ARG 0.011 0.001 ARG 7 348 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 7227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 252 time to evaluate : 5.864 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: U 244 MET cc_start: -0.0769 (ptt) cc_final: -0.1298 (ptt) REVERT: 4 153 MET cc_start: 0.2411 (ppp) cc_final: 0.2039 (ppp) REVERT: 0 61 MET cc_start: 0.3121 (mtm) cc_final: 0.1957 (ptp) REVERT: 0 435 MET cc_start: 0.1476 (mmp) cc_final: 0.1263 (mmp) outliers start: 41 outliers final: 14 residues processed: 272 average time/residue: 0.5752 time to fit residues: 277.4166 Evaluate side-chains 249 residues out of total 7227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 235 time to evaluate : 7.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain G residue 44 TYR Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain Q residue 380 ASP Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 468 MET Chi-restraints excluded: chain 7 residue 474 MET Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 716 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 394 optimal weight: 8.9990 chunk 220 optimal weight: 20.0000 chunk 591 optimal weight: 50.0000 chunk 483 optimal weight: 40.0000 chunk 195 optimal weight: 5.9990 chunk 711 optimal weight: 50.0000 chunk 768 optimal weight: 8.9990 chunk 633 optimal weight: 40.0000 chunk 705 optimal weight: 5.9990 chunk 242 optimal weight: 10.0000 chunk 570 optimal weight: 40.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS A 760 GLN ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 HIS A1354 ASN ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN E 136 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN ** M 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 300 GLN ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 141 ASN ** O 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 379 ASN ** 4 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 161 ASN ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 212 ASN ** 6 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 349 ASN ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4597 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 65862 Z= 0.416 Angle : 0.800 11.475 89392 Z= 0.414 Chirality : 0.047 0.319 10069 Planarity : 0.006 0.074 11234 Dihedral : 13.345 172.993 10059 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 27.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.78 % Favored : 89.16 % Rotamer: Outliers : 1.85 % Allowed : 11.05 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.59 % Twisted General : 0.17 % 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: -2.56 (0.09), residues: 7932 helix: -0.65 (0.09), residues: 3116 sheet: -2.09 (0.16), residues: 912 loop : -2.52 (0.09), residues: 3904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 170 HIS 0.039 0.002 HIS I 79 PHE 0.025 0.002 PHE 3 47 TYR 0.032 0.002 TYR H 115 ARG 0.015 0.001 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 7227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 233 time to evaluate : 6.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 HIS cc_start: 0.6510 (OUTLIER) cc_final: 0.5977 (m170) REVERT: C 230 MET cc_start: 0.7073 (mpp) cc_final: 0.6869 (mpp) REVERT: L 50 ASP cc_start: 0.3397 (OUTLIER) cc_final: 0.3146 (t0) REVERT: U 244 MET cc_start: -0.0467 (ptt) cc_final: -0.1244 (ptt) REVERT: 1 385 MET cc_start: -0.1039 (ttp) cc_final: -0.1593 (ptp) REVERT: 4 153 MET cc_start: 0.2941 (ppp) cc_final: 0.2586 (ppp) REVERT: 4 206 MET cc_start: 0.2608 (mpp) cc_final: 0.1882 (mpp) REVERT: 0 61 MET cc_start: 0.2021 (mtm) cc_final: 0.1180 (ptm) REVERT: 0 485 MET cc_start: -0.0219 (mmt) cc_final: -0.0972 (mmt) REVERT: 3 61 LYS cc_start: -0.0712 (tmtt) cc_final: -0.1276 (tmtt) outliers start: 119 outliers final: 49 residues processed: 334 average time/residue: 0.5571 time to fit residues: 332.4741 Evaluate side-chains 276 residues out of total 7227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 225 time to evaluate : 5.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 862 ASN Chi-restraints excluded: chain A residue 930 ASP Chi-restraints excluded: chain A residue 980 ASP Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 921 ASP Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain G residue 44 TYR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 83 ASN Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain Q residue 380 ASP Chi-restraints excluded: chain Q residue 386 MET Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 167 VAL Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 622 MET Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 7 residue 337 VAL Chi-restraints excluded: chain 7 residue 474 MET Chi-restraints excluded: chain 7 residue 501 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 702 optimal weight: 6.9990 chunk 534 optimal weight: 50.0000 chunk 369 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 339 optimal weight: 4.9990 chunk 477 optimal weight: 40.0000 chunk 713 optimal weight: 40.0000 chunk 755 optimal weight: 30.0000 chunk 373 optimal weight: 9.9990 chunk 676 optimal weight: 50.0000 chunk 203 optimal weight: 7.9990 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN I 79 HIS I 87 GLN ** M 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN ** 4 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 140 GLN ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 163 GLN ** 6 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 212 ASN ** 6 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4518 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 65862 Z= 0.247 Angle : 0.664 15.993 89392 Z= 0.346 Chirality : 0.044 0.417 10069 Planarity : 0.005 0.074 11234 Dihedral : 13.077 170.402 10056 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.71 % Favored : 91.23 % Rotamer: Outliers : 1.83 % Allowed : 13.00 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.59 % Twisted General : 0.14 % 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: -2.06 (0.09), residues: 7932 helix: -0.20 (0.09), residues: 3121 sheet: -1.93 (0.16), residues: 919 loop : -2.23 (0.10), residues: 3892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 192 HIS 0.008 0.001 HIS B 984 PHE 0.026 0.002 PHE 3 47 TYR 0.030 0.001 TYR 7 365 ARG 0.017 0.000 ARG 7 303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 7227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 233 time to evaluate : 5.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 93 MET cc_start: 0.3244 (ppp) cc_final: 0.2608 (tmm) REVERT: U 244 MET cc_start: -0.0532 (ptt) cc_final: -0.1289 (ptt) REVERT: 1 385 MET cc_start: -0.1427 (ttp) cc_final: -0.2140 (ptp) REVERT: 4 153 MET cc_start: 0.2929 (ppp) cc_final: 0.2632 (ppp) REVERT: 0 61 MET cc_start: 0.2873 (mtm) cc_final: 0.1723 (ptm) REVERT: 0 435 MET cc_start: 0.1822 (mmp) cc_final: 0.1102 (mmp) REVERT: 0 485 MET cc_start: -0.0444 (mmt) cc_final: -0.0955 (mmt) REVERT: 7 622 MET cc_start: -0.1108 (OUTLIER) cc_final: -0.1760 (mmm) REVERT: 3 61 LYS cc_start: -0.0783 (tmtt) cc_final: -0.1371 (tmtt) outliers start: 118 outliers final: 58 residues processed: 333 average time/residue: 0.5644 time to fit residues: 335.3903 Evaluate side-chains 285 residues out of total 7227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 226 time to evaluate : 5.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 862 ASN Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1278 ASN Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 921 ASP Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain G residue 44 TYR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain I residue 83 ASN Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 117 ASN Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain Q residue 380 ASP Chi-restraints excluded: chain Q residue 386 MET Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain O residue 197 MET Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 233 VAL Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 167 VAL Chi-restraints excluded: chain 0 residue 290 VAL Chi-restraints excluded: chain 0 residue 349 LEU Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 440 CYS Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 7 residue 348 ARG Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 474 MET Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 514 THR Chi-restraints excluded: chain 7 residue 622 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 629 optimal weight: 9.9990 chunk 429 optimal weight: 40.0000 chunk 10 optimal weight: 20.0000 chunk 562 optimal weight: 20.0000 chunk 311 optimal weight: 7.9990 chunk 645 optimal weight: 7.9990 chunk 522 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 385 optimal weight: 7.9990 chunk 678 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 GLN ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 GLN B1104 HIS E 3 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 ASN ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 251 ASN 1 273 ASN ** 4 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 212 ASN ** 6 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4671 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 65862 Z= 0.438 Angle : 0.792 17.761 89392 Z= 0.409 Chirality : 0.047 0.419 10069 Planarity : 0.006 0.074 11234 Dihedral : 13.222 173.042 10056 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 28.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.12 % Favored : 88.78 % Rotamer: Outliers : 2.95 % Allowed : 14.01 % Favored : 83.04 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.59 % Twisted General : 0.16 % 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: -2.27 (0.09), residues: 7932 helix: -0.33 (0.09), residues: 3103 sheet: -2.04 (0.16), residues: 931 loop : -2.39 (0.09), residues: 3898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 170 HIS 0.065 0.002 HIS I 79 PHE 0.025 0.002 PHE C 62 TYR 0.029 0.002 TYR 7 365 ARG 0.008 0.001 ARG H 145 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 7227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 226 time to evaluate : 6.916 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: A 923 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6270 (mm) REVERT: D 40 HIS cc_start: 0.2637 (OUTLIER) cc_final: 0.1400 (m-70) REVERT: E 57 MET cc_start: 0.6341 (ppp) cc_final: 0.5921 (ppp) REVERT: U 244 MET cc_start: -0.0550 (ptt) cc_final: -0.1276 (ptt) REVERT: 1 350 ARG cc_start: -0.1244 (OUTLIER) cc_final: -0.2188 (pmt-80) REVERT: 0 61 MET cc_start: 0.2879 (mtm) cc_final: 0.1679 (ptm) REVERT: 0 485 MET cc_start: -0.0134 (mmt) cc_final: -0.1114 (mmt) REVERT: 7 459 MET cc_start: -0.2917 (mmp) cc_final: -0.3491 (mmt) REVERT: 7 622 MET cc_start: -0.0778 (mmm) cc_final: -0.1402 (mmm) REVERT: 3 61 LYS cc_start: -0.0636 (tmtt) cc_final: -0.1201 (tmtt) outliers start: 190 outliers final: 112 residues processed: 395 average time/residue: 0.5528 time to fit residues: 392.1145 Evaluate side-chains 337 residues out of total 7227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 222 time to evaluate : 5.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 862 ASN Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 930 ASP Chi-restraints excluded: chain A residue 980 ASP Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1278 ASN Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain A residue 1359 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 921 ASP Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1099 VAL Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain G residue 44 TYR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain I residue 83 ASN Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 38 GLU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 117 ASN Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain Q residue 380 ASP Chi-restraints excluded: chain Q residue 386 MET Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain O residue 104 MET Chi-restraints excluded: chain O residue 203 VAL Chi-restraints excluded: chain O residue 233 VAL Chi-restraints excluded: chain 1 residue 350 ARG Chi-restraints excluded: chain 4 residue 252 MET Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 167 VAL Chi-restraints excluded: chain 0 residue 290 VAL Chi-restraints excluded: chain 0 residue 349 LEU Chi-restraints excluded: chain 0 residue 389 GLU Chi-restraints excluded: chain 0 residue 472 MET Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 6 residue 126 LEU Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 310 VAL Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 7 residue 337 VAL Chi-restraints excluded: chain 7 residue 348 ARG Chi-restraints excluded: chain 7 residue 349 ASN Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 456 THR Chi-restraints excluded: chain 7 residue 474 MET Chi-restraints excluded: chain 7 residue 742 MET Chi-restraints excluded: chain 7 residue 745 ILE Chi-restraints excluded: chain 3 residue 30 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 254 optimal weight: 6.9990 chunk 680 optimal weight: 30.0000 chunk 149 optimal weight: 5.9990 chunk 443 optimal weight: 50.0000 chunk 186 optimal weight: 5.9990 chunk 756 optimal weight: 6.9990 chunk 628 optimal weight: 8.9990 chunk 350 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 250 optimal weight: 0.9990 chunk 397 optimal weight: 3.9990 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 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 HIS ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 ASN ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 699 GLN ** 0 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 212 ASN ** 2 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4548 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 65862 Z= 0.218 Angle : 0.645 16.343 89392 Z= 0.333 Chirality : 0.043 0.291 10069 Planarity : 0.004 0.074 11234 Dihedral : 13.005 171.121 10056 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 21.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.23 % Favored : 91.70 % Rotamer: Outliers : 2.18 % Allowed : 15.41 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.59 % Twisted General : 0.12 % 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: -1.81 (0.09), residues: 7932 helix: 0.06 (0.09), residues: 3114 sheet: -1.88 (0.16), residues: 966 loop : -2.11 (0.10), residues: 3852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 192 HIS 0.019 0.001 HIS I 79 PHE 0.029 0.001 PHE 3 47 TYR 0.031 0.001 TYR 7 365 ARG 0.006 0.000 ARG 7 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 7227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 226 time to evaluate : 5.954 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: B 809 MET cc_start: 0.4580 (ptm) cc_final: 0.4346 (ptm) REVERT: C 75 MET cc_start: 0.5700 (mmp) cc_final: 0.5418 (mmp) REVERT: G 119 LEU cc_start: -0.1030 (OUTLIER) cc_final: -0.1258 (mt) REVERT: U 244 MET cc_start: -0.0581 (ptt) cc_final: -0.1292 (ptt) REVERT: 0 61 MET cc_start: 0.2773 (mtm) cc_final: 0.1548 (ptm) REVERT: 0 231 ILE cc_start: -0.2279 (OUTLIER) cc_final: -0.2898 (tt) REVERT: 0 485 MET cc_start: -0.0159 (mmt) cc_final: -0.0622 (mmt) REVERT: 7 459 MET cc_start: -0.2749 (mmp) cc_final: -0.3331 (mmt) REVERT: 7 622 MET cc_start: -0.1135 (OUTLIER) cc_final: -0.1521 (mmm) REVERT: 3 61 LYS cc_start: -0.0469 (tmtt) cc_final: -0.1183 (tmtt) outliers start: 140 outliers final: 89 residues processed: 345 average time/residue: 0.5754 time to fit residues: 355.3142 Evaluate side-chains 317 residues out of total 7227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 225 time to evaluate : 5.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 862 ASN Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 921 ASP Chi-restraints excluded: chain B residue 1006 ILE Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain G residue 44 TYR Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 38 GLU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 301 THR Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain Q residue 380 ASP Chi-restraints excluded: chain Q residue 386 MET Chi-restraints excluded: chain R residue 121 ASP Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 142 PHE Chi-restraints excluded: chain O residue 197 MET Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 233 VAL Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 167 VAL Chi-restraints excluded: chain 0 residue 231 ILE Chi-restraints excluded: chain 0 residue 290 VAL Chi-restraints excluded: chain 0 residue 389 GLU Chi-restraints excluded: chain 0 residue 495 MET Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 2 residue 52 PHE Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 7 residue 337 VAL Chi-restraints excluded: chain 7 residue 343 PHE Chi-restraints excluded: chain 7 residue 348 ARG Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 456 THR Chi-restraints excluded: chain 7 residue 474 MET Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 514 THR Chi-restraints excluded: chain 7 residue 622 MET Chi-restraints excluded: chain 7 residue 742 MET Chi-restraints excluded: chain 7 residue 745 ILE Chi-restraints excluded: chain 3 residue 30 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 729 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 431 optimal weight: 5.9990 chunk 552 optimal weight: 50.0000 chunk 428 optimal weight: 0.8980 chunk 636 optimal weight: 0.9980 chunk 422 optimal weight: 30.0000 chunk 753 optimal weight: 30.0000 chunk 471 optimal weight: 1.9990 chunk 459 optimal weight: 50.0000 chunk 347 optimal weight: 7.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 212 ASN ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 251 ASN X 265 ASN ** 4 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 707 ASN ** 0 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4547 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 65862 Z= 0.225 Angle : 0.642 16.104 89392 Z= 0.328 Chirality : 0.043 0.551 10069 Planarity : 0.005 0.143 11234 Dihedral : 12.885 173.551 10056 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.94 % Favored : 91.00 % Rotamer: Outliers : 2.19 % Allowed : 16.03 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.59 % Twisted General : 0.07 % 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: -1.61 (0.09), residues: 7932 helix: 0.25 (0.09), residues: 3119 sheet: -1.78 (0.16), residues: 986 loop : -2.02 (0.10), residues: 3827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 170 HIS 0.009 0.001 HIS L 53 PHE 0.024 0.001 PHE 3 47 TYR 0.030 0.001 TYR 7 365 ARG 0.020 0.000 ARG 7 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 7227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 227 time to evaluate : 5.934 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: B 1098 MET cc_start: 0.5885 (mpp) cc_final: 0.5364 (mpp) REVERT: C 75 MET cc_start: 0.5721 (mmp) cc_final: 0.5393 (mmp) REVERT: L 50 ASP cc_start: 0.2525 (OUTLIER) cc_final: 0.1590 (t70) REVERT: U 244 MET cc_start: -0.0616 (ptt) cc_final: -0.1625 (ptt) REVERT: 0 61 MET cc_start: 0.2830 (mtm) cc_final: 0.1552 (ptm) REVERT: 0 485 MET cc_start: -0.0359 (mmt) cc_final: -0.0840 (mmt) REVERT: 7 304 GLU cc_start: -0.1575 (OUTLIER) cc_final: -0.2154 (pt0) REVERT: 7 459 MET cc_start: -0.2855 (mmp) cc_final: -0.3429 (mmt) REVERT: 7 622 MET cc_start: -0.1214 (OUTLIER) cc_final: -0.1603 (mmm) REVERT: 3 61 LYS cc_start: -0.0538 (tmtt) cc_final: -0.1169 (tmtt) outliers start: 141 outliers final: 100 residues processed: 347 average time/residue: 0.5544 time to fit residues: 344.6984 Evaluate side-chains 328 residues out of total 7227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 225 time to evaluate : 5.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 862 ASN Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 980 ASP Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1231 ASP Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1278 ASN Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 921 ASP Chi-restraints excluded: chain B residue 1006 ILE Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain G residue 44 TYR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 38 GLU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 301 THR Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain Q residue 380 ASP Chi-restraints excluded: chain Q residue 386 MET Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 151 LEU Chi-restraints excluded: chain O residue 104 MET Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 233 VAL Chi-restraints excluded: chain 4 residue 252 MET Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 167 VAL Chi-restraints excluded: chain 0 residue 290 VAL Chi-restraints excluded: chain 0 residue 679 MET Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 6 residue 126 LEU Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 2 residue 52 PHE Chi-restraints excluded: chain 2 residue 97 MET Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 7 residue 269 LEU Chi-restraints excluded: chain 7 residue 302 GLU Chi-restraints excluded: chain 7 residue 304 GLU Chi-restraints excluded: chain 7 residue 337 VAL Chi-restraints excluded: chain 7 residue 343 PHE Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 449 GLU Chi-restraints excluded: chain 7 residue 474 MET Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 514 THR Chi-restraints excluded: chain 7 residue 622 MET Chi-restraints excluded: chain 7 residue 745 ILE Chi-restraints excluded: chain 3 residue 30 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 466 optimal weight: 50.0000 chunk 300 optimal weight: 7.9990 chunk 450 optimal weight: 50.0000 chunk 227 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 479 optimal weight: 20.0000 chunk 513 optimal weight: 30.0000 chunk 372 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 592 optimal weight: 10.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN B 499 ASN ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 251 ASN ** 4 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 577 GLN 0 628 GLN ** 0 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 425 ASN ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4703 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 65862 Z= 0.416 Angle : 0.784 17.071 89392 Z= 0.401 Chirality : 0.046 0.571 10069 Planarity : 0.006 0.116 11234 Dihedral : 13.201 174.496 10056 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 28.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.77 % Favored : 89.15 % Rotamer: Outliers : 2.61 % Allowed : 16.40 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.59 % Twisted General : 0.09 % 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: -2.00 (0.09), residues: 7932 helix: -0.12 (0.09), residues: 3114 sheet: -1.79 (0.16), residues: 939 loop : -2.26 (0.10), residues: 3879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 170 HIS 0.014 0.002 HIS A 399 PHE 0.024 0.002 PHE B 963 TYR 0.030 0.002 TYR 7 365 ARG 0.015 0.001 ARG 7 303 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 7227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 225 time to evaluate : 5.943 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: A 81 PHE cc_start: 0.6209 (OUTLIER) cc_final: 0.5600 (m-80) REVERT: A 923 LEU cc_start: 0.6518 (OUTLIER) cc_final: 0.6234 (mm) REVERT: B 1098 MET cc_start: 0.5938 (mpp) cc_final: 0.5601 (mpp) REVERT: D 40 HIS cc_start: 0.2679 (OUTLIER) cc_final: 0.1499 (m-70) REVERT: L 50 ASP cc_start: 0.1521 (OUTLIER) cc_final: 0.1218 (t70) REVERT: U 244 MET cc_start: -0.0467 (ptt) cc_final: -0.1299 (ptt) REVERT: 0 61 MET cc_start: 0.2168 (mtm) cc_final: 0.1318 (ptm) REVERT: 0 346 MET cc_start: -0.1401 (tpp) cc_final: -0.2873 (tmm) REVERT: 0 485 MET cc_start: -0.0238 (mmt) cc_final: -0.0839 (mmt) REVERT: 0 553 MET cc_start: 0.5986 (ppp) cc_final: 0.5737 (ppp) REVERT: 7 304 GLU cc_start: -0.1403 (OUTLIER) cc_final: -0.1992 (pt0) REVERT: 7 459 MET cc_start: -0.2598 (mmp) cc_final: -0.2938 (mmt) REVERT: 7 622 MET cc_start: -0.0838 (OUTLIER) cc_final: -0.1159 (mmm) REVERT: 3 61 LYS cc_start: -0.0778 (tmtt) cc_final: -0.1013 (tmtt) outliers start: 168 outliers final: 120 residues processed: 370 average time/residue: 0.5524 time to fit residues: 366.9088 Evaluate side-chains 347 residues out of total 7227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 221 time to evaluate : 5.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 862 ASN Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 980 ASP Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1231 ASP Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1278 ASN Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain A residue 1359 ASP Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 921 ASP Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1006 ILE Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain G residue 44 TYR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 38 GLU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 117 ASN Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 301 THR Chi-restraints excluded: chain Q residue 380 ASP Chi-restraints excluded: chain Q residue 386 MET Chi-restraints excluded: chain R residue 121 ASP Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 142 PHE Chi-restraints excluded: chain O residue 104 MET Chi-restraints excluded: chain O residue 115 ILE Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 233 VAL Chi-restraints excluded: chain 4 residue 252 MET Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 167 VAL Chi-restraints excluded: chain 0 residue 231 ILE Chi-restraints excluded: chain 0 residue 290 VAL Chi-restraints excluded: chain 0 residue 679 MET Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 6 residue 126 LEU Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 384 MET Chi-restraints excluded: chain 2 residue 48 MET Chi-restraints excluded: chain 2 residue 52 PHE Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 7 residue 269 LEU Chi-restraints excluded: chain 7 residue 304 GLU Chi-restraints excluded: chain 7 residue 337 VAL Chi-restraints excluded: chain 7 residue 343 PHE Chi-restraints excluded: chain 7 residue 449 GLU Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 514 THR Chi-restraints excluded: chain 7 residue 561 MET Chi-restraints excluded: chain 7 residue 622 MET Chi-restraints excluded: chain 7 residue 745 ILE Chi-restraints excluded: chain 3 residue 30 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 685 optimal weight: 4.9990 chunk 722 optimal weight: 50.0000 chunk 658 optimal weight: 7.9990 chunk 702 optimal weight: 8.9990 chunk 721 optimal weight: 50.0000 chunk 422 optimal weight: 9.9990 chunk 305 optimal weight: 7.9990 chunk 551 optimal weight: 9.9990 chunk 215 optimal weight: 0.9990 chunk 634 optimal weight: 8.9990 chunk 664 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 303 GLN ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 403 HIS ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4640 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 65862 Z= 0.296 Angle : 0.693 16.878 89392 Z= 0.354 Chirality : 0.044 0.440 10069 Planarity : 0.005 0.071 11234 Dihedral : 13.134 172.771 10056 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 24.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.24 % Favored : 90.68 % Rotamer: Outliers : 2.10 % Allowed : 17.06 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.29 % Twisted General : 0.10 % 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: -1.79 (0.09), residues: 7932 helix: 0.06 (0.09), residues: 3115 sheet: -1.72 (0.16), residues: 962 loop : -2.13 (0.10), residues: 3855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 170 HIS 0.015 0.001 HIS 0 66 PHE 0.024 0.002 PHE 3 47 TYR 0.032 0.002 TYR 7 365 ARG 0.009 0.000 ARG 7 303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 7227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 222 time to evaluate : 5.871 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: A 923 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.6242 (mm) REVERT: B 1098 MET cc_start: 0.5902 (mpp) cc_final: 0.5550 (mpp) REVERT: D 40 HIS cc_start: 0.2376 (OUTLIER) cc_final: 0.1362 (m-70) REVERT: U 244 MET cc_start: -0.0235 (ptt) cc_final: -0.1255 (ptt) REVERT: 0 61 MET cc_start: 0.2242 (mtm) cc_final: 0.1308 (ptm) REVERT: 0 346 MET cc_start: -0.1844 (tpp) cc_final: -0.3114 (tmm) REVERT: 0 485 MET cc_start: -0.0193 (mmt) cc_final: -0.0777 (mmt) REVERT: 0 553 MET cc_start: 0.5904 (ppp) cc_final: 0.5684 (ppp) REVERT: 7 304 GLU cc_start: -0.1501 (OUTLIER) cc_final: -0.2128 (pt0) REVERT: 7 459 MET cc_start: -0.2297 (mmp) cc_final: -0.3150 (mmt) REVERT: 7 622 MET cc_start: -0.1101 (OUTLIER) cc_final: -0.1512 (mmm) REVERT: 3 61 LYS cc_start: -0.0869 (tmtt) cc_final: -0.1071 (tmtt) outliers start: 135 outliers final: 111 residues processed: 342 average time/residue: 0.5391 time to fit residues: 332.0960 Evaluate side-chains 336 residues out of total 7227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 221 time to evaluate : 5.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 862 ASN Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1231 ASP Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1278 ASN Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain A residue 1359 ASP Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 921 ASP Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1006 ILE Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain G residue 44 TYR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 38 GLU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 301 THR Chi-restraints excluded: chain M residue 303 GLN Chi-restraints excluded: chain Q residue 386 MET Chi-restraints excluded: chain R residue 98 ASN Chi-restraints excluded: chain R residue 121 ASP Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain O residue 104 MET Chi-restraints excluded: chain O residue 115 ILE Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 233 VAL Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 4 residue 252 MET Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 167 VAL Chi-restraints excluded: chain 0 residue 679 MET Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 6 residue 126 LEU Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 356 VAL Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 7 residue 269 LEU Chi-restraints excluded: chain 7 residue 304 GLU Chi-restraints excluded: chain 7 residue 337 VAL Chi-restraints excluded: chain 7 residue 343 PHE Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 449 GLU Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 514 THR Chi-restraints excluded: chain 7 residue 622 MET Chi-restraints excluded: chain 7 residue 745 ILE Chi-restraints excluded: chain 3 residue 30 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 699 optimal weight: 20.0000 chunk 461 optimal weight: 2.9990 chunk 742 optimal weight: 40.0000 chunk 453 optimal weight: 20.0000 chunk 352 optimal weight: 9.9990 chunk 516 optimal weight: 50.0000 chunk 779 optimal weight: 50.0000 chunk 717 optimal weight: 20.0000 chunk 620 optimal weight: 50.0000 chunk 64 optimal weight: 0.9980 chunk 479 optimal weight: 30.0000 overall best weight: 10.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 HIS ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 331 HIS ** 4 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 265 ASN 0 350 HIS ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 352 ASN ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4805 moved from start: 0.5332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.141 65862 Z= 0.514 Angle : 0.895 19.770 89392 Z= 0.456 Chirality : 0.049 0.453 10069 Planarity : 0.006 0.080 11234 Dihedral : 13.557 174.005 10056 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 34.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.29 % Favored : 87.63 % Rotamer: Outliers : 2.19 % Allowed : 17.34 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.59 % Twisted General : 0.12 % 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: -2.36 (0.09), residues: 7932 helix: -0.46 (0.09), residues: 3144 sheet: -1.92 (0.17), residues: 934 loop : -2.46 (0.09), residues: 3854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP C 170 HIS 0.016 0.002 HIS 0 66 PHE 0.028 0.003 PHE B 963 TYR 0.034 0.002 TYR 7 365 ARG 0.014 0.001 ARG A 416 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 7227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 221 time to evaluate : 5.933 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: A 108 MET cc_start: 0.5438 (mmt) cc_final: 0.5235 (mmm) REVERT: A 923 LEU cc_start: 0.6550 (OUTLIER) cc_final: 0.6226 (mm) REVERT: B 1098 MET cc_start: 0.5917 (mpp) cc_final: 0.5660 (mpp) REVERT: D 40 HIS cc_start: 0.2973 (OUTLIER) cc_final: 0.1819 (m-70) REVERT: U 244 MET cc_start: -0.0359 (ptt) cc_final: -0.1524 (ptt) REVERT: 1 350 ARG cc_start: -0.0690 (OUTLIER) cc_final: -0.1313 (pmt-80) REVERT: 1 385 MET cc_start: -0.1508 (ttp) cc_final: -0.3546 (mtm) REVERT: 0 61 MET cc_start: 0.1948 (mtm) cc_final: 0.1129 (ptm) REVERT: 0 485 MET cc_start: -0.0028 (mmt) cc_final: -0.0642 (mmt) REVERT: 0 553 MET cc_start: 0.5906 (ppp) cc_final: 0.5697 (ppp) REVERT: 7 304 GLU cc_start: -0.1455 (OUTLIER) cc_final: -0.2016 (pt0) REVERT: 7 459 MET cc_start: -0.2632 (mmp) cc_final: -0.2894 (mmt) REVERT: 7 622 MET cc_start: -0.1018 (OUTLIER) cc_final: -0.1781 (mmm) outliers start: 141 outliers final: 118 residues processed: 347 average time/residue: 0.5507 time to fit residues: 341.6023 Evaluate side-chains 342 residues out of total 7227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 219 time to evaluate : 5.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 862 ASN Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 980 ASP Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1231 ASP Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1278 ASN Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain A residue 1359 ASP Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1408 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 921 ASP Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1006 ILE Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1219 ASP Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain G residue 44 TYR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 38 GLU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 303 GLN Chi-restraints excluded: chain Q residue 386 MET Chi-restraints excluded: chain R residue 98 ASN Chi-restraints excluded: chain R residue 121 ASP Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain O residue 104 MET Chi-restraints excluded: chain O residue 115 ILE Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 233 VAL Chi-restraints excluded: chain 1 residue 350 ARG Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 4 residue 252 MET Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 167 VAL Chi-restraints excluded: chain 0 residue 679 MET Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 6 residue 126 LEU Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 356 VAL Chi-restraints excluded: chain 2 residue 48 MET Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 7 residue 269 LEU Chi-restraints excluded: chain 7 residue 304 GLU Chi-restraints excluded: chain 7 residue 337 VAL Chi-restraints excluded: chain 7 residue 343 PHE Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 449 GLU Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 514 THR Chi-restraints excluded: chain 7 residue 622 MET Chi-restraints excluded: chain 7 residue 745 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 782 random chunks: chunk 380 optimal weight: 5.9990 chunk 492 optimal weight: 10.0000 chunk 660 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 chunk 572 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 172 optimal weight: 0.7980 chunk 621 optimal weight: 30.0000 chunk 260 optimal weight: 3.9990 chunk 638 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1195 HIS ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 303 GLN ** U 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 379 ASN ** 4 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 269 GLN ** 6 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 633 GLN ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.055956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.047235 restraints weight = 812887.613| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 5.42 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3805 r_free = 0.3805 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 363 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3804 r_free = 0.3804 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 363 | |-----------------------------------------------------------------------------| r_final: 0.3804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.5537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 65862 Z= 0.258 Angle : 0.699 18.282 89392 Z= 0.357 Chirality : 0.044 0.407 10069 Planarity : 0.005 0.068 11234 Dihedral : 13.328 171.500 10056 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 24.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.20 % Favored : 90.73 % Rotamer: Outliers : 1.99 % Allowed : 17.68 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.29 % Twisted General : 0.12 % 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: -1.93 (0.09), residues: 7932 helix: -0.07 (0.09), residues: 3130 sheet: -1.75 (0.16), residues: 965 loop : -2.22 (0.10), residues: 3837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 2 201 HIS 0.008 0.001 HIS 0 294 PHE 0.032 0.002 PHE C 62 TYR 0.034 0.002 TYR 7 365 ARG 0.007 0.001 ARG 7 466 =============================================================================== Job complete usr+sys time: 9499.10 seconds wall clock time: 172 minutes 22.44 seconds (10342.44 seconds total)