Starting phenix.real_space_refine on Thu Feb 15 06:05:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml0_23904/02_2024/7ml0_23904_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml0_23904/02_2024/7ml0_23904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml0_23904/02_2024/7ml0_23904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml0_23904/02_2024/7ml0_23904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml0_23904/02_2024/7ml0_23904_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml0_23904/02_2024/7ml0_23904_updated.pdb" } resolution = 3.0 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 17 6.06 5 P 132 5.49 5 Mg 1 5.21 5 S 354 5.16 5 C 40068 2.51 5 N 11287 2.21 5 O 12351 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 GLU 291": "OE1" <-> "OE2" Residue "A GLU 500": "OE1" <-> "OE2" Residue "A GLU 678": "OE1" <-> "OE2" Residue "A GLU 812": "OE1" <-> "OE2" Residue "A GLU 833": "OE1" <-> "OE2" Residue "A GLU 1050": "OE1" <-> "OE2" Residue "A GLU 1074": "OE1" <-> "OE2" Residue "A GLU 1167": "OE1" <-> "OE2" Residue "A PHE 1174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1351": "OE1" <-> "OE2" Residue "A GLU 1448": "OE1" <-> "OE2" Residue "B PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B GLU 641": "OE1" <-> "OE2" Residue "B ARG 884": "NH1" <-> "NH2" Residue "C TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 194": "OE1" <-> "OE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C GLU 233": "OE1" <-> "OE2" Residue "D GLU 43": "OE1" <-> "OE2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "E GLU 66": "OE1" <-> "OE2" Residue "E GLU 67": "OE1" <-> "OE2" Residue "E PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 203": "OE1" <-> "OE2" Residue "F GLU 112": "OE1" <-> "OE2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "H ARG 80": "NH1" <-> "NH2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "H TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "I PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 30": "NH1" <-> "NH2" Residue "I PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 63": "NH1" <-> "NH2" Residue "M ASP 103": "OD1" <-> "OD2" Residue "M PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 215": "NH1" <-> "NH2" Residue "M GLU 306": "OE1" <-> "OE2" Residue "M ARG 320": "NH1" <-> "NH2" Residue "Q TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 343": "NH1" <-> "NH2" Residue "Q TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "W ARG 18": "NH1" <-> "NH2" Residue "W PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 60": "NH1" <-> "NH2" Residue "W ARG 62": "NH1" <-> "NH2" Residue "W ARG 65": "NH1" <-> "NH2" Residue "W ARG 108": "NH1" <-> "NH2" Residue "W ARG 144": "NH1" <-> "NH2" Residue "W ARG 193": "NH1" <-> "NH2" Residue "X ARG 197": "NH1" <-> "NH2" Residue "X PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 276": "NH1" <-> "NH2" Residue "O PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 287": "OE1" <-> "OE2" Residue "0 GLU 370": "OE1" <-> "OE2" Residue "0 ARG 375": "NH1" <-> "NH2" Residue "0 PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 421": "OE1" <-> "OE2" Residue "0 ASP 441": "OD1" <-> "OD2" Residue "0 GLU 572": "OE1" <-> "OE2" Residue "0 TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 286": "NH1" <-> "NH2" Residue "4 GLU 55": "OE1" <-> "OE2" Residue "4 ASP 122": "OD1" <-> "OD2" Residue "4 ARG 175": "NH1" <-> "NH2" Residue "4 ARG 273": "NH1" <-> "NH2" Residue "6 TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 378": "NH1" <-> "NH2" Residue "2 ARG 450": "NH1" <-> "NH2" Residue "2 GLU 455": "OE1" <-> "OE2" Residue "2 GLU 463": "OE1" <-> "OE2" Residue "2 TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 13": "OD1" <-> "OD2" Residue "5 GLU 33": "OE1" <-> "OE2" Residue "5 ARG 56": "NH1" <-> "NH2" Residue "3 PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 433": "OE1" <-> "OE2" Residue "7 PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 695": "NH1" <-> "NH2" Residue "7 GLU 755": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 64214 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 10996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1398, 10996 Classifications: {'peptide': 1398} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 1333} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 9132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1147, 9132 Classifications: {'peptide': 1147} Link IDs: {'PTRANS': 51, 'TRANS': 1095} Chain breaks: 6 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: "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: "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: "T" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1345 Classifications: {'DNA': 66} Link IDs: {'rna3p': 65} Chain: "N" Number of atoms: 1361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1361 Classifications: {'DNA': 66} Link IDs: {'rna3p': 65} Chain: "0" Number of atoms: 6099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 6099 Classifications: {'peptide': 753} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 720} Chain breaks: 1 Chain: "1" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2415 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 179} Link IDs: {'PTRANS': 12, 'TRANS': 354} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 460 Unresolved non-hydrogen angles: 630 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'UNK:plan-1': 105, 'TYR:plan': 3, 'ASN:plan1': 9, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 240 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: "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: {'PCIS': 1, 'PTRANS': 19, '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: 3020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3020 Classifications: {'peptide': 461} Incomplete info: {'backbone_only': 154, 'truncation_to_alanine': 14} Link IDs: {'CIS': 2, 'PTRANS': 17, 'TRANS': 441} 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: "3" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 890 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 5, 'TRANS': 131} Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 153 Chain: "7" Number of atoms: 4478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 4478 Classifications: {'peptide': 638} Incomplete info: {'backbone_only': 162} Link IDs: {'PTRANS': 26, 'TRANS': 611} 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: "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: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 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: "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 812 SG CYS A 107 86.929 122.076 129.030 1.00 0.00 S ATOM 836 SG CYS A 110 85.408 120.929 132.177 1.00 0.00 S ATOM 1141 SG CYS A 148 88.983 122.484 131.866 1.00 0.00 S ATOM 1210 SG CYS A 167 87.715 118.987 130.006 1.00 0.00 S ATOM 507 SG CYS A 67 43.024 135.295 116.911 1.00 0.00 S ATOM 529 SG CYS A 70 42.781 136.307 120.842 1.00 0.00 S ATOM 582 SG CYS A 77 44.380 138.594 117.920 1.00 0.00 S ATOM 19646 SG CYS B1163 51.099 133.916 133.459 1.00 0.00 S ATOM 19664 SG CYS B1166 53.739 133.428 130.738 1.00 0.00 S ATOM 19789 SG CYS B1182 50.405 131.918 130.379 1.00 0.00 S ATOM 19808 SG CYS B1185 53.062 130.589 132.705 1.00 0.00 S ATOM 20775 SG CYS C 86 11.666 193.004 95.361 1.00 0.00 S ATOM 20792 SG CYS C 88 12.850 189.542 94.463 1.00 0.00 S ATOM 20825 SG CYS C 92 11.285 192.291 92.074 1.00 0.00 S ATOM 20848 SG CYS C 95 14.952 192.330 93.550 1.00 0.00 S ATOM 28338 SG CYS I 7 131.916 157.685 89.452 1.00 0.00 S ATOM 28363 SG CYS I 10 129.335 154.563 90.066 1.00 0.00 S ATOM 28529 SG CYS I 29 130.780 155.727 92.766 1.00 0.00 S ATOM 28553 SG CYS I 32 133.062 154.341 89.936 1.00 0.00 S ATOM 28880 SG CYS I 75 119.372 199.643 91.844 1.00 0.00 S ATOM 28902 SG CYS I 78 117.814 201.524 89.071 1.00 0.00 S ATOM 29118 SG CYS I 103 117.341 197.493 89.271 1.00 0.00 S ATOM 29138 SG CYS I 106 119.789 198.957 87.809 1.00 0.00 S ATOM 29283 SG CYS J 7 44.075 203.717 92.221 1.00 0.00 S ATOM 29306 SG CYS J 10 41.899 207.117 93.280 1.00 0.00 S ATOM 29586 SG CYS J 45 45.711 206.706 93.683 1.00 0.00 S ATOM 29592 SG CYS J 46 44.211 207.199 90.624 1.00 0.00 S ATOM 30715 SG CYS L 31 41.860 167.530 67.080 1.00 0.00 S ATOM 30735 SG CYS L 34 39.563 168.141 63.716 1.00 0.00 S ATOM 30839 SG CYS L 48 39.825 165.082 65.628 1.00 0.00 S ATOM 30862 SG CYS L 51 42.747 165.996 63.635 1.00 0.00 S ATOM 31090 SG CYS M 24 21.250 150.660 115.457 1.00 0.00 S ATOM 31112 SG CYS M 27 18.082 152.195 114.179 1.00 0.00 S ATOM 31256 SG CYS M 45 21.271 153.065 112.292 1.00 0.00 S ATOM 31275 SG CYS M 48 21.059 154.210 115.662 1.00 0.00 S ATOM 36546 SG CYS W 124 32.814 121.264 115.166 1.00 0.00 S ATOM 36567 SG CYS W 127 36.037 122.636 115.899 1.00 0.00 S ATOM 36752 SG CYS W 149 33.328 124.016 117.809 1.00 0.00 S ATOM 36772 SG CYS W 152 33.386 124.726 113.887 1.00 0.00 S ATOM 43158 SG CYS 0 115 79.418 48.500 145.584 1.00117.61 S ATOM 43300 SG CYS 0 133 75.364 48.789 149.293 1.00 46.59 S ATOM 43786 SG CYS 0 191 77.614 42.995 149.268 1.00115.32 S ATOM 52570 SG CYS 4 289 143.775 25.361 147.277 1.00 0.00 S ATOM 52589 SG CYS 4 292 144.945 24.961 150.914 1.00 0.00 S ATOM 52674 SG CYS 4 305 144.412 22.238 149.175 1.00 0.00 S ATOM 52690 SG CYS 4 308 141.514 24.002 150.641 1.00 0.00 S ATOM 54988 SG CYS 6 403 160.271 45.760 171.697 1.00 0.00 S ATOM 55010 SG CYS 6 406 161.969 48.514 170.431 1.00 0.00 S ATOM 55178 SG CYS 6 437 158.522 49.502 171.113 1.00 0.00 S ATOM 55194 SG CYS 6 440 158.998 46.824 168.442 1.00 0.00 S ATOM 55136 SG CYS 6 429 151.471 37.087 170.157 1.00 0.00 S ATOM 55152 SG CYS 6 432 154.573 35.851 171.352 1.00 0.00 S ATOM 55272 SG CYS 6 451 154.312 36.553 167.439 1.00 0.00 S ATOM 55287 SG CYS 6 454 152.641 33.688 168.840 1.00 0.00 S ATOM 54633 SG CYS 6 349 153.687 28.479 129.172 1.00 0.00 S ATOM 54654 SG CYS 6 352 154.272 30.079 125.907 1.00 0.00 S ATOM 54723 SG CYS 6 363 151.345 31.339 127.755 1.00 0.00 S ATOM 54741 SG CYS 6 366 150.791 28.054 127.005 1.00 0.00 S ATOM 54550 SG CYS 6 336 156.768 40.814 123.576 1.00 30.00 S ATOM 54561 SG CYS 6 338 154.232 40.625 126.420 1.00 30.00 S ATOM 54688 SG CYS 6 357 157.088 42.783 126.845 1.00 30.00 S ATOM 58859 SG CYS 3 13 52.260 93.067 132.503 1.00163.05 S ATOM 58880 SG CYS 3 16 53.516 95.846 130.154 1.00164.11 S ATOM 59075 SG CYS 3 39 53.361 96.376 133.787 1.00156.98 S ATOM 59096 SG CYS 3 42 50.145 96.338 131.846 1.00154.76 S ATOM 59028 SG CYS 3 34 42.850 87.804 138.504 1.00151.96 S ATOM 59186 SG CYS 3 54 43.523 90.024 135.473 1.00157.81 S ATOM 59224 SG CYS 3 59 40.489 87.768 135.276 1.00157.50 S Residues with excluded nonbonded symmetry interactions: 11 residue: pdb=" P DT T 100 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 100 " occ=0.00 residue: pdb=" P DT T 102 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 102 " occ=0.00 residue: pdb=" P DA T 109 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA T 109 " occ=0.00 residue: pdb=" P DT T 114 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 114 " occ=0.00 residue: pdb=" P DT T 121 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 121 " occ=0.00 residue: pdb=" P DA N 45 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 45 " occ=0.00 residue: pdb=" P DA N 52 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 52 " occ=0.00 residue: pdb=" P DT N 55 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT N 55 " occ=0.00 residue: pdb=" P DT N 57 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT N 57 " occ=0.00 residue: pdb=" P DA N 64 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 64 " occ=0.00 residue: pdb=" P DA N 66 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 66 " occ=0.00 Time building chain proxies: 25.36, per 1000 atoms: 0.39 Number of scatterers: 64214 At special positions: 0 Unit cell: (218.36, 246.98, 200.34, 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 354 16.00 P 132 15.00 Mg 1 11.99 O 12351 8.00 N 11287 7.00 C 40068 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: 22.23 Conformation dependent library (CDL) restraints added in 8.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 801 " pdb="FE4 SF4 0 801 " - pdb=" SG CYS 0 191 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 133 " pdb="FE1 SF4 0 801 " - pdb=" SG CYS 0 115 " pdb="FE2 SF4 0 801 " - pdb=" SD MET 0 136 " pdb="FE4 SF4 0 801 " - pdb=" SG CYS 0 156 " Number of angles added : 15 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 16 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 42 " 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 54 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 59 " 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 4 308 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 289 " pdb=" ZN 6 501 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 406 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 440 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 403 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 437 " pdb=" ZN 6 502 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 454 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 432 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 429 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 451 " pdb=" ZN 6 503 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 349 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 366 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 363 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 352 " pdb=" ZN 6 504 " pdb="ZN ZN 6 504 " - pdb=" ND1 HIS 6 339 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 357 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 336 " pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " 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 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " 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 ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 48 " 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 W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 127 " 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 152 " Number of angles added : 93 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14770 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 310 helices and 55 sheets defined 38.9% alpha, 9.2% beta 58 base pairs and 107 stacking pairs defined. Time for finding SS restraints: 22.42 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 96 through 105 removed outlier: 3.876A pdb=" N VAL A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N CYS A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 131 through 142 removed outlier: 3.667A pdb=" N ALA A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.515A pdb=" N HIS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 222 Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 261 through 281 removed outlier: 3.689A pdb=" N LEU A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 304 removed outlier: 3.682A pdb=" N SER A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 329 removed outlier: 3.656A pdb=" N LEU A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 325 through 329' Processing helix chain 'A' and resid 335 through 339 Processing helix chain 'A' and resid 368 through 371 No H-bonds generated for 'chain 'A' and resid 368 through 371' Processing helix chain 'A' and resid 385 through 394 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 473 through 478 Proline residue: A 477 - end of helix Processing helix chain 'A' and resid 497 through 504 Processing helix chain 'A' and resid 508 through 510 No H-bonds generated for 'chain 'A' and resid 508 through 510' Processing helix chain 'A' and resid 526 through 535 Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 574 through 581 removed outlier: 4.058A 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 637 Processing helix chain 'A' and resid 639 through 660 removed outlier: 3.672A pdb=" N GLY A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 669 Processing helix chain 'A' and resid 673 through 698 removed outlier: 3.551A pdb=" N ALA A 686 " --> pdb=" O THR A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 736 removed outlier: 3.676A pdb=" N ASN A 736 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 748 Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 794 through 797 No H-bonds generated for 'chain 'A' and resid 794 through 797' Processing helix chain 'A' and resid 810 through 844 removed outlier: 3.534A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (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 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' 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 914 through 919 removed outlier: 4.192A pdb=" N SER A 917 " --> pdb=" O GLU A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 946 removed outlier: 3.805A pdb=" N LEU A 928 " --> pdb=" O LYS A 924 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP A 930 " --> pdb=" O GLN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 971 Processing helix chain 'A' and resid 983 through 996 removed outlier: 4.367A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) removed outlier: 4.149A 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 removed outlier: 3.625A pdb=" N ASP A1043 " --> pdb=" O LYS A1039 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP A1044 " --> pdb=" O GLN A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1077 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1097 through 1105 Processing helix chain 'A' and resid 1128 through 1138 Processing helix chain 'A' and resid 1143 through 1145 No H-bonds generated for 'chain 'A' and resid 1143 through 1145' Processing helix chain 'A' and resid 1164 through 1174 removed outlier: 3.909A pdb=" N GLU A1168 " --> pdb=" O PRO A1164 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU A1172 " --> pdb=" O GLU A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1202 No H-bonds generated for 'chain 'A' and resid 1199 through 1202' Processing helix chain 'A' and resid 1209 through 1219 Processing helix chain 'A' and resid 1257 through 1269 removed outlier: 3.565A pdb=" N ASN A1265 " --> pdb=" O LYS A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1316 No H-bonds generated for 'chain 'A' and resid 1313 through 1316' Processing helix chain 'A' and resid 1332 through 1359 removed outlier: 7.069A pdb=" N ILE A1341 " --> pdb=" O GLU A1337 " (cutoff:3.500A) removed outlier: 9.288A pdb=" N GLU A1342 " --> pdb=" O VAL A1338 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1376 removed outlier: 3.515A pdb=" N THR A1376 " --> pdb=" O VAL A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1391 No H-bonds generated for 'chain 'A' and resid 1389 through 1391' Processing helix chain 'A' and resid 1396 through 1401 removed outlier: 4.021A pdb=" N SER A1401 " --> pdb=" O LEU A1397 " (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 Processing helix chain 'B' and resid 27 through 41 removed outlier: 3.525A pdb=" N SER B 30 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 34 " --> pdb=" O TRP B 31 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 41 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 56 removed outlier: 3.671A pdb=" N PHE B 51 " --> pdb=" O GLN B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 66 removed outlier: 4.275A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 294 through 300 removed outlier: 3.512A pdb=" N GLU B 299 " --> pdb=" O GLY B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Proline residue: B 316 - end of helix removed outlier: 3.655A pdb=" N ASP B 320 " --> pdb=" O PRO B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 337 removed outlier: 4.236A pdb=" N ARG B 337 " --> pdb=" O PHE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 359 removed outlier: 3.614A pdb=" N GLN B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 389 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: 3.599A pdb=" N THR B 419 " --> pdb=" O GLN B 415 " (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: 3.575A pdb=" N SER B 455 " --> pdb=" O LYS B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 495 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 removed outlier: 3.642A pdb=" N GLU B 560 " --> pdb=" O THR B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 593 through 606 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 removed outlier: 3.665A pdb=" N THR B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 686 Processing helix chain 'B' and resid 697 through 700 Processing helix chain 'B' and resid 707 through 711 Processing helix chain 'B' and resid 745 through 748 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 759 through 761 No H-bonds generated for 'chain 'B' and resid 759 through 761' Processing helix chain 'B' and resid 764 through 776 removed outlier: 4.710A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 810 Processing helix chain 'B' and resid 843 through 847 Processing helix chain 'B' and resid 928 through 931 No H-bonds generated for 'chain 'B' and resid 928 through 931' 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 1020 Proline residue: B1018 - end of helix Processing helix chain 'B' and resid 1023 through 1038 Processing helix chain 'B' and resid 1052 through 1062 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 1122 through 1124 No H-bonds generated for 'chain 'B' and resid 1122 through 1124' Processing helix chain 'B' and resid 1132 through 1141 Processing helix chain 'B' and resid 1144 through 1149 Processing helix chain 'B' and resid 1198 through 1208 Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 60 through 69 removed outlier: 3.663A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) 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 197 through 200 No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 205 through 208 Processing helix chain 'C' and resid 240 through 264 removed outlier: 3.611A pdb=" N THR C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 3.850A 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: 3.532A pdb=" N LYS D 60 " --> pdb=" O ARG D 56 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS D 71 " --> pdb=" O ARG D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 133 removed outlier: 4.605A pdb=" N GLU D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 150 removed outlier: 3.508A pdb=" N TYR D 147 " --> pdb=" O ASN D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 169 removed outlier: 4.332A pdb=" N SER D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 Processing helix chain 'D' and resid 189 through 194 Processing helix chain 'D' and resid 204 through 217 removed outlier: 3.572A pdb=" N ILE D 210 " --> pdb=" O GLU D 206 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 26 Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'E' and resid 39 through 43 Processing helix chain 'E' and resid 55 through 58 No H-bonds generated for 'chain 'E' and resid 55 through 58' Processing helix chain 'E' and resid 66 through 71 removed outlier: 3.542A pdb=" N SER E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 103 removed outlier: 3.522A pdb=" N ILE E 98 " --> pdb=" O LYS E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 123 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 167 removed outlier: 3.732A 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 103 Processing helix chain 'F' and resid 117 through 127 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 22 through 34 Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'H' and resid 129 through 134 removed outlier: 5.313A pdb=" N ASN H 134 " --> pdb=" O ARG H 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'J' and resid 18 through 27 Processing helix chain 'J' and resid 32 through 39 removed outlier: 4.148A pdb=" N SER J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 52 removed outlier: 3.825A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 Processing helix chain 'K' and resid 40 through 52 removed outlier: 3.865A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 111 removed outlier: 3.712A pdb=" N LYS K 88 " --> pdb=" O LYS K 84 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU K 108 " --> pdb=" O ASN K 104 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU K 111 " --> pdb=" O THR K 107 " (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 61 through 64 No H-bonds generated for 'chain 'M' and resid 61 through 64' Processing helix chain 'M' and resid 85 through 88 No H-bonds generated for 'chain 'M' and resid 85 through 88' Processing helix chain 'M' and resid 104 through 116 removed outlier: 5.248A pdb=" N GLU M 109 " --> pdb=" O ARG M 105 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN M 114 " --> pdb=" O LEU M 110 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLY M 115 " --> pdb=" O ASN M 111 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LYS M 116 " --> pdb=" O LYS M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 139 removed outlier: 4.703A pdb=" N ALA M 128 " --> pdb=" O GLU M 125 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA M 131 " --> pdb=" O ALA M 128 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS M 137 " --> pdb=" O THR M 134 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ASP M 138 " --> pdb=" O MET M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 157 removed outlier: 3.794A pdb=" N ASP M 148 " --> pdb=" O LYS M 144 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS M 155 " --> pdb=" O LYS M 151 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N CYS M 157 " --> pdb=" O ALA M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 169 through 182 removed outlier: 4.094A pdb=" N ILE M 176 " --> pdb=" O MET M 172 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU M 177 " --> pdb=" O ALA M 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 195 Processing helix chain 'M' and resid 202 through 217 removed outlier: 3.550A pdb=" N ILE M 209 " --> pdb=" O LYS M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 235 through 246 Proline residue: M 240 - end of helix removed outlier: 3.969A pdb=" N SER M 244 " --> pdb=" O ARG M 241 " (cutoff:3.500A) Processing helix chain 'M' and resid 250 through 266 removed outlier: 3.551A pdb=" N ALA M 256 " --> pdb=" O VAL M 252 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU M 257 " --> pdb=" O THR M 253 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR M 258 " --> pdb=" O THR M 254 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE M 266 " --> pdb=" O LYS M 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 275 through 288 removed outlier: 3.877A pdb=" N SER M 281 " --> pdb=" O ILE M 277 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE M 282 " --> pdb=" O ALA M 278 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 302 removed outlier: 3.909A pdb=" N GLN M 300 " --> pdb=" O ALA M 296 " (cutoff:3.500A) Processing helix chain 'M' and resid 307 through 317 removed outlier: 3.615A pdb=" N ILE M 315 " --> pdb=" O SER M 311 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU M 316 " --> pdb=" O GLY M 312 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 34 removed outlier: 4.169A pdb=" N ARG Q 28 " --> pdb=" O ASP Q 25 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE Q 31 " --> pdb=" O ARG Q 28 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N MET Q 34 " --> pdb=" O PHE Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 109 through 113 Processing helix chain 'Q' and resid 130 through 132 No H-bonds generated for 'chain 'Q' and resid 130 through 132' Processing helix chain 'Q' and resid 338 through 344 Processing helix chain 'Q' and resid 408 through 414 Processing helix chain 'R' and resid 75 through 81 Processing helix chain 'R' and resid 234 through 245 removed outlier: 3.794A pdb=" N ILE R 243 " --> pdb=" O GLN R 239 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS R 245 " --> pdb=" O ARG R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 265 removed outlier: 3.589A pdb=" N MET R 263 " --> pdb=" O VAL R 259 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER R 264 " --> pdb=" O GLY R 260 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N HIS R 265 " --> pdb=" O VAL R 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 259 through 265' Processing helix chain 'R' and resid 296 through 309 Processing helix chain 'R' and resid 315 through 322 removed outlier: 3.512A pdb=" N ARG R 321 " --> pdb=" O GLY R 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 326 through 334 removed outlier: 3.774A pdb=" N LEU R 333 " --> pdb=" O LEU R 329 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP R 334 " --> pdb=" O LYS R 330 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 19 Processing helix chain 'W' and resid 23 through 33 removed outlier: 3.811A pdb=" N VAL W 28 " --> pdb=" O PHE W 25 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP W 30 " --> pdb=" O LEU W 27 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA W 31 " --> pdb=" O VAL W 28 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 47 Processing helix chain 'W' and resid 55 through 63 removed outlier: 3.573A pdb=" N ARG W 60 " --> pdb=" O PRO W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 91 through 110 Processing helix chain 'W' and resid 133 through 139 Processing helix chain 'W' and resid 162 through 178 removed outlier: 3.529A pdb=" N GLN W 178 " --> pdb=" O ARG W 174 " (cutoff:3.500A) Processing helix chain 'W' and resid 182 through 190 Processing helix chain 'X' and resid 125 through 138 Processing helix chain 'X' and resid 144 through 150 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 213 removed outlier: 3.787A pdb=" N ASP X 212 " --> pdb=" O LYS X 208 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 223 removed outlier: 3.672A pdb=" N ASN X 222 " --> pdb=" O ASP X 218 " (cutoff:3.500A) Processing helix chain 'X' and resid 257 through 265 Processing helix chain 'X' and resid 273 through 281 removed outlier: 3.574A pdb=" N GLN X 279 " --> pdb=" O PRO X 275 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 88 Processing helix chain 'O' and resid 129 through 146 Processing helix chain 'O' and resid 172 through 178 Processing helix chain 'O' and resid 220 through 236 Proline residue: O 232 - end of helix Processing helix chain '0' and resid 19 through 33 Processing helix chain '0' and resid 48 through 62 removed outlier: 3.668A pdb=" N LEU 0 55 " --> pdb=" O SER 0 51 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA 0 58 " --> pdb=" O SER 0 54 " (cutoff:3.500A) Processing helix chain '0' and resid 76 through 96 Processing helix chain '0' and resid 118 through 122 Processing helix chain '0' and resid 126 through 136 Processing helix chain '0' and resid 139 through 146 Processing helix chain '0' and resid 158 through 165 Processing helix chain '0' and resid 178 through 187 removed outlier: 3.977A pdb=" N LYS 0 183 " --> pdb=" O GLU 0 179 " (cutoff:3.500A) Processing helix chain '0' and resid 192 through 201 removed outlier: 4.891A pdb=" N SER 0 201 " --> pdb=" O ARG 0 197 " (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 237 through 248 removed outlier: 4.823A pdb=" N ASP 0 241 " --> pdb=" O HIS 0 238 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU 0 248 " --> pdb=" O CYS 0 244 " (cutoff:3.500A) Processing helix chain '0' and resid 254 through 277 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 Processing helix chain '0' and resid 328 through 347 removed outlier: 4.180A pdb=" N LYS 0 347 " --> pdb=" O LYS 0 343 " (cutoff:3.500A) Processing helix chain '0' and resid 356 through 366 removed outlier: 3.719A pdb=" N HIS 0 362 " --> pdb=" O SER 0 358 " (cutoff:3.500A) Processing helix chain '0' and resid 371 through 386 removed outlier: 3.968A pdb=" N PHE 0 376 " --> pdb=" O LYS 0 372 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N SER 0 378 " --> pdb=" O LEU 0 374 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLU 0 379 " --> pdb=" O ARG 0 375 " (cutoff:3.500A) Processing helix chain '0' and resid 394 through 411 removed outlier: 3.737A pdb=" N ALA 0 398 " --> pdb=" O GLU 0 394 " (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 442 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 removed outlier: 3.604A pdb=" N SER 0 524 " --> pdb=" O ARG 0 520 " (cutoff:3.500A) Processing helix chain '0' and resid 544 through 556 Processing helix chain '0' and resid 559 through 566 removed outlier: 3.548A pdb=" N VAL 0 563 " --> pdb=" O ILE 0 559 " (cutoff:3.500A) Processing helix chain '0' and resid 576 through 591 removed outlier: 3.655A pdb=" N GLU 0 584 " --> pdb=" O SER 0 580 " (cutoff:3.500A) Processing helix chain '0' and resid 605 through 609 Processing helix chain '0' and resid 633 through 645 removed outlier: 3.720A pdb=" N PHE 0 641 " --> pdb=" O ALA 0 637 " (cutoff:3.500A) Processing helix chain '0' and resid 650 through 669 removed outlier: 3.581A pdb=" N MET 0 659 " --> pdb=" O SER 0 655 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN 0 664 " --> pdb=" O ARG 0 660 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU 0 666 " --> pdb=" O ALA 0 662 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ARG 0 668 " --> pdb=" O GLN 0 664 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL 0 669 " --> pdb=" O CYS 0 665 " (cutoff:3.500A) Processing helix chain '0' and resid 684 through 692 removed outlier: 3.511A pdb=" N ARG 0 690 " --> pdb=" O SER 0 687 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER 0 691 " --> pdb=" O ARG 0 688 " (cutoff:3.500A) Processing helix chain '0' and resid 695 through 700 Processing helix chain '0' and resid 710 through 725 removed outlier: 3.529A pdb=" N SER 0 715 " --> pdb=" O ASP 0 711 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN 0 716 " --> pdb=" O MET 0 712 " (cutoff:3.500A) Processing helix chain '0' and resid 733 through 738 removed outlier: 3.862A pdb=" N VAL 0 738 " --> pdb=" O GLY 0 735 " (cutoff:3.500A) Processing helix chain '0' and resid 744 through 753 Processing helix chain '1' and resid 171 through 176 Processing helix chain '1' and resid 178 through 185 Processing helix chain '1' and resid 189 through 199 removed outlier: 4.615A pdb=" N THR 1 198 " --> pdb=" O VAL 1 194 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL 1 199 " --> pdb=" O PHE 1 195 " (cutoff:3.500A) Processing helix chain '1' and resid 206 through 224 removed outlier: 3.764A pdb=" N SER 1 211 " --> pdb=" O SER 1 207 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR 1 212 " --> pdb=" O GLU 1 208 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ARG 1 213 " --> pdb=" O PHE 1 209 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE 1 214 " --> pdb=" O TRP 1 210 " (cutoff:3.500A) Proline residue: 1 215 - end of helix removed outlier: 3.830A pdb=" N UNK 1 224 " --> pdb=" O PHE 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 231 through 239 removed outlier: 4.382A pdb=" N UNK 1 237 " --> pdb=" O VAL 1 233 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N UNK 1 238 " --> pdb=" O UNK 1 234 " (cutoff:3.500A) Proline residue: 1 239 - end of helix Processing helix chain '1' and resid 252 through 262 Processing helix chain '1' and resid 264 through 273 Processing helix chain '1' and resid 283 through 294 removed outlier: 3.637A pdb=" N SER 1 289 " --> pdb=" O ALA 1 285 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER 1 290 " --> pdb=" O ARG 1 286 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS 1 291 " --> pdb=" O PHE 1 287 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU 1 292 " --> pdb=" O PHE 1 288 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE 1 293 " --> pdb=" O SER 1 289 " (cutoff:3.500A) Processing helix chain '1' and resid 309 through 329 removed outlier: 4.106A pdb=" N LEU 1 315 " --> pdb=" O UNK 1 312 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N UNK 1 316 " --> pdb=" O UNK 1 313 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N UNK 1 319 " --> pdb=" O UNK 1 316 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N UNK 1 320 " --> pdb=" O UNK 1 317 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N UNK 1 323 " --> pdb=" O UNK 1 320 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS 1 324 " --> pdb=" O PHE 1 321 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N UNK 1 325 " --> pdb=" O UNK 1 322 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N UNK 1 326 " --> pdb=" O UNK 1 323 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N UNK 1 328 " --> pdb=" O UNK 1 325 " (cutoff:3.500A) Processing helix chain '1' and resid 339 through 344 Processing helix chain '1' and resid 372 through 390 Processing helix chain '1' and resid 469 through 482 Processing helix chain '1' and resid 497 through 515 removed outlier: 3.615A pdb=" N ILE 1 509 " --> pdb=" O THR 1 505 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ASN 1 510 " --> pdb=" O UNK 1 506 " (cutoff:3.500A) Processing helix chain '1' and resid 541 through 566 removed outlier: 3.874A pdb=" N LEU 1 547 " --> pdb=" O PRO 1 543 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU 1 548 " --> pdb=" O ILE 1 544 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE 1 566 " --> pdb=" O LYS 1 562 " (cutoff:3.500A) Processing helix chain '1' and resid 576 through 604 removed outlier: 3.529A pdb=" N LYS 1 580 " --> pdb=" O ALA 1 576 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU 1 601 " --> pdb=" O PHE 1 597 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN 1 602 " --> pdb=" O GLN 1 598 " (cutoff:3.500A) Processing helix chain '1' and resid 607 through 638 removed outlier: 3.580A pdb=" N ALA 1 614 " --> pdb=" O ASN 1 610 " (cutoff:3.500A) Proline residue: 1 618 - end of helix Processing helix chain '4' and resid 34 through 42 Processing helix chain '4' and resid 50 through 67 removed outlier: 3.510A pdb=" N GLU 4 55 " --> pdb=" O ILE 4 51 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN 4 62 " --> pdb=" O ILE 4 58 " (cutoff:3.500A) Processing helix chain '4' and resid 118 through 134 removed outlier: 3.804A pdb=" N GLU 4 128 " --> pdb=" O THR 4 124 " (cutoff:3.500A) Processing helix chain '4' and resid 138 through 142 Processing helix chain '4' and resid 149 through 166 Processing helix chain '4' and resid 191 through 206 Proline residue: 4 195 - end of helix removed outlier: 3.579A pdb=" N PHE 4 201 " --> pdb=" O ASN 4 198 " (cutoff:3.500A) Processing helix chain '4' and resid 222 through 231 Processing helix chain '4' and resid 244 through 251 removed outlier: 4.034A pdb=" N ALA 4 249 " --> pdb=" O GLN 4 246 " (cutoff:3.500A) Processing helix chain '4' and resid 314 through 322 removed outlier: 3.875A pdb=" N LYS 4 321 " --> pdb=" O ILE 4 317 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG 4 322 " --> pdb=" O ALA 4 318 " (cutoff:3.500A) Processing helix chain '6' and resid 134 through 137 Processing helix chain '6' and resid 145 through 163 removed outlier: 3.748A pdb=" N ASP 6 155 " --> pdb=" O GLN 6 151 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE 6 156 " --> pdb=" O TYR 6 152 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS 6 158 " --> pdb=" O ILE 6 154 " (cutoff:3.500A) Processing helix chain '6' and resid 189 through 201 removed outlier: 3.912A pdb=" N LYS 6 197 " --> pdb=" O ILE 6 193 " (cutoff:3.500A) Processing helix chain '6' and resid 210 through 220 removed outlier: 3.507A pdb=" N GLU 6 215 " --> pdb=" O GLN 6 211 " (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 305 removed outlier: 3.820A pdb=" N GLU 6 299 " --> pdb=" O THR 6 295 " (cutoff:3.500A) Processing helix chain '6' and resid 374 through 380 removed outlier: 3.627A pdb=" N SER 6 379 " --> pdb=" O HIS 6 375 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR 6 380 " --> pdb=" O LEU 6 376 " (cutoff:3.500A) 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 11 through 16 Processing helix chain '2' and resid 19 through 27 removed outlier: 4.108A pdb=" N THR 2 27 " --> pdb=" O ASN 2 23 " (cutoff:3.500A) Processing helix chain '2' and resid 29 through 38 Processing helix chain '2' and resid 41 through 51 Processing helix chain '2' and resid 60 through 65 Processing helix chain '2' and resid 71 through 84 removed outlier: 4.026A pdb=" N GLN 2 75 " --> pdb=" O LYS 2 71 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER 2 80 " --> pdb=" O ASN 2 76 " (cutoff:3.500A) Processing helix chain '2' and resid 102 through 112 removed outlier: 3.588A pdb=" N ALA 2 111 " --> pdb=" O SER 2 107 " (cutoff:3.500A) Processing helix chain '2' and resid 138 through 151 removed outlier: 4.128A pdb=" N LYS 2 142 " --> pdb=" O TYR 2 138 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU 2 147 " --> pdb=" O TRP 2 143 " (cutoff:3.500A) Processing helix chain '2' and resid 161 through 170 Processing helix chain '2' and resid 186 through 193 Processing helix chain '2' and resid 197 through 210 removed outlier: 4.491A pdb=" N GLN 2 206 " --> pdb=" O THR 2 202 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR 2 207 " --> pdb=" O LEU 2 203 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU 2 208 " --> pdb=" O LEU 2 204 " (cutoff:3.500A) Processing helix chain '2' and resid 218 through 230 removed outlier: 3.673A pdb=" N PHE 2 224 " --> pdb=" O ASP 2 220 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU 2 228 " --> pdb=" O PHE 2 224 " (cutoff:3.500A) Processing helix chain '2' and resid 244 through 256 Processing helix chain '2' and resid 273 through 279 removed outlier: 3.787A pdb=" N THR 2 279 " --> pdb=" O ALA 2 275 " (cutoff:3.500A) Processing helix chain '2' and resid 356 through 363 removed outlier: 4.307A pdb=" N PHE 2 363 " --> pdb=" O VAL 2 359 " (cutoff:3.500A) Processing helix chain '2' and resid 380 through 389 removed outlier: 3.874A pdb=" N ARG 2 384 " --> pdb=" O ARG 2 380 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG 2 385 " --> pdb=" O GLU 2 381 " (cutoff:3.500A) removed outlier: 4.303A 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 408 Processing helix chain '2' and resid 411 through 414 No H-bonds generated for 'chain '2' and resid 411 through 414' Processing helix chain '2' and resid 422 through 424 No H-bonds generated for 'chain '2' and resid 422 through 424' Processing helix chain '2' and resid 436 through 449 Processing helix chain '2' and resid 475 through 478 No H-bonds generated for 'chain '2' and resid 475 through 478' Processing helix chain '2' and resid 486 through 488 No H-bonds generated for 'chain '2' and resid 486 through 488' Processing helix chain '5' and resid 14 through 27 Processing helix chain '5' and resid 47 through 61 Processing helix chain '3' and resid 40 through 47 Processing helix chain '3' and resid 65 through 67 No H-bonds generated for 'chain '3' and resid 65 through 67' Processing helix chain '3' and resid 76 through 94 removed outlier: 3.832A pdb=" N ASN 3 93 " --> pdb=" O PHE 3 89 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS 3 94 " --> pdb=" O ASN 3 90 " (cutoff:3.500A) Processing helix chain '3' and resid 103 through 122 Processing helix chain '3' and resid 128 through 142 Processing helix chain '7' and resid 125 through 128 No H-bonds generated for 'chain '7' and resid 125 through 128' Processing helix chain '7' and resid 151 through 159 removed outlier: 4.206A pdb=" N ASP 7 155 " --> pdb=" O GLN 7 152 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE 7 156 " --> pdb=" O ALA 7 153 " (cutoff:3.500A) Processing helix chain '7' and resid 177 through 185 removed outlier: 3.961A pdb=" N TYR 7 181 " --> pdb=" O ALA 7 177 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL 7 184 " --> pdb=" O LEU 7 180 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N SER 7 185 " --> pdb=" O TYR 7 181 " (cutoff:3.500A) Processing helix chain '7' and resid 190 through 199 removed outlier: 3.736A pdb=" N ILE 7 194 " --> pdb=" O THR 7 190 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG 7 199 " --> pdb=" O SER 7 195 " (cutoff:3.500A) Processing helix chain '7' and resid 207 through 216 Processing helix chain '7' and resid 242 through 244 No H-bonds generated for 'chain '7' and resid 242 through 244' Processing helix chain '7' and resid 305 through 307 No H-bonds generated for 'chain '7' and resid 305 through 307' Processing helix chain '7' and resid 326 through 332 removed outlier: 4.546A pdb=" N GLN 7 331 " --> pdb=" O LYS 7 327 " (cutoff:3.500A) Processing helix chain '7' and resid 367 through 373 removed outlier: 3.842A pdb=" N MET 7 373 " --> pdb=" O SER 7 369 " (cutoff:3.500A) Processing helix chain '7' and resid 392 through 401 removed outlier: 3.834A pdb=" N ALA 7 399 " --> pdb=" O VAL 7 395 " (cutoff:3.500A) Processing helix chain '7' and resid 417 through 419 No H-bonds generated for 'chain '7' and resid 417 through 419' 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 removed outlier: 3.598A pdb=" N MET 7 474 " --> pdb=" O GLN 7 471 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ASP 7 475 " --> pdb=" O LYS 7 472 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE 7 476 " --> pdb=" O VAL 7 473 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU 7 477 " --> pdb=" O MET 7 474 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR 7 478 " --> pdb=" O ASP 7 475 " (cutoff:3.500A) Processing helix chain '7' and resid 495 through 502 removed outlier: 6.312A pdb=" N ARG 7 500 " --> pdb=" O ALA 7 496 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL 7 501 " --> pdb=" O MET 7 497 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL 7 502 " --> pdb=" O PHE 7 498 " (cutoff:3.500A) Processing helix chain '7' and resid 563 through 569 removed outlier: 4.364A pdb=" N GLU 7 568 " --> pdb=" O GLU 7 564 " (cutoff:3.500A) Processing helix chain '7' and resid 575 through 582 removed outlier: 3.856A pdb=" N LEU 7 579 " --> pdb=" O LYS 7 576 " (cutoff:3.500A) Processing helix chain '7' and resid 585 through 600 removed outlier: 3.933A pdb=" N GLN 7 589 " --> pdb=" O PRO 7 585 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE 7 593 " --> pdb=" O GLN 7 589 " (cutoff:3.500A) Processing helix chain '7' and resid 612 through 621 removed outlier: 4.610A pdb=" N GLU 7 617 " --> pdb=" O TYR 7 613 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU 7 620 " --> pdb=" O GLN 7 616 " (cutoff:3.500A) Processing helix chain '7' and resid 634 through 639 removed outlier: 3.897A pdb=" N ILE 7 639 " --> pdb=" O ARG 7 636 " (cutoff:3.500A) Processing helix chain '7' and resid 658 through 660 No H-bonds generated for 'chain '7' and resid 658 through 660' Processing helix chain '7' and resid 680 through 691 removed outlier: 3.514A pdb=" N GLY 7 688 " --> pdb=" O ALA 7 684 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG 7 689 " --> pdb=" O GLN 7 685 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE 7 690 " --> pdb=" O ARG 7 686 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU 7 691 " --> pdb=" O LEU 7 687 " (cutoff:3.500A) Processing helix chain '7' and resid 716 through 725 removed outlier: 4.394A pdb=" N PHE 7 725 " --> pdb=" O LYS 7 721 " (cutoff:3.500A) Processing helix chain '7' and resid 727 through 729 No H-bonds generated for 'chain '7' and resid 727 through 729' Processing helix chain '7' and resid 753 through 769 removed outlier: 3.507A pdb=" N GLN 7 761 " --> pdb=" O ARG 7 757 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU 7 765 " --> pdb=" O GLN 7 761 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS 7 766 " --> pdb=" O GLU 7 762 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN 7 767 " --> pdb=" O VAL 7 763 " (cutoff:3.500A) 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 173 through 176 Processing sheet with id= C, first strand: chain 'A' and resid 250 through 252 Processing sheet with id= D, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.573A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.240A 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: 4.008A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.976A 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 Processing sheet with id= H, first strand: chain 'A' and resid 879 through 882 Processing sheet with id= I, first strand: chain 'A' and resid 1226 through 1228 Processing sheet with id= J, first strand: chain 'A' and resid 1285 through 1288 Processing sheet with id= K, first strand: chain 'B' and resid 69 through 73 Processing sheet with id= L, first strand: chain 'B' and resid 95 through 97 removed outlier: 4.035A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= N, first strand: chain 'B' and resid 203 through 205 Processing sheet with id= O, first strand: chain 'B' and resid 404 through 407 Processing sheet with id= P, first strand: chain 'B' and resid 223 through 227 removed outlier: 6.933A pdb=" N LEU B 258 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL B 237 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL B 256 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLU B 239 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU B 254 " --> pdb=" O GLU B 239 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 614 through 618 removed outlier: 6.426A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 634 through 638 Processing sheet with id= S, first strand: chain 'B' and resid 793 through 796 removed outlier: 5.733A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 821 through 827 removed outlier: 4.606A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N MET B 841 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR B 993 " --> pdb=" O MET B 841 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 915 through 917 Processing sheet with id= V, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id= W, first strand: chain 'C' and resid 228 through 233 removed outlier: 6.233A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 97 through 104 removed outlier: 5.717A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.605A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 36 through 38 removed outlier: 3.827A pdb=" N GLN D 37 " --> pdb=" O GLU D 45 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.805A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.672A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N MET E 215 " --> pdb=" O PRO E 176 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ILE E 178 " --> pdb=" O MET E 215 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 133 through 137 Processing sheet with id= AD, first strand: chain 'G' and resid 2 through 13 removed outlier: 4.568A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 86 through 90 removed outlier: 4.546A pdb=" N ARG G 142 " --> pdb=" O ILE G 171 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY G 169 " --> pdb=" O ARG G 144 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 98 through 103 removed outlier: 3.556A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL G 110 " --> pdb=" O PHE G 99 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 146 through 151 removed outlier: 5.390A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'H' and resid 7 through 11 removed outlier: 3.554A pdb=" N ASP H 8 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR H 56 " --> pdb=" O ARG H 145 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG H 145 " --> pdb=" O THR H 56 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU H 126 " --> pdb=" O LYS H 37 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'I' and resid 16 through 19 Processing sheet with id= AJ, first strand: chain 'I' and resid 83 through 87 Processing sheet with id= AK, first strand: chain 'K' and resid 19 through 22 Processing sheet with id= AL, first strand: chain 'M' and resid 34 through 37 removed outlier: 3.598A pdb=" N SER M 53 " --> pdb=" O VAL M 43 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N CYS M 45 " --> pdb=" O VAL M 51 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL M 51 " --> pdb=" O CYS M 45 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'R' and resid 135 through 137 Processing sheet with id= AN, first strand: chain 'R' and resid 66 through 72 removed outlier: 7.722A pdb=" N LEU R 70 " --> pdb=" O CYS R 219 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLU R 221 " --> pdb=" O LEU R 70 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ARG R 72 " --> pdb=" O GLU R 221 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLN R 223 " --> pdb=" O ARG R 72 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'W' and resid 69 through 71 Processing sheet with id= AP, first strand: chain 'W' and resid 122 through 124 Processing sheet with id= AQ, first strand: chain 'O' and resid 72 through 75 removed outlier: 4.120A pdb=" N LYS O 120 " --> pdb=" O PHE O 116 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'O' and resid 193 through 196 removed outlier: 5.244A pdb=" N SER O 163 " --> pdb=" O LEU O 67 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU O 67 " --> pdb=" O SER O 163 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain '0' and resid 2 through 4 Processing sheet with id= AT, first strand: chain '0' and resid 205 through 209 removed outlier: 6.844A pdb=" N ILE 0 69 " --> pdb=" O ILE 0 206 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N TYR 0 208 " --> pdb=" O ILE 0 69 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR 0 71 " --> pdb=" O TYR 0 208 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE 0 231 " --> pdb=" O ILE 0 70 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N CYS 0 72 " --> pdb=" O ILE 0 231 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE 0 233 " --> pdb=" O CYS 0 72 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain '0' and resid 352 through 355 removed outlier: 3.557A pdb=" N GLU 0 421 " --> pdb=" O ILE 0 434 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain '0' and resid 493 through 497 removed outlier: 3.630A pdb=" N MET 0 622 " --> pdb=" O VAL 0 680 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU 0 598 " --> pdb=" O VAL 0 539 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N PHE 0 541 " --> pdb=" O LEU 0 598 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N SER 0 600 " --> pdb=" O PHE 0 541 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain '4' and resid 83 through 85 removed outlier: 8.518A pdb=" N ALA 4 74 " --> pdb=" O SER 4 24 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU 4 26 " --> pdb=" O ALA 4 74 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ILE 4 76 " --> pdb=" O LEU 4 26 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL 4 28 " --> pdb=" O ILE 4 76 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ALA 4 78 " --> pdb=" O VAL 4 28 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ILE 4 30 " --> pdb=" O ALA 4 78 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LYS 4 173 " --> pdb=" O LEU 4 25 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N THR 4 27 " --> pdb=" O LYS 4 173 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ARG 4 175 " --> pdb=" O THR 4 27 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILE 4 29 " --> pdb=" O ARG 4 175 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU 4 177 " --> pdb=" O ILE 4 29 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLU 4 31 " --> pdb=" O LEU 4 177 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU 4 179 " --> pdb=" O GLU 4 31 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain '6' and resid 178 through 183 removed outlier: 6.679A pdb=" N ILE 6 171 " --> pdb=" O VAL 6 182 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N THR 6 229 " --> pdb=" O SER 6 125 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE 6 127 " --> pdb=" O THR 6 229 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLU 6 231 " --> pdb=" O ILE 6 127 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N THR 6 129 " --> pdb=" O GLU 6 231 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU 6 233 " --> pdb=" O THR 6 129 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ASP 6 131 " --> pdb=" O LEU 6 233 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL 6 235 " --> pdb=" O ASP 6 131 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG 6 260 " --> pdb=" O VAL 6 232 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ILE 6 234 " --> pdb=" O ARG 6 260 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS 6 262 " --> pdb=" O ILE 6 234 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain '2' and resid 87 through 90 removed outlier: 3.556A pdb=" N ASN 2 99 " --> pdb=" O ILE 2 88 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain '2' and resid 365 through 369 removed outlier: 4.276A pdb=" N HIS 2 365 " --> pdb=" O GLN 2 377 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN 2 377 " --> pdb=" O HIS 2 365 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU 2 375 " --> pdb=" O LYS 2 367 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain '5' and resid 8 through 10 Processing sheet with id= BB, first strand: chain '7' and resid 382 through 385 removed outlier: 4.483A pdb=" N GLY 7 382 " --> pdb=" O LYS 7 510 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR 7 514 " --> pdb=" O ILE 7 384 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE 7 485 " --> pdb=" O LEU 7 511 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LEU 7 513 " --> pdb=" O ILE 7 485 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU 7 487 " --> pdb=" O LEU 7 513 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain '7' and resid 732 through 736 removed outlier: 3.502A pdb=" N CYS 7 554 " --> pdb=" O ALA 7 732 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU 7 556 " --> pdb=" O LYS 7 734 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP 7 558 " --> pdb=" O ILE 7 736 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N PHE 7 705 " --> pdb=" O ALA 7 555 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N VAL 7 557 " --> pdb=" O PHE 7 705 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N SER 7 707 " --> pdb=" O VAL 7 557 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N CYS 7 559 " --> pdb=" O SER 7 707 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL 7 709 " --> pdb=" O CYS 7 559 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N LEU 7 670 " --> pdb=" O TYR 7 706 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU 7 708 " --> pdb=" O LEU 7 670 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLN 7 672 " --> pdb=" O LEU 7 708 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N SER 7 710 " --> pdb=" O GLN 7 672 " (cutoff:3.500A) 2057 hydrogen bonds defined for protein. 5721 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 127 hydrogen bonds 246 hydrogen bond angles 0 basepair planarities 58 basepair parallelities 107 stacking parallelities Total time for adding SS restraints: 23.92 Time building geometry restraints manager: 24.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.40: 26365 1.40 - 1.62: 38647 1.62 - 1.84: 544 1.84 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 65568 Sorted by residual: bond pdb=" C SER A 354 " pdb=" N GLY A 355 " ideal model delta sigma weight residual 1.332 1.228 0.105 1.91e-02 2.74e+03 3.00e+01 bond pdb=" C LYS A 569 " pdb=" N PRO A 570 " ideal model delta sigma weight residual 1.330 1.269 0.062 1.19e-02 7.06e+03 2.68e+01 bond pdb=" CA GLU A1404 " pdb=" CB GLU A1404 " ideal model delta sigma weight residual 1.531 1.374 0.157 3.12e-02 1.03e+03 2.53e+01 bond pdb=" C CYS I 32 " pdb=" N SER I 33 " ideal model delta sigma weight residual 1.332 1.266 0.066 1.40e-02 5.10e+03 2.23e+01 bond pdb=" C ASN 6 188 " pdb=" N PRO 6 189 " ideal model delta sigma weight residual 1.336 1.283 0.053 1.20e-02 6.94e+03 1.94e+01 ... (remaining 65563 not shown) Histogram of bond angle deviations from ideal: 73.62 - 86.54: 12 86.54 - 99.46: 73 99.46 - 112.38: 36384 112.38 - 125.30: 51429 125.30 - 138.22: 1183 Bond angle restraints: 89081 Sorted by residual: angle pdb=" C ASN B1013 " pdb=" N PRO B1014 " pdb=" CA PRO B1014 " ideal model delta sigma weight residual 119.56 129.73 -10.17 1.02e+00 9.61e-01 9.94e+01 angle pdb=" C UNK 1 506 " pdb=" N ILE 1 507 " pdb=" CA ILE 1 507 " ideal model delta sigma weight residual 121.70 109.86 11.84 1.80e+00 3.09e-01 4.33e+01 angle pdb=" N ASN W 116 " pdb=" CA ASN W 116 " pdb=" C ASN W 116 " ideal model delta sigma weight residual 108.07 116.83 -8.76 1.38e+00 5.25e-01 4.03e+01 angle pdb=" N ILE 7 333 " pdb=" CA ILE 7 333 " pdb=" C ILE 7 333 " ideal model delta sigma weight residual 112.29 106.67 5.62 9.40e-01 1.13e+00 3.57e+01 angle pdb=" N GLN A 71 " pdb=" CA GLN A 71 " pdb=" C GLN A 71 " ideal model delta sigma weight residual 109.86 118.54 -8.68 1.55e+00 4.16e-01 3.13e+01 ... (remaining 89076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 33071 17.99 - 35.98: 3996 35.98 - 53.98: 1692 53.98 - 71.97: 503 71.97 - 89.96: 111 Dihedral angle restraints: 39373 sinusoidal: 16332 harmonic: 23041 Sorted by residual: dihedral pdb=" CA GLN A 71 " pdb=" C GLN A 71 " pdb=" N GLU A 72 " pdb=" CA GLU A 72 " ideal model delta harmonic sigma weight residual -180.00 -125.54 -54.46 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA TYR M 30 " pdb=" C TYR M 30 " pdb=" N PRO M 31 " pdb=" CA PRO M 31 " ideal model delta harmonic sigma weight residual 180.00 127.38 52.62 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CA ASP 4 255 " pdb=" C ASP 4 255 " pdb=" N PRO 4 256 " pdb=" CA PRO 4 256 " ideal model delta harmonic sigma weight residual 180.00 -131.72 -48.28 0 5.00e+00 4.00e-02 9.32e+01 ... (remaining 39370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 7497 0.068 - 0.135: 2210 0.135 - 0.203: 286 0.203 - 0.270: 22 0.270 - 0.338: 6 Chirality restraints: 10021 Sorted by residual: chirality pdb=" CB VAL J 14 " pdb=" CA VAL J 14 " pdb=" CG1 VAL J 14 " pdb=" CG2 VAL J 14 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CB VAL B 211 " pdb=" CA VAL B 211 " pdb=" CG1 VAL B 211 " pdb=" CG2 VAL B 211 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB VAL A 622 " pdb=" CA VAL A 622 " pdb=" CG1 VAL A 622 " pdb=" CG2 VAL A 622 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 10018 not shown) Planarity restraints: 11132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 756 " -0.051 5.00e-02 4.00e+02 7.63e-02 9.32e+00 pdb=" N PRO B 757 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 757 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 757 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN 7 431 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO 7 432 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO 7 432 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO 7 432 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP 4 255 " 0.046 5.00e-02 4.00e+02 6.96e-02 7.75e+00 pdb=" N PRO 4 256 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO 4 256 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO 4 256 " 0.039 5.00e-02 4.00e+02 ... (remaining 11129 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 1452 2.51 - 3.11: 59206 3.11 - 3.70: 110485 3.70 - 4.30: 154962 4.30 - 4.90: 235427 Nonbonded interactions: 561532 Sorted by model distance: nonbonded pdb=" O GLN 2 466 " pdb=" N LEU 2 470 " model vdw 1.912 2.520 nonbonded pdb=" OH TYR 2 350 " pdb=" O TRP 7 133 " model vdw 1.930 2.440 nonbonded pdb=" OD1 ASN 5 43 " pdb=" OG SER 5 45 " model vdw 1.951 2.440 nonbonded pdb=" N2 DG T 119 " pdb=" O2 DC N 47 " model vdw 1.957 2.496 nonbonded pdb=" CB CYS 0 156 " pdb=" S1 SF4 0 801 " model vdw 1.968 3.040 ... (remaining 561527 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: 4.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 22.180 Check model and map are aligned: 0.740 Set scattering table: 0.440 Process input model: 163.520 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.190 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:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 204.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6152 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 : 0.018 0.157 65568 Z= 1.200 Angle : 1.120 18.715 89081 Z= 0.603 Chirality : 0.061 0.338 10021 Planarity : 0.006 0.076 11132 Dihedral : 19.834 89.962 24603 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 37.28 Ramachandran Plot: Outliers : 0.27 % Allowed : 15.57 % Favored : 84.17 % Rotamer: Outliers : 20.13 % Allowed : 14.64 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 1.47 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.08), residues: 7844 helix: -2.54 (0.08), residues: 2659 sheet: -1.99 (0.16), residues: 897 loop : -2.77 (0.09), residues: 4288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP C 192 HIS 0.017 0.002 HIS B 363 PHE 0.038 0.003 PHE Q 347 TYR 0.039 0.003 TYR E 187 ARG 0.020 0.001 ARG J 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1549 residues out of total 7137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1279 poor density : 270 time to evaluate : 5.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7983 (ttt-90) REVERT: A 510 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7709 (mm-40) REVERT: A 839 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7437 (ttm-80) REVERT: A 845 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8372 (mp) REVERT: A 1187 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.6726 (pt0) REVERT: A 1327 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7823 (tt) REVERT: B 587 HIS cc_start: 0.7722 (OUTLIER) cc_final: 0.6901 (m90) REVERT: B 1108 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7882 (mtm110) REVERT: C 106 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.6016 (mt-10) REVERT: J 17 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7859 (mptt) REVERT: J 59 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7814 (mttt) REVERT: M 96 ILE cc_start: 0.2955 (OUTLIER) cc_final: 0.2507 (pp) REVERT: M 104 MET cc_start: 0.2460 (OUTLIER) cc_final: -0.0647 (mpt) REVERT: M 236 LEU cc_start: 0.5377 (OUTLIER) cc_final: 0.4859 (mp) REVERT: Q 347 PHE cc_start: 0.6074 (OUTLIER) cc_final: 0.5679 (p90) REVERT: 0 37 ASN cc_start: 0.5120 (OUTLIER) cc_final: 0.4540 (m-40) REVERT: 0 346 MET cc_start: 0.5168 (tpp) cc_final: 0.4867 (tpp) REVERT: 0 347 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.6603 (mmtp) REVERT: 0 413 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7315 (pm20) REVERT: 0 605 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8601 (pmtt) REVERT: 0 632 SER cc_start: 0.6362 (OUTLIER) cc_final: 0.6122 (t) REVERT: 1 209 PHE cc_start: 0.5682 (OUTLIER) cc_final: 0.5462 (t80) REVERT: 1 287 PHE cc_start: 0.4279 (OUTLIER) cc_final: 0.3706 (t80) REVERT: 6 118 TYR cc_start: 0.5864 (OUTLIER) cc_final: 0.5038 (m-80) REVERT: 6 139 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7694 (mmmt) REVERT: 6 193 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7597 (mm) REVERT: 6 239 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8899 (tm) REVERT: 2 13 TYR cc_start: 0.8662 (t80) cc_final: 0.8402 (OUTLIER) REVERT: 2 14 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8589 (mt) REVERT: 2 17 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8846 (tp) REVERT: 2 55 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7879 (p0) REVERT: 2 373 MET cc_start: 0.6633 (tpt) cc_final: 0.5662 (tpt) REVERT: 3 25 ASP cc_start: 0.6393 (OUTLIER) cc_final: 0.6029 (p0) REVERT: 3 73 PHE cc_start: 0.6983 (OUTLIER) cc_final: 0.6710 (m-80) REVERT: 7 311 ASP cc_start: 0.8802 (p0) cc_final: 0.8431 (m-30) REVERT: 7 365 TYR cc_start: 0.0254 (OUTLIER) cc_final: -0.1807 (m-80) REVERT: 7 447 GLN cc_start: 0.2424 (OUTLIER) cc_final: 0.1211 (mp10) outliers start: 1279 outliers final: 580 residues processed: 1501 average time/residue: 1.2371 time to fit residues: 2475.1083 Evaluate side-chains 863 residues out of total 7137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 612 poor density : 251 time to evaluate : 5.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 92 HIS Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 839 ARG Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 862 ASN Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 930 ASP Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 980 ASP Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1130 GLN Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1187 GLN Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1205 LYS Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain A residue 1211 GLN Chi-restraints excluded: chain A residue 1230 GLU Chi-restraints excluded: chain A residue 1239 ARG Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1269 GLU Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1325 THR Chi-restraints excluded: chain A residue 1327 ILE Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1350 LYS Chi-restraints excluded: chain A residue 1361 SER Chi-restraints excluded: chain A residue 1372 VAL Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 398 ARG Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 827 ILE Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 858 SER Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 881 ASN Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 906 SER Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 986 GLN Chi-restraints excluded: chain B residue 987 LYS Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1056 SER Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1108 ARG Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1145 SER Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1170 THR Chi-restraints excluded: chain B residue 1201 LYS Chi-restraints excluded: chain B residue 1215 ARG Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 148 GLU Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 134 ASN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 106 CYS Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 17 LYS Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 103 THR 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 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 62 GLU Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 104 MET Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 142 LEU Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 209 ILE Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 234 GLN Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain M residue 315 ILE Chi-restraints excluded: chain M residue 323 LEU Chi-restraints excluded: chain Q residue 27 MET Chi-restraints excluded: chain Q residue 104 ARG Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 118 LEU Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 336 ASP Chi-restraints excluded: chain Q residue 347 PHE Chi-restraints excluded: chain Q residue 358 TYR Chi-restraints excluded: chain Q residue 385 THR Chi-restraints excluded: chain Q residue 392 VAL Chi-restraints excluded: chain Q residue 396 THR Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 96 ARG Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 262 THR Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain W residue 5 ILE Chi-restraints excluded: chain W residue 6 ASP Chi-restraints excluded: chain W residue 16 VAL Chi-restraints excluded: chain W residue 91 TYR Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain W residue 120 ASN Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 141 ASN Chi-restraints excluded: chain W residue 149 CYS Chi-restraints excluded: chain W residue 169 GLN Chi-restraints excluded: chain X residue 192 LEU Chi-restraints excluded: chain X residue 209 ASP Chi-restraints excluded: chain X residue 256 ASP Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 178 SER Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 17 ILE Chi-restraints excluded: chain 0 residue 28 ILE Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 37 ASN Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 73 SER Chi-restraints excluded: chain 0 residue 78 GLU Chi-restraints excluded: chain 0 residue 80 GLU Chi-restraints excluded: chain 0 residue 94 THR Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 131 GLU Chi-restraints excluded: chain 0 residue 137 THR Chi-restraints excluded: chain 0 residue 150 GLU Chi-restraints excluded: chain 0 residue 155 LEU Chi-restraints excluded: chain 0 residue 201 SER Chi-restraints excluded: chain 0 residue 204 ASN Chi-restraints excluded: chain 0 residue 209 SER Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 245 ILE Chi-restraints excluded: chain 0 residue 255 ASP Chi-restraints excluded: chain 0 residue 257 LEU Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 321 ILE Chi-restraints excluded: chain 0 residue 339 ILE Chi-restraints excluded: chain 0 residue 347 LYS Chi-restraints excluded: chain 0 residue 351 VAL Chi-restraints excluded: chain 0 residue 354 GLU Chi-restraints excluded: chain 0 residue 360 LEU Chi-restraints excluded: chain 0 residue 407 THR Chi-restraints excluded: chain 0 residue 413 GLU Chi-restraints excluded: chain 0 residue 416 PHE Chi-restraints excluded: chain 0 residue 418 LEU Chi-restraints excluded: chain 0 residue 423 TYR Chi-restraints excluded: chain 0 residue 438 THR Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 498 THR Chi-restraints excluded: chain 0 residue 533 THR Chi-restraints excluded: chain 0 residue 559 ILE Chi-restraints excluded: chain 0 residue 563 VAL Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 591 SER Chi-restraints excluded: chain 0 residue 594 ARG Chi-restraints excluded: chain 0 residue 605 LYS Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 632 SER Chi-restraints excluded: chain 0 residue 649 ARG Chi-restraints excluded: chain 0 residue 651 ASN Chi-restraints excluded: chain 0 residue 655 SER Chi-restraints excluded: chain 0 residue 657 ASP Chi-restraints excluded: chain 0 residue 673 LYS Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 678 VAL Chi-restraints excluded: chain 0 residue 683 ASP Chi-restraints excluded: chain 0 residue 689 LYS Chi-restraints excluded: chain 0 residue 706 LEU Chi-restraints excluded: chain 0 residue 716 ASN Chi-restraints excluded: chain 0 residue 717 THR Chi-restraints excluded: chain 0 residue 739 TRP Chi-restraints excluded: chain 0 residue 741 TYR Chi-restraints excluded: chain 0 residue 743 ASP Chi-restraints excluded: chain 1 residue 185 LEU Chi-restraints excluded: chain 1 residue 209 PHE Chi-restraints excluded: chain 1 residue 210 TRP Chi-restraints excluded: chain 1 residue 211 SER Chi-restraints excluded: chain 1 residue 213 ARG Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 271 THR Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 1 residue 374 ILE Chi-restraints excluded: chain 1 residue 381 LEU Chi-restraints excluded: chain 1 residue 561 LEU Chi-restraints excluded: chain 1 residue 621 ASN Chi-restraints excluded: chain 4 residue 22 SER Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 43 GLU Chi-restraints excluded: chain 4 residue 122 ASP Chi-restraints excluded: chain 4 residue 133 PHE Chi-restraints excluded: chain 4 residue 137 LYS Chi-restraints excluded: chain 4 residue 179 LEU Chi-restraints excluded: chain 4 residue 180 THR Chi-restraints excluded: chain 4 residue 194 ILE Chi-restraints excluded: chain 4 residue 200 ILE Chi-restraints excluded: chain 4 residue 202 SER Chi-restraints excluded: chain 4 residue 212 VAL Chi-restraints excluded: chain 4 residue 222 THR Chi-restraints excluded: chain 4 residue 227 THR Chi-restraints excluded: chain 4 residue 228 THR Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 253 PHE Chi-restraints excluded: chain 4 residue 260 PRO Chi-restraints excluded: chain 4 residue 269 SER Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 274 THR Chi-restraints excluded: chain 4 residue 276 CYS Chi-restraints excluded: chain 4 residue 288 ILE Chi-restraints excluded: chain 6 residue 114 ASN Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 119 GLN Chi-restraints excluded: chain 6 residue 139 LYS Chi-restraints excluded: chain 6 residue 146 HIS Chi-restraints excluded: chain 6 residue 155 ASP Chi-restraints excluded: chain 6 residue 158 HIS Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 6 residue 193 ILE Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 238 SER Chi-restraints excluded: chain 6 residue 239 LEU Chi-restraints excluded: chain 6 residue 243 ASP Chi-restraints excluded: chain 6 residue 261 VAL Chi-restraints excluded: chain 6 residue 280 THR Chi-restraints excluded: chain 6 residue 282 TYR Chi-restraints excluded: chain 6 residue 289 LYS Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 310 VAL Chi-restraints excluded: chain 6 residue 317 PHE Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 319 LEU Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 406 CYS Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 14 LEU Chi-restraints excluded: chain 2 residue 17 ILE Chi-restraints excluded: chain 2 residue 21 VAL Chi-restraints excluded: chain 2 residue 28 SER Chi-restraints excluded: chain 2 residue 53 ASN Chi-restraints excluded: chain 2 residue 55 ASN Chi-restraints excluded: chain 2 residue 60 LEU Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 80 SER Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 2 residue 208 LEU Chi-restraints excluded: chain 2 residue 284 THR Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 350 TYR Chi-restraints excluded: chain 2 residue 353 SER Chi-restraints excluded: chain 2 residue 356 GLN Chi-restraints excluded: chain 2 residue 370 PHE Chi-restraints excluded: chain 2 residue 372 ASN Chi-restraints excluded: chain 2 residue 379 THR Chi-restraints excluded: chain 2 residue 389 ASN Chi-restraints excluded: chain 2 residue 391 ILE Chi-restraints excluded: chain 2 residue 395 GLN Chi-restraints excluded: chain 2 residue 408 MET Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 450 ARG Chi-restraints excluded: chain 2 residue 457 SER Chi-restraints excluded: chain 2 residue 462 PHE Chi-restraints excluded: chain 2 residue 470 LEU Chi-restraints excluded: chain 2 residue 486 ASP Chi-restraints excluded: chain 2 residue 489 LYS Chi-restraints excluded: chain 2 residue 495 LYS Chi-restraints excluded: chain 2 residue 508 LYS Chi-restraints excluded: chain 5 residue 9 LEU Chi-restraints excluded: chain 5 residue 13 ASP Chi-restraints excluded: chain 5 residue 26 LYS Chi-restraints excluded: chain 5 residue 33 GLU Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 5 residue 46 LYS Chi-restraints excluded: chain 5 residue 47 VAL Chi-restraints excluded: chain 3 residue 25 ASP Chi-restraints excluded: chain 3 residue 44 ASP Chi-restraints excluded: chain 3 residue 49 LEU Chi-restraints excluded: chain 3 residue 73 PHE Chi-restraints excluded: chain 7 residue 302 GLU Chi-restraints excluded: chain 7 residue 309 ASP Chi-restraints excluded: chain 7 residue 315 SER Chi-restraints excluded: chain 7 residue 316 PHE Chi-restraints excluded: chain 7 residue 320 ASN Chi-restraints excluded: chain 7 residue 331 GLN Chi-restraints excluded: chain 7 residue 360 THR Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 378 ARG Chi-restraints excluded: chain 7 residue 398 THR Chi-restraints excluded: chain 7 residue 402 THR Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 419 GLN Chi-restraints excluded: chain 7 residue 428 CYS Chi-restraints excluded: chain 7 residue 431 GLN Chi-restraints excluded: chain 7 residue 439 THR Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 447 GLN Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 456 THR Chi-restraints excluded: chain 7 residue 473 VAL Chi-restraints excluded: chain 7 residue 475 ASP Chi-restraints excluded: chain 7 residue 490 VAL Chi-restraints excluded: chain 7 residue 498 PHE Chi-restraints excluded: chain 7 residue 499 ARG Chi-restraints excluded: chain 7 residue 500 ARG Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 505 ILE Chi-restraints excluded: chain 7 residue 518 VAL Chi-restraints excluded: chain 7 residue 527 LEU Chi-restraints excluded: chain 7 residue 541 MET Chi-restraints excluded: chain 7 residue 545 GLN Chi-restraints excluded: chain 7 residue 549 ILE Chi-restraints excluded: chain 7 residue 562 THR Chi-restraints excluded: chain 7 residue 565 PHE Chi-restraints excluded: chain 7 residue 571 ARG Chi-restraints excluded: chain 7 residue 576 LYS Chi-restraints excluded: chain 7 residue 579 LEU Chi-restraints excluded: chain 7 residue 656 LYS Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 695 ARG Chi-restraints excluded: chain 7 residue 697 ASN Chi-restraints excluded: chain 7 residue 712 ASP Chi-restraints excluded: chain 7 residue 717 TYR Chi-restraints excluded: chain 7 residue 719 SER Chi-restraints excluded: chain 7 residue 735 VAL Chi-restraints excluded: chain 7 residue 761 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 654 optimal weight: 2.9990 chunk 587 optimal weight: 2.9990 chunk 325 optimal weight: 4.9990 chunk 200 optimal weight: 0.9990 chunk 396 optimal weight: 5.9990 chunk 313 optimal weight: 1.9990 chunk 607 optimal weight: 6.9990 chunk 235 optimal weight: 0.9990 chunk 369 optimal weight: 0.9990 chunk 452 optimal weight: 0.0370 chunk 703 optimal weight: 6.9990 overall best weight: 1.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN A 451 HIS A 757 ASN A 865 GLN A1040 GLN A1048 ASN ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 GLN B 794 ASN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN G 117 GLN I 23 ASN I 46 HIS I 89 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN ** M 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 GLN ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 GLN ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 164 ASN ** 6 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 227 HIS 6 249 GLN ** 6 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 407 GLN 2 403 HIS ** 2 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 9 ASN ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 431 GLN ** 7 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5900 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 65568 Z= 0.244 Angle : 0.788 15.790 89081 Z= 0.410 Chirality : 0.047 0.392 10021 Planarity : 0.005 0.074 11132 Dihedral : 17.610 89.966 11344 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.23 % Favored : 90.57 % Rotamer: Outliers : 10.62 % Allowed : 21.44 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 1.18 % Twisted General : 0.28 % 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: -2.62 (0.09), residues: 7844 helix: -1.01 (0.09), residues: 2948 sheet: -1.69 (0.16), residues: 925 loop : -2.33 (0.10), residues: 3971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 31 HIS 0.015 0.001 HIS 1 563 PHE 0.044 0.002 PHE 1 564 TYR 0.025 0.002 TYR M 313 ARG 0.008 0.001 ARG 5 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 7137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 675 poor density : 264 time to evaluate : 5.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 CYS cc_start: 0.6731 (OUTLIER) cc_final: 0.6505 (t) REVERT: A 845 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7963 (mp) REVERT: A 1187 GLN cc_start: 0.6959 (OUTLIER) cc_final: 0.6430 (pt0) REVERT: B 351 TYR cc_start: 0.6460 (OUTLIER) cc_final: 0.6228 (t80) REVERT: G 69 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.5998 (tt0) REVERT: M 52 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7458 (mt) REVERT: M 96 ILE cc_start: 0.3075 (OUTLIER) cc_final: 0.2734 (pp) REVERT: M 236 LEU cc_start: 0.5421 (OUTLIER) cc_final: 0.4972 (mp) REVERT: 1 287 PHE cc_start: 0.3845 (OUTLIER) cc_final: 0.3296 (t80) REVERT: 6 118 TYR cc_start: 0.5255 (OUTLIER) cc_final: 0.4542 (m-80) REVERT: 2 13 TYR cc_start: 0.8596 (t80) cc_final: 0.8281 (t80) REVERT: 2 61 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7703 (p0) REVERT: 2 81 MET cc_start: 0.9214 (ptp) cc_final: 0.9010 (mpp) REVERT: 7 309 ASP cc_start: 0.4079 (OUTLIER) cc_final: 0.3847 (m-30) REVERT: 7 365 TYR cc_start: 0.0537 (OUTLIER) cc_final: -0.1194 (m-80) REVERT: 7 447 GLN cc_start: 0.0803 (OUTLIER) cc_final: 0.0278 (mp10) REVERT: 7 454 VAL cc_start: 0.7215 (OUTLIER) cc_final: 0.6813 (m) REVERT: 7 456 THR cc_start: 0.5111 (OUTLIER) cc_final: 0.4821 (t) REVERT: 7 459 MET cc_start: 0.7527 (ttp) cc_final: 0.7284 (ttp) outliers start: 675 outliers final: 337 residues processed: 907 average time/residue: 1.1446 time to fit residues: 1418.7579 Evaluate side-chains 599 residues out of total 7137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 353 poor density : 246 time to evaluate : 5.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 839 ARG Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 862 ASN Chi-restraints excluded: chain A residue 865 GLN Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1130 GLN Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1187 GLN Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1205 LYS Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1211 GLN Chi-restraints excluded: chain A residue 1239 ARG Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1361 SER Chi-restraints excluded: chain A residue 1372 VAL Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1038 SER Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1201 LYS Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 148 GLU Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain M residue 142 LEU Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 181 ARG Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 198 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 234 GLN Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain Q residue 104 ARG Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 132 ASP Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 358 TYR Chi-restraints excluded: chain Q residue 359 ASN Chi-restraints excluded: chain Q residue 392 VAL Chi-restraints excluded: chain R residue 96 ARG Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 262 THR Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain W residue 6 ASP Chi-restraints excluded: chain W residue 30 ASP Chi-restraints excluded: chain W residue 91 TYR Chi-restraints excluded: chain W residue 103 HIS Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain X residue 192 LEU Chi-restraints excluded: chain X residue 209 ASP Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain X residue 256 ASP Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain 0 residue 17 ILE Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 73 SER Chi-restraints excluded: chain 0 residue 78 GLU Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 137 THR Chi-restraints excluded: chain 0 residue 155 LEU Chi-restraints excluded: chain 0 residue 190 LEU Chi-restraints excluded: chain 0 residue 204 ASN Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 255 ASP Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 321 ILE Chi-restraints excluded: chain 0 residue 327 ARG Chi-restraints excluded: chain 0 residue 407 THR Chi-restraints excluded: chain 0 residue 416 PHE Chi-restraints excluded: chain 0 residue 418 LEU Chi-restraints excluded: chain 0 residue 421 GLU Chi-restraints excluded: chain 0 residue 438 THR Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 498 THR Chi-restraints excluded: chain 0 residue 559 ILE Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 591 SER Chi-restraints excluded: chain 0 residue 594 ARG Chi-restraints excluded: chain 0 residue 649 ARG Chi-restraints excluded: chain 0 residue 651 ASN Chi-restraints excluded: chain 0 residue 655 SER Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 683 ASP Chi-restraints excluded: chain 0 residue 706 LEU Chi-restraints excluded: chain 0 residue 717 THR Chi-restraints excluded: chain 0 residue 739 TRP Chi-restraints excluded: chain 0 residue 741 TYR Chi-restraints excluded: chain 0 residue 743 ASP Chi-restraints excluded: chain 1 residue 213 ARG Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 4 residue 22 SER Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 179 LEU Chi-restraints excluded: chain 4 residue 194 ILE Chi-restraints excluded: chain 4 residue 212 VAL Chi-restraints excluded: chain 4 residue 222 THR Chi-restraints excluded: chain 4 residue 227 THR Chi-restraints excluded: chain 4 residue 228 THR Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 253 PHE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 6 residue 114 ASN Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 145 ARG Chi-restraints excluded: chain 6 residue 155 ASP Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 6 residue 191 ASP Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 238 SER Chi-restraints excluded: chain 6 residue 239 LEU Chi-restraints excluded: chain 6 residue 243 ASP Chi-restraints excluded: chain 6 residue 282 TYR Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 317 PHE Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 406 CYS Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 21 VAL Chi-restraints excluded: chain 2 residue 53 ASN Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 2 residue 284 THR Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 350 TYR Chi-restraints excluded: chain 2 residue 351 SER Chi-restraints excluded: chain 2 residue 353 SER Chi-restraints excluded: chain 2 residue 356 GLN Chi-restraints excluded: chain 2 residue 366 LEU Chi-restraints excluded: chain 2 residue 372 ASN Chi-restraints excluded: chain 2 residue 379 THR Chi-restraints excluded: chain 2 residue 389 ASN Chi-restraints excluded: chain 2 residue 391 ILE Chi-restraints excluded: chain 2 residue 395 GLN Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 462 PHE Chi-restraints excluded: chain 2 residue 470 LEU Chi-restraints excluded: chain 2 residue 486 ASP Chi-restraints excluded: chain 2 residue 489 LYS Chi-restraints excluded: chain 2 residue 503 ASP Chi-restraints excluded: chain 5 residue 13 ASP Chi-restraints excluded: chain 5 residue 47 VAL Chi-restraints excluded: chain 5 residue 52 HIS Chi-restraints excluded: chain 3 residue 49 LEU Chi-restraints excluded: chain 7 residue 309 ASP Chi-restraints excluded: chain 7 residue 316 PHE Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 398 THR Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 428 CYS Chi-restraints excluded: chain 7 residue 439 THR Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 447 GLN Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 456 THR Chi-restraints excluded: chain 7 residue 498 PHE Chi-restraints excluded: chain 7 residue 500 ARG Chi-restraints excluded: chain 7 residue 505 ILE Chi-restraints excluded: chain 7 residue 518 VAL Chi-restraints excluded: chain 7 residue 527 LEU Chi-restraints excluded: chain 7 residue 531 ILE Chi-restraints excluded: chain 7 residue 549 ILE Chi-restraints excluded: chain 7 residue 565 PHE Chi-restraints excluded: chain 7 residue 571 ARG Chi-restraints excluded: chain 7 residue 573 THR Chi-restraints excluded: chain 7 residue 576 LYS Chi-restraints excluded: chain 7 residue 579 LEU Chi-restraints excluded: chain 7 residue 656 LYS Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 695 ARG Chi-restraints excluded: chain 7 residue 697 ASN Chi-restraints excluded: chain 7 residue 712 ASP Chi-restraints excluded: chain 7 residue 717 TYR Chi-restraints excluded: chain 7 residue 729 GLN Chi-restraints excluded: chain 7 residue 735 VAL Chi-restraints excluded: chain 7 residue 736 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 391 optimal weight: 5.9990 chunk 218 optimal weight: 8.9990 chunk 585 optimal weight: 9.9990 chunk 479 optimal weight: 40.0000 chunk 194 optimal weight: 9.9990 chunk 705 optimal weight: 30.0000 chunk 761 optimal weight: 30.0000 chunk 627 optimal weight: 7.9990 chunk 699 optimal weight: 40.0000 chunk 240 optimal weight: 4.9990 chunk 565 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 ASN A 865 GLN A1048 ASN ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 ASN ** B 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS C 203 GLN C 231 ASN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN H 33 GLN I 23 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 165 ASN ** O 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 555 GLN ** 1 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 164 ASN ** 6 168 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** ** 2 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 761 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6020 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.096 65568 Z= 0.644 Angle : 0.849 15.549 89081 Z= 0.439 Chirality : 0.050 0.326 10021 Planarity : 0.006 0.074 11132 Dihedral : 16.513 89.311 10746 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 26.33 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.17 % Favored : 88.58 % Rotamer: Outliers : 10.01 % Allowed : 22.60 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 1.18 % Twisted General : 0.24 % 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: -2.55 (0.09), residues: 7844 helix: -0.93 (0.09), residues: 2979 sheet: -1.58 (0.16), residues: 948 loop : -2.36 (0.10), residues: 3917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 7 558 HIS 0.013 0.002 HIS B 363 PHE 0.025 0.002 PHE Q 347 TYR 0.035 0.002 TYR 2 13 ARG 0.007 0.001 ARG 4 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 7137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 636 poor density : 250 time to evaluate : 5.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 CYS cc_start: 0.6784 (OUTLIER) cc_final: 0.6491 (t) REVERT: A 839 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7417 (ttm-80) REVERT: A 845 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8239 (mp) REVERT: A 1102 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7204 (mtmt) REVERT: A 1187 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6666 (pt0) REVERT: G 69 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.6165 (tt0) REVERT: M 52 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7600 (mt) REVERT: M 96 ILE cc_start: 0.3363 (OUTLIER) cc_final: 0.2948 (pp) REVERT: M 236 LEU cc_start: 0.5521 (OUTLIER) cc_final: 0.5037 (mp) REVERT: M 317 TYR cc_start: 0.2538 (OUTLIER) cc_final: 0.2185 (t80) REVERT: 6 118 TYR cc_start: 0.5440 (OUTLIER) cc_final: 0.4657 (m-80) REVERT: 7 309 ASP cc_start: 0.4307 (OUTLIER) cc_final: 0.2955 (m-30) REVERT: 7 311 ASP cc_start: 0.8672 (p0) cc_final: 0.8336 (m-30) REVERT: 7 365 TYR cc_start: 0.0641 (OUTLIER) cc_final: -0.0889 (m-80) REVERT: 7 447 GLN cc_start: 0.1451 (OUTLIER) cc_final: 0.0914 (mp10) REVERT: 7 676 HIS cc_start: 0.1988 (OUTLIER) cc_final: 0.0474 (p-80) outliers start: 636 outliers final: 396 residues processed: 860 average time/residue: 1.0767 time to fit residues: 1282.2217 Evaluate side-chains 652 residues out of total 7137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 411 poor density : 241 time to evaluate : 5.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 505 CYS Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 839 ARG Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 862 ASN Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1130 GLN Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1187 GLN Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1205 LYS Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1211 GLN Chi-restraints excluded: chain A residue 1239 ARG Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1361 SER Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1201 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 148 GLU Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 104 MET Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain M residue 142 LEU Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 181 ARG Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 198 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 234 GLN Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 317 TYR Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 358 TYR Chi-restraints excluded: chain Q residue 359 ASN Chi-restraints excluded: chain Q residue 392 VAL Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 262 THR Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain W residue 6 ASP Chi-restraints excluded: chain W residue 30 ASP Chi-restraints excluded: chain W residue 103 HIS Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 120 ASN Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 143 ASP Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain X residue 251 ASN Chi-restraints excluded: chain X residue 256 ASP Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 17 ILE Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 73 SER Chi-restraints excluded: chain 0 residue 94 THR Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 137 THR Chi-restraints excluded: chain 0 residue 142 LYS Chi-restraints excluded: chain 0 residue 153 VAL Chi-restraints excluded: chain 0 residue 155 LEU Chi-restraints excluded: chain 0 residue 190 LEU Chi-restraints excluded: chain 0 residue 204 ASN Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 249 SER Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 321 ILE Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 407 THR Chi-restraints excluded: chain 0 residue 416 PHE Chi-restraints excluded: chain 0 residue 418 LEU Chi-restraints excluded: chain 0 residue 438 THR Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 498 THR Chi-restraints excluded: chain 0 residue 515 ASP Chi-restraints excluded: chain 0 residue 559 ILE Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 591 SER Chi-restraints excluded: chain 0 residue 594 ARG Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 632 SER Chi-restraints excluded: chain 0 residue 649 ARG Chi-restraints excluded: chain 0 residue 651 ASN Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 683 ASP Chi-restraints excluded: chain 0 residue 706 LEU Chi-restraints excluded: chain 0 residue 717 THR Chi-restraints excluded: chain 0 residue 739 TRP Chi-restraints excluded: chain 0 residue 741 TYR Chi-restraints excluded: chain 0 residue 743 ASP Chi-restraints excluded: chain 1 residue 213 ARG Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 1 residue 382 SER Chi-restraints excluded: chain 4 residue 22 SER Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 180 THR Chi-restraints excluded: chain 4 residue 202 SER Chi-restraints excluded: chain 4 residue 208 CYS Chi-restraints excluded: chain 4 residue 212 VAL Chi-restraints excluded: chain 4 residue 222 THR Chi-restraints excluded: chain 4 residue 227 THR Chi-restraints excluded: chain 4 residue 228 THR Chi-restraints excluded: chain 4 residue 234 VAL Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 253 PHE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 274 THR Chi-restraints excluded: chain 6 residue 114 ASN Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 128 LEU Chi-restraints excluded: chain 6 residue 146 HIS Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 6 residue 191 ASP Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 238 SER Chi-restraints excluded: chain 6 residue 243 ASP Chi-restraints excluded: chain 6 residue 282 TYR Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 310 VAL Chi-restraints excluded: chain 6 residue 317 PHE Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 406 CYS Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 53 ASN Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 2 residue 284 THR Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 350 TYR Chi-restraints excluded: chain 2 residue 353 SER Chi-restraints excluded: chain 2 residue 366 LEU Chi-restraints excluded: chain 2 residue 379 THR Chi-restraints excluded: chain 2 residue 389 ASN Chi-restraints excluded: chain 2 residue 391 ILE Chi-restraints excluded: chain 2 residue 408 MET Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 457 SER Chi-restraints excluded: chain 2 residue 462 PHE Chi-restraints excluded: chain 2 residue 470 LEU Chi-restraints excluded: chain 2 residue 486 ASP Chi-restraints excluded: chain 2 residue 488 LYS Chi-restraints excluded: chain 2 residue 489 LYS Chi-restraints excluded: chain 2 residue 508 LYS Chi-restraints excluded: chain 5 residue 13 ASP Chi-restraints excluded: chain 5 residue 33 GLU Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 5 residue 47 VAL Chi-restraints excluded: chain 5 residue 52 HIS Chi-restraints excluded: chain 3 residue 25 ASP Chi-restraints excluded: chain 3 residue 49 LEU Chi-restraints excluded: chain 3 residue 60 ASP Chi-restraints excluded: chain 7 residue 309 ASP Chi-restraints excluded: chain 7 residue 316 PHE Chi-restraints excluded: chain 7 residue 322 SER Chi-restraints excluded: chain 7 residue 361 GLN Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 392 LYS Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 439 THR Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 447 GLN Chi-restraints excluded: chain 7 residue 500 ARG Chi-restraints excluded: chain 7 residue 505 ILE Chi-restraints excluded: chain 7 residue 518 VAL Chi-restraints excluded: chain 7 residue 527 LEU Chi-restraints excluded: chain 7 residue 531 ILE Chi-restraints excluded: chain 7 residue 549 ILE Chi-restraints excluded: chain 7 residue 565 PHE Chi-restraints excluded: chain 7 residue 571 ARG Chi-restraints excluded: chain 7 residue 573 THR Chi-restraints excluded: chain 7 residue 576 LYS Chi-restraints excluded: chain 7 residue 579 LEU Chi-restraints excluded: chain 7 residue 656 LYS Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 695 ARG Chi-restraints excluded: chain 7 residue 697 ASN Chi-restraints excluded: chain 7 residue 712 ASP Chi-restraints excluded: chain 7 residue 717 TYR Chi-restraints excluded: chain 7 residue 729 GLN Chi-restraints excluded: chain 7 residue 735 VAL Chi-restraints excluded: chain 7 residue 736 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 696 optimal weight: 6.9990 chunk 530 optimal weight: 20.0000 chunk 365 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 336 optimal weight: 30.0000 chunk 473 optimal weight: 10.0000 chunk 707 optimal weight: 50.0000 chunk 749 optimal weight: 20.0000 chunk 369 optimal weight: 1.9990 chunk 670 optimal weight: 20.0000 chunk 201 optimal weight: 0.8980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS A1048 ASN ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS C 203 GLN C 231 ASN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN F 104 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 164 ASN ** 6 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 76 ASN ** 2 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 644 GLN ** 7 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 761 GLN 7 767 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 65568 Z= 0.261 Angle : 0.711 13.866 89081 Z= 0.364 Chirality : 0.045 0.414 10021 Planarity : 0.005 0.069 11132 Dihedral : 15.992 89.709 10690 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.31 % Favored : 91.50 % Rotamer: Outliers : 8.11 % Allowed : 23.88 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 1.18 % Twisted General : 0.18 % 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: -1.95 (0.09), residues: 7844 helix: -0.34 (0.09), residues: 2941 sheet: -1.32 (0.17), residues: 927 loop : -2.05 (0.10), residues: 3976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 263 HIS 0.013 0.001 HIS W 103 PHE 0.019 0.001 PHE 5 49 TYR 0.028 0.001 TYR 1 630 ARG 0.013 0.000 ARG 0 638 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 7137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 515 poor density : 258 time to evaluate : 5.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 TYR cc_start: 0.7437 (OUTLIER) cc_final: 0.6110 (p90) REVERT: A 839 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7460 (ttm-80) REVERT: A 845 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7954 (mp) REVERT: A 862 ASN cc_start: 0.7726 (OUTLIER) cc_final: 0.7440 (m110) REVERT: B 351 TYR cc_start: 0.6439 (OUTLIER) cc_final: 0.6172 (t80) REVERT: M 96 ILE cc_start: 0.3534 (OUTLIER) cc_final: 0.3032 (pp) REVERT: M 236 LEU cc_start: 0.5350 (OUTLIER) cc_final: 0.4954 (mp) REVERT: M 317 TYR cc_start: 0.2414 (OUTLIER) cc_final: 0.2070 (t80) REVERT: 0 740 SER cc_start: 0.3732 (OUTLIER) cc_final: 0.3523 (p) REVERT: 1 287 PHE cc_start: 0.3702 (OUTLIER) cc_final: 0.3250 (t80) REVERT: 6 118 TYR cc_start: 0.5019 (OUTLIER) cc_final: 0.4191 (m-80) REVERT: 2 61 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7583 (p0) REVERT: 2 81 MET cc_start: 0.9217 (ptp) cc_final: 0.8981 (mpp) REVERT: 7 309 ASP cc_start: 0.3919 (OUTLIER) cc_final: 0.2662 (m-30) REVERT: 7 311 ASP cc_start: 0.8305 (p0) cc_final: 0.8016 (m-30) REVERT: 7 365 TYR cc_start: 0.0931 (OUTLIER) cc_final: -0.0917 (m-80) REVERT: 7 676 HIS cc_start: 0.1806 (OUTLIER) cc_final: 0.0522 (p-80) REVERT: 7 695 ARG cc_start: 0.1097 (OUTLIER) cc_final: -0.0650 (ppt170) outliers start: 515 outliers final: 317 residues processed: 749 average time/residue: 1.1447 time to fit residues: 1176.3493 Evaluate side-chains 579 residues out of total 7137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 333 poor density : 246 time to evaluate : 5.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 839 ARG Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 862 ASN Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1130 GLN Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1211 GLN Chi-restraints excluded: chain A residue 1220 PHE Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1038 SER Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1201 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 148 GLU Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 3 ASN Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain M residue 142 LEU Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 317 TYR Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 358 TYR Chi-restraints excluded: chain Q residue 359 ASN Chi-restraints excluded: chain Q residue 392 VAL Chi-restraints excluded: chain R residue 98 ASN Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 262 THR Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain W residue 6 ASP Chi-restraints excluded: chain W residue 103 HIS Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 120 ASN Chi-restraints excluded: chain X residue 193 LEU Chi-restraints excluded: chain X residue 217 CYS Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain X residue 256 ASP Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 137 THR Chi-restraints excluded: chain 0 residue 142 LYS Chi-restraints excluded: chain 0 residue 153 VAL Chi-restraints excluded: chain 0 residue 204 ASN Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 249 SER Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 321 ILE Chi-restraints excluded: chain 0 residue 361 GLN Chi-restraints excluded: chain 0 residue 402 ILE Chi-restraints excluded: chain 0 residue 407 THR Chi-restraints excluded: chain 0 residue 416 PHE Chi-restraints excluded: chain 0 residue 438 THR Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 498 THR Chi-restraints excluded: chain 0 residue 515 ASP Chi-restraints excluded: chain 0 residue 533 THR Chi-restraints excluded: chain 0 residue 559 ILE Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 594 ARG Chi-restraints excluded: chain 0 residue 649 ARG Chi-restraints excluded: chain 0 residue 651 ASN Chi-restraints excluded: chain 0 residue 673 LYS Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 683 ASP Chi-restraints excluded: chain 0 residue 689 LYS Chi-restraints excluded: chain 0 residue 706 LEU Chi-restraints excluded: chain 0 residue 739 TRP Chi-restraints excluded: chain 0 residue 740 SER Chi-restraints excluded: chain 0 residue 741 TYR Chi-restraints excluded: chain 0 residue 743 ASP Chi-restraints excluded: chain 1 residue 213 ARG Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 1 residue 382 SER Chi-restraints excluded: chain 1 residue 383 GLU Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 73 VAL Chi-restraints excluded: chain 4 residue 202 SER Chi-restraints excluded: chain 4 residue 212 VAL Chi-restraints excluded: chain 4 residue 222 THR Chi-restraints excluded: chain 4 residue 227 THR Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 6 residue 114 ASN Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 128 LEU Chi-restraints excluded: chain 6 residue 146 HIS Chi-restraints excluded: chain 6 residue 155 ASP Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 238 SER Chi-restraints excluded: chain 6 residue 282 TYR Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 317 PHE Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 406 CYS Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 53 ASN Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 350 TYR Chi-restraints excluded: chain 2 residue 351 SER Chi-restraints excluded: chain 2 residue 353 SER Chi-restraints excluded: chain 2 residue 366 LEU Chi-restraints excluded: chain 2 residue 372 ASN Chi-restraints excluded: chain 2 residue 379 THR Chi-restraints excluded: chain 2 residue 389 ASN Chi-restraints excluded: chain 2 residue 391 ILE Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 462 PHE Chi-restraints excluded: chain 2 residue 470 LEU Chi-restraints excluded: chain 2 residue 486 ASP Chi-restraints excluded: chain 2 residue 489 LYS Chi-restraints excluded: chain 2 residue 508 LYS Chi-restraints excluded: chain 5 residue 13 ASP Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 5 residue 47 VAL Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 49 LEU Chi-restraints excluded: chain 3 residue 60 ASP Chi-restraints excluded: chain 7 residue 309 ASP Chi-restraints excluded: chain 7 residue 316 PHE Chi-restraints excluded: chain 7 residue 361 GLN Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 392 LYS Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 439 THR Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 500 ARG Chi-restraints excluded: chain 7 residue 505 ILE Chi-restraints excluded: chain 7 residue 518 VAL Chi-restraints excluded: chain 7 residue 522 ASP Chi-restraints excluded: chain 7 residue 527 LEU Chi-restraints excluded: chain 7 residue 531 ILE Chi-restraints excluded: chain 7 residue 571 ARG Chi-restraints excluded: chain 7 residue 573 THR Chi-restraints excluded: chain 7 residue 576 LYS Chi-restraints excluded: chain 7 residue 613 TYR Chi-restraints excluded: chain 7 residue 656 LYS Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 695 ARG Chi-restraints excluded: chain 7 residue 712 ASP Chi-restraints excluded: chain 7 residue 717 TYR Chi-restraints excluded: chain 7 residue 735 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 623 optimal weight: 6.9990 chunk 425 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 557 optimal weight: 10.0000 chunk 309 optimal weight: 7.9990 chunk 639 optimal weight: 6.9990 chunk 517 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 382 optimal weight: 10.0000 chunk 672 optimal weight: 40.0000 chunk 189 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 ASN ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 GLN B 887 HIS C 203 GLN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN I 23 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 117 ASN ** M 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 251 ASN ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 164 ASN ** 6 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 403 HIS ** 2 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5989 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 65568 Z= 0.550 Angle : 0.791 15.091 89081 Z= 0.405 Chirality : 0.048 0.305 10021 Planarity : 0.005 0.071 11132 Dihedral : 15.814 93.065 10603 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 23.97 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.12 % Favored : 89.65 % Rotamer: Outliers : 8.39 % Allowed : 24.21 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 1.18 % 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: -2.02 (0.09), residues: 7844 helix: -0.38 (0.09), residues: 2955 sheet: -1.39 (0.16), residues: 975 loop : -2.11 (0.10), residues: 3914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 7 558 HIS 0.013 0.001 HIS W 103 PHE 0.021 0.002 PHE K 71 TYR 0.045 0.002 TYR 2 13 ARG 0.011 0.001 ARG 0 638 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 7137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 533 poor density : 250 time to evaluate : 5.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.5544 (OUTLIER) cc_final: 0.5268 (pt0) REVERT: A 465 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.6503 (p90) REVERT: A 839 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7431 (ttm-80) REVERT: A 845 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8300 (mp) REVERT: A 862 ASN cc_start: 0.7959 (OUTLIER) cc_final: 0.7637 (m110) REVERT: B 287 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6240 (mtt90) REVERT: B 351 TYR cc_start: 0.6198 (OUTLIER) cc_final: 0.5843 (t80) REVERT: M 52 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7576 (mt) REVERT: M 96 ILE cc_start: 0.3651 (OUTLIER) cc_final: 0.3135 (pp) REVERT: M 236 LEU cc_start: 0.5467 (OUTLIER) cc_final: 0.5057 (mp) REVERT: M 317 TYR cc_start: 0.2013 (OUTLIER) cc_final: 0.1749 (t80) REVERT: 6 118 TYR cc_start: 0.5075 (OUTLIER) cc_final: 0.4272 (m-80) REVERT: 7 309 ASP cc_start: 0.4016 (OUTLIER) cc_final: 0.2643 (m-30) REVERT: 7 311 ASP cc_start: 0.8498 (p0) cc_final: 0.8227 (m-30) REVERT: 7 326 VAL cc_start: 0.4960 (t) cc_final: 0.3622 (p) REVERT: 7 365 TYR cc_start: 0.1088 (OUTLIER) cc_final: -0.0410 (m-80) REVERT: 7 447 GLN cc_start: 0.1187 (OUTLIER) cc_final: 0.0659 (mp10) REVERT: 7 452 LEU cc_start: 0.5988 (OUTLIER) cc_final: 0.5382 (tt) REVERT: 7 676 HIS cc_start: 0.1789 (OUTLIER) cc_final: 0.0670 (p-80) REVERT: 7 695 ARG cc_start: 0.1050 (OUTLIER) cc_final: -0.0315 (ppt170) outliers start: 533 outliers final: 353 residues processed: 755 average time/residue: 1.0997 time to fit residues: 1147.2084 Evaluate side-chains 618 residues out of total 7137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 371 poor density : 247 time to evaluate : 5.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 839 ARG Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 862 ASN Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1130 GLN Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1201 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 106 MET Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 148 GLU Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 20 LYS Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain M residue 142 LEU Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 198 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 234 GLN Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 317 TYR Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 132 ASP Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 358 TYR Chi-restraints excluded: chain Q residue 359 ASN Chi-restraints excluded: chain Q residue 392 VAL Chi-restraints excluded: chain R residue 98 ASN Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 256 ASP Chi-restraints excluded: chain R residue 262 THR Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain W residue 6 ASP Chi-restraints excluded: chain W residue 103 HIS Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 120 ASN Chi-restraints excluded: chain X residue 217 CYS Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain X residue 256 ASP Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 73 SER Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 137 THR Chi-restraints excluded: chain 0 residue 142 LYS Chi-restraints excluded: chain 0 residue 204 ASN Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 249 SER Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 318 THR Chi-restraints excluded: chain 0 residue 321 ILE Chi-restraints excluded: chain 0 residue 324 ASN Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 361 GLN Chi-restraints excluded: chain 0 residue 402 ILE Chi-restraints excluded: chain 0 residue 407 THR Chi-restraints excluded: chain 0 residue 416 PHE Chi-restraints excluded: chain 0 residue 418 LEU Chi-restraints excluded: chain 0 residue 438 THR Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 462 THR Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 498 THR Chi-restraints excluded: chain 0 residue 515 ASP Chi-restraints excluded: chain 0 residue 533 THR Chi-restraints excluded: chain 0 residue 559 ILE Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 649 ARG Chi-restraints excluded: chain 0 residue 651 ASN Chi-restraints excluded: chain 0 residue 673 LYS Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 683 ASP Chi-restraints excluded: chain 0 residue 706 LEU Chi-restraints excluded: chain 0 residue 739 TRP Chi-restraints excluded: chain 0 residue 741 TYR Chi-restraints excluded: chain 0 residue 743 ASP Chi-restraints excluded: chain 1 residue 213 ARG Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 1 residue 383 GLU Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 4 residue 73 VAL Chi-restraints excluded: chain 4 residue 202 SER Chi-restraints excluded: chain 4 residue 208 CYS Chi-restraints excluded: chain 4 residue 222 THR Chi-restraints excluded: chain 4 residue 227 THR Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 274 THR Chi-restraints excluded: chain 6 residue 114 ASN Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 128 LEU Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 145 ARG Chi-restraints excluded: chain 6 residue 146 HIS Chi-restraints excluded: chain 6 residue 155 ASP Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 6 residue 191 ASP Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 250 THR Chi-restraints excluded: chain 6 residue 282 TYR Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 317 PHE Chi-restraints excluded: chain 6 residue 318 THR Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 406 CYS Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 53 ASN Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 2 residue 284 THR Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 350 TYR Chi-restraints excluded: chain 2 residue 351 SER Chi-restraints excluded: chain 2 residue 366 LEU Chi-restraints excluded: chain 2 residue 372 ASN Chi-restraints excluded: chain 2 residue 379 THR Chi-restraints excluded: chain 2 residue 389 ASN Chi-restraints excluded: chain 2 residue 391 ILE Chi-restraints excluded: chain 2 residue 408 MET Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 457 SER Chi-restraints excluded: chain 2 residue 462 PHE Chi-restraints excluded: chain 2 residue 486 ASP Chi-restraints excluded: chain 2 residue 489 LYS Chi-restraints excluded: chain 2 residue 508 LYS Chi-restraints excluded: chain 5 residue 13 ASP Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 5 residue 47 VAL Chi-restraints excluded: chain 3 residue 25 ASP Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 60 ASP Chi-restraints excluded: chain 7 residue 309 ASP Chi-restraints excluded: chain 7 residue 316 PHE Chi-restraints excluded: chain 7 residue 322 SER Chi-restraints excluded: chain 7 residue 361 GLN Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 439 THR Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 447 GLN Chi-restraints excluded: chain 7 residue 452 LEU Chi-restraints excluded: chain 7 residue 500 ARG Chi-restraints excluded: chain 7 residue 518 VAL Chi-restraints excluded: chain 7 residue 522 ASP Chi-restraints excluded: chain 7 residue 527 LEU Chi-restraints excluded: chain 7 residue 531 ILE Chi-restraints excluded: chain 7 residue 565 PHE Chi-restraints excluded: chain 7 residue 571 ARG Chi-restraints excluded: chain 7 residue 576 LYS Chi-restraints excluded: chain 7 residue 656 LYS Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 695 ARG Chi-restraints excluded: chain 7 residue 697 ASN Chi-restraints excluded: chain 7 residue 712 ASP Chi-restraints excluded: chain 7 residue 717 TYR Chi-restraints excluded: chain 7 residue 735 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 252 optimal weight: 1.9990 chunk 674 optimal weight: 20.0000 chunk 148 optimal weight: 0.9990 chunk 439 optimal weight: 20.0000 chunk 184 optimal weight: 2.9990 chunk 749 optimal weight: 20.0000 chunk 622 optimal weight: 8.9990 chunk 347 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 248 optimal weight: 0.9990 chunk 393 optimal weight: 20.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 HIS ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS C 203 GLN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 117 ASN ** M 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 251 ASN ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 164 ASN ** 0 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 164 ASN ** 6 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 500 GLN ** 5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 419 GLN ** 7 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 729 GLN 7 761 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5871 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 65568 Z= 0.207 Angle : 0.698 17.554 89081 Z= 0.352 Chirality : 0.044 0.319 10021 Planarity : 0.004 0.081 11132 Dihedral : 15.416 88.670 10577 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.65 % Favored : 92.19 % Rotamer: Outliers : 6.60 % Allowed : 25.75 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 1.18 % Twisted General : 0.15 % 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: -1.58 (0.10), residues: 7844 helix: 0.03 (0.10), residues: 2948 sheet: -1.11 (0.17), residues: 928 loop : -1.90 (0.10), residues: 3968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP X 263 HIS 0.012 0.001 HIS B 363 PHE 0.022 0.001 PHE 5 49 TYR 0.041 0.001 TYR 2 13 ARG 0.015 0.000 ARG 7 344 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 7137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 419 poor density : 254 time to evaluate : 5.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.5574 (OUTLIER) cc_final: 0.5085 (pt0) REVERT: A 465 TYR cc_start: 0.7504 (OUTLIER) cc_final: 0.6355 (p90) REVERT: A 625 SER cc_start: 0.7975 (OUTLIER) cc_final: 0.7727 (p) REVERT: A 839 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7410 (ttm-80) REVERT: A 845 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7952 (mp) REVERT: G 122 ASN cc_start: 0.2864 (OUTLIER) cc_final: 0.2433 (m110) REVERT: J 49 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.6800 (mmm) REVERT: M 96 ILE cc_start: 0.3598 (OUTLIER) cc_final: 0.3116 (pp) REVERT: M 236 LEU cc_start: 0.5315 (OUTLIER) cc_final: 0.4904 (mp) REVERT: M 317 TYR cc_start: 0.1989 (OUTLIER) cc_final: 0.1689 (t80) REVERT: 0 498 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7148 (p) REVERT: 6 118 TYR cc_start: 0.4982 (OUTLIER) cc_final: 0.4161 (m-80) REVERT: 2 61 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7553 (p0) REVERT: 7 309 ASP cc_start: 0.3655 (OUTLIER) cc_final: 0.2355 (m-30) REVERT: 7 311 ASP cc_start: 0.8235 (p0) cc_final: 0.7974 (m-30) REVERT: 7 326 VAL cc_start: 0.4794 (t) cc_final: 0.3429 (p) REVERT: 7 365 TYR cc_start: 0.1380 (OUTLIER) cc_final: -0.0566 (m-80) REVERT: 7 445 MET cc_start: 0.2525 (ptt) cc_final: 0.1990 (pp-130) REVERT: 7 452 LEU cc_start: 0.5816 (OUTLIER) cc_final: 0.5156 (tt) REVERT: 7 676 HIS cc_start: 0.2101 (OUTLIER) cc_final: 0.1184 (p-80) REVERT: 7 695 ARG cc_start: 0.0954 (OUTLIER) cc_final: -0.0534 (ppt170) REVERT: 7 716 MET cc_start: 0.2849 (mpp) cc_final: 0.2329 (mtm) outliers start: 419 outliers final: 263 residues processed: 654 average time/residue: 1.1571 time to fit residues: 1040.6087 Evaluate side-chains 527 residues out of total 7137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 246 time to evaluate : 5.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 839 ARG Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1130 GLN Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1220 PHE Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1201 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 146 LYS Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 23 ASN Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 234 GLN Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 317 TYR Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 358 TYR Chi-restraints excluded: chain Q residue 359 ASN Chi-restraints excluded: chain Q residue 392 VAL Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 262 THR Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain W residue 6 ASP Chi-restraints excluded: chain W residue 103 HIS Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 115 LYS Chi-restraints excluded: chain W residue 120 ASN Chi-restraints excluded: chain X residue 217 CYS Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain X residue 256 ASP Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 73 SER Chi-restraints excluded: chain 0 residue 80 GLU Chi-restraints excluded: chain 0 residue 109 THR Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 137 THR Chi-restraints excluded: chain 0 residue 142 LYS Chi-restraints excluded: chain 0 residue 162 LEU Chi-restraints excluded: chain 0 residue 204 ASN Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 249 SER Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 318 THR Chi-restraints excluded: chain 0 residue 321 ILE Chi-restraints excluded: chain 0 residue 324 ASN Chi-restraints excluded: chain 0 residue 361 GLN Chi-restraints excluded: chain 0 residue 402 ILE Chi-restraints excluded: chain 0 residue 407 THR Chi-restraints excluded: chain 0 residue 435 MET Chi-restraints excluded: chain 0 residue 438 THR Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 498 THR Chi-restraints excluded: chain 0 residue 515 ASP Chi-restraints excluded: chain 0 residue 533 THR Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 683 ASP Chi-restraints excluded: chain 0 residue 706 LEU Chi-restraints excluded: chain 0 residue 739 TRP Chi-restraints excluded: chain 0 residue 741 TYR Chi-restraints excluded: chain 0 residue 743 ASP Chi-restraints excluded: chain 1 residue 213 ARG Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 202 SER Chi-restraints excluded: chain 4 residue 222 THR Chi-restraints excluded: chain 4 residue 227 THR Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 128 LEU Chi-restraints excluded: chain 6 residue 145 ARG Chi-restraints excluded: chain 6 residue 146 HIS Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 238 SER Chi-restraints excluded: chain 6 residue 282 TYR Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 317 PHE Chi-restraints excluded: chain 6 residue 406 CYS Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 53 ASN Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 2 residue 284 THR Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 350 TYR Chi-restraints excluded: chain 2 residue 366 LEU Chi-restraints excluded: chain 2 residue 389 ASN Chi-restraints excluded: chain 2 residue 391 ILE Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 450 ARG Chi-restraints excluded: chain 2 residue 462 PHE Chi-restraints excluded: chain 2 residue 486 ASP Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 5 residue 47 VAL Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 60 ASP Chi-restraints excluded: chain 7 residue 309 ASP Chi-restraints excluded: chain 7 residue 316 PHE Chi-restraints excluded: chain 7 residue 343 PHE Chi-restraints excluded: chain 7 residue 361 GLN Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 439 THR Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 446 PHE Chi-restraints excluded: chain 7 residue 452 LEU Chi-restraints excluded: chain 7 residue 500 ARG Chi-restraints excluded: chain 7 residue 522 ASP Chi-restraints excluded: chain 7 residue 527 LEU Chi-restraints excluded: chain 7 residue 531 ILE Chi-restraints excluded: chain 7 residue 565 PHE Chi-restraints excluded: chain 7 residue 572 GLU Chi-restraints excluded: chain 7 residue 576 LYS Chi-restraints excluded: chain 7 residue 584 ASN Chi-restraints excluded: chain 7 residue 656 LYS Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 695 ARG Chi-restraints excluded: chain 7 residue 712 ASP Chi-restraints excluded: chain 7 residue 717 TYR Chi-restraints excluded: chain 7 residue 735 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 722 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 427 optimal weight: 20.0000 chunk 547 optimal weight: 4.9990 chunk 424 optimal weight: 20.0000 chunk 631 optimal weight: 9.9990 chunk 418 optimal weight: 20.0000 chunk 746 optimal weight: 0.0060 chunk 467 optimal weight: 10.0000 chunk 455 optimal weight: 5.9990 chunk 344 optimal weight: 0.9990 overall best weight: 3.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 862 ASN A1048 ASN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS C 203 GLN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 117 ASN ** M 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 251 ASN ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 114 ASN 6 164 ASN ** 6 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 466 GLN ** 5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 65568 Z= 0.313 Angle : 0.708 14.805 89081 Z= 0.357 Chirality : 0.044 0.302 10021 Planarity : 0.004 0.073 11132 Dihedral : 15.184 88.990 10508 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.47 % Favored : 91.36 % Rotamer: Outliers : 6.22 % Allowed : 25.97 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 1.18 % 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: -1.48 (0.10), residues: 7844 helix: 0.13 (0.10), residues: 2944 sheet: -1.11 (0.17), residues: 959 loop : -1.85 (0.10), residues: 3941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 263 HIS 0.013 0.001 HIS B 363 PHE 0.025 0.001 PHE G 3 TYR 0.035 0.001 TYR 2 13 ARG 0.011 0.000 ARG 0 649 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 7137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 395 poor density : 252 time to evaluate : 5.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.5532 (OUTLIER) cc_final: 0.5272 (pt0) REVERT: A 465 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.6494 (p90) REVERT: A 845 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8210 (mp) REVERT: G 122 ASN cc_start: 0.3038 (OUTLIER) cc_final: 0.2631 (m110) REVERT: J 49 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.6845 (mmm) REVERT: K 70 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.6693 (ttp80) REVERT: M 96 ILE cc_start: 0.3668 (OUTLIER) cc_final: 0.3161 (pp) REVERT: M 236 LEU cc_start: 0.5292 (OUTLIER) cc_final: 0.4946 (mp) REVERT: M 317 TYR cc_start: 0.1884 (OUTLIER) cc_final: 0.1586 (t80) REVERT: 0 498 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7158 (p) REVERT: 6 118 TYR cc_start: 0.4978 (OUTLIER) cc_final: 0.4177 (m-80) REVERT: 7 309 ASP cc_start: 0.3670 (OUTLIER) cc_final: 0.2369 (m-30) REVERT: 7 311 ASP cc_start: 0.8418 (p0) cc_final: 0.8185 (m-30) REVERT: 7 326 VAL cc_start: 0.5113 (t) cc_final: 0.3824 (p) REVERT: 7 365 TYR cc_start: 0.1157 (OUTLIER) cc_final: -0.0916 (m-80) REVERT: 7 445 MET cc_start: 0.2339 (ptt) cc_final: 0.1486 (ppp) REVERT: 7 452 LEU cc_start: 0.5557 (OUTLIER) cc_final: 0.4943 (tt) REVERT: 7 676 HIS cc_start: 0.2015 (OUTLIER) cc_final: 0.1148 (p-80) REVERT: 7 716 MET cc_start: 0.2844 (mpp) cc_final: 0.2409 (mtm) outliers start: 395 outliers final: 270 residues processed: 628 average time/residue: 1.1586 time to fit residues: 996.6119 Evaluate side-chains 531 residues out of total 7137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 246 time to evaluate : 5.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1130 GLN Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1220 PHE Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1201 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 3 ASN Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 234 GLN Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 317 TYR Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 358 TYR Chi-restraints excluded: chain Q residue 359 ASN Chi-restraints excluded: chain R residue 98 ASN Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 262 THR Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain W residue 103 HIS Chi-restraints excluded: chain W residue 115 LYS Chi-restraints excluded: chain W residue 120 ASN Chi-restraints excluded: chain X residue 217 CYS Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 73 SER Chi-restraints excluded: chain 0 residue 80 GLU Chi-restraints excluded: chain 0 residue 109 THR Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 137 THR Chi-restraints excluded: chain 0 residue 162 LEU Chi-restraints excluded: chain 0 residue 204 ASN Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 249 SER Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 318 THR Chi-restraints excluded: chain 0 residue 361 GLN Chi-restraints excluded: chain 0 residue 402 ILE Chi-restraints excluded: chain 0 residue 407 THR Chi-restraints excluded: chain 0 residue 435 MET Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 462 THR Chi-restraints excluded: chain 0 residue 498 THR Chi-restraints excluded: chain 0 residue 515 ASP Chi-restraints excluded: chain 0 residue 533 THR Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 683 ASP Chi-restraints excluded: chain 0 residue 706 LEU Chi-restraints excluded: chain 0 residue 741 TYR Chi-restraints excluded: chain 1 residue 213 ARG Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 4 residue 202 SER Chi-restraints excluded: chain 4 residue 222 THR Chi-restraints excluded: chain 4 residue 227 THR Chi-restraints excluded: chain 4 residue 234 VAL Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 128 LEU Chi-restraints excluded: chain 6 residue 145 ARG Chi-restraints excluded: chain 6 residue 146 HIS Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 6 residue 191 ASP Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 238 SER Chi-restraints excluded: chain 6 residue 282 TYR Chi-restraints excluded: chain 6 residue 291 LEU Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 297 LEU Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 317 PHE Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 406 CYS Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 53 ASN Chi-restraints excluded: chain 2 residue 57 VAL Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 350 TYR Chi-restraints excluded: chain 2 residue 351 SER Chi-restraints excluded: chain 2 residue 366 LEU Chi-restraints excluded: chain 2 residue 389 ASN Chi-restraints excluded: chain 2 residue 391 ILE Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 462 PHE Chi-restraints excluded: chain 2 residue 486 ASP Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 5 residue 47 VAL Chi-restraints excluded: chain 3 residue 25 ASP Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 60 ASP Chi-restraints excluded: chain 7 residue 309 ASP Chi-restraints excluded: chain 7 residue 316 PHE Chi-restraints excluded: chain 7 residue 322 SER Chi-restraints excluded: chain 7 residue 352 LEU Chi-restraints excluded: chain 7 residue 361 GLN Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 452 LEU Chi-restraints excluded: chain 7 residue 500 ARG Chi-restraints excluded: chain 7 residue 522 ASP Chi-restraints excluded: chain 7 residue 527 LEU Chi-restraints excluded: chain 7 residue 531 ILE Chi-restraints excluded: chain 7 residue 561 MET Chi-restraints excluded: chain 7 residue 572 GLU Chi-restraints excluded: chain 7 residue 576 LYS Chi-restraints excluded: chain 7 residue 584 ASN Chi-restraints excluded: chain 7 residue 613 TYR Chi-restraints excluded: chain 7 residue 656 LYS Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 712 ASP Chi-restraints excluded: chain 7 residue 717 TYR Chi-restraints excluded: chain 7 residue 735 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 462 optimal weight: 30.0000 chunk 298 optimal weight: 8.9990 chunk 446 optimal weight: 8.9990 chunk 225 optimal weight: 0.0370 chunk 146 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 474 optimal weight: 50.0000 chunk 508 optimal weight: 30.0000 chunk 369 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 587 optimal weight: 10.0000 overall best weight: 1.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 HIS ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS C 203 GLN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 117 ASN ** M 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 251 ASN ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 88 ASN ** 0 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 164 ASN ** 6 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 729 GLN 7 767 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5863 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 65568 Z= 0.218 Angle : 0.707 16.132 89081 Z= 0.353 Chirality : 0.044 0.311 10021 Planarity : 0.004 0.073 11132 Dihedral : 14.954 88.582 10472 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.78 % Favored : 92.07 % Rotamer: Outliers : 5.49 % Allowed : 26.41 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.59 % Twisted General : 0.11 % 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: -1.31 (0.10), residues: 7844 helix: 0.29 (0.10), residues: 2948 sheet: -0.83 (0.17), residues: 930 loop : -1.81 (0.10), residues: 3966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP X 263 HIS 0.012 0.001 HIS B 363 PHE 0.022 0.001 PHE 5 49 TYR 0.038 0.001 TYR 2 13 ARG 0.009 0.000 ARG 1 350 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 7137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 349 poor density : 256 time to evaluate : 5.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.5509 (OUTLIER) cc_final: 0.5253 (pt0) REVERT: A 465 TYR cc_start: 0.7503 (OUTLIER) cc_final: 0.6532 (p90) REVERT: A 845 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8047 (mp) REVERT: A 1417 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.5971 (tm-30) REVERT: F 148 VAL cc_start: 0.8223 (OUTLIER) cc_final: 0.7951 (m) REVERT: G 122 ASN cc_start: 0.3051 (OUTLIER) cc_final: 0.2694 (m110) REVERT: J 49 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.6773 (mmm) REVERT: K 10 PHE cc_start: 0.4617 (OUTLIER) cc_final: 0.4318 (m-80) REVERT: M 96 ILE cc_start: 0.3667 (OUTLIER) cc_final: 0.3208 (pp) REVERT: M 236 LEU cc_start: 0.5186 (OUTLIER) cc_final: 0.4874 (mp) REVERT: M 317 TYR cc_start: 0.1933 (OUTLIER) cc_final: 0.1622 (t80) REVERT: 0 221 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7662 (pmt-80) REVERT: 0 498 THR cc_start: 0.7847 (OUTLIER) cc_final: 0.7080 (p) REVERT: 0 525 MET cc_start: 0.7524 (ppp) cc_final: 0.7133 (ppp) REVERT: 6 118 TYR cc_start: 0.5038 (OUTLIER) cc_final: 0.4233 (m-80) REVERT: 7 309 ASP cc_start: 0.3464 (OUTLIER) cc_final: 0.2182 (m-30) REVERT: 7 311 ASP cc_start: 0.8245 (p0) cc_final: 0.8028 (m-30) REVERT: 7 326 VAL cc_start: 0.4819 (t) cc_final: 0.3505 (p) REVERT: 7 365 TYR cc_start: 0.1086 (OUTLIER) cc_final: -0.0945 (m-80) REVERT: 7 452 LEU cc_start: 0.5626 (OUTLIER) cc_final: 0.5063 (tt) REVERT: 7 716 MET cc_start: 0.2880 (mpp) cc_final: 0.2431 (mtm) outliers start: 349 outliers final: 241 residues processed: 587 average time/residue: 1.1469 time to fit residues: 924.7635 Evaluate side-chains 510 residues out of total 7137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 252 time to evaluate : 5.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 865 GLN Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1130 GLN Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1220 PHE Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1201 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 106 MET Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 117 ASN Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 234 GLN Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 317 TYR Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 358 TYR Chi-restraints excluded: chain Q residue 359 ASN Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 103 HIS Chi-restraints excluded: chain W residue 120 ASN Chi-restraints excluded: chain X residue 217 CYS Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain 0 residue 73 SER Chi-restraints excluded: chain 0 residue 80 GLU Chi-restraints excluded: chain 0 residue 109 THR Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 137 THR Chi-restraints excluded: chain 0 residue 162 LEU Chi-restraints excluded: chain 0 residue 204 ASN Chi-restraints excluded: chain 0 residue 209 SER Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 249 SER Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 318 THR Chi-restraints excluded: chain 0 residue 321 ILE Chi-restraints excluded: chain 0 residue 324 ASN Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 361 GLN Chi-restraints excluded: chain 0 residue 407 THR Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 462 THR Chi-restraints excluded: chain 0 residue 498 THR Chi-restraints excluded: chain 0 residue 515 ASP Chi-restraints excluded: chain 0 residue 533 THR Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 651 ASN Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 683 ASP Chi-restraints excluded: chain 0 residue 706 LEU Chi-restraints excluded: chain 0 residue 741 TYR Chi-restraints excluded: chain 0 residue 743 ASP Chi-restraints excluded: chain 1 residue 213 ARG Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 227 THR Chi-restraints excluded: chain 4 residue 234 VAL Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 274 THR Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 128 LEU Chi-restraints excluded: chain 6 residue 145 ARG Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 238 SER Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 282 TYR Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 297 LEU Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 317 PHE Chi-restraints excluded: chain 6 residue 406 CYS Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 53 ASN Chi-restraints excluded: chain 2 residue 57 VAL Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 343 THR Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 350 TYR Chi-restraints excluded: chain 2 residue 351 SER Chi-restraints excluded: chain 2 residue 366 LEU Chi-restraints excluded: chain 2 residue 389 ASN Chi-restraints excluded: chain 2 residue 391 ILE Chi-restraints excluded: chain 2 residue 462 PHE Chi-restraints excluded: chain 2 residue 486 ASP Chi-restraints excluded: chain 2 residue 508 LYS Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 5 residue 47 VAL Chi-restraints excluded: chain 5 residue 49 PHE Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 7 residue 309 ASP Chi-restraints excluded: chain 7 residue 316 PHE Chi-restraints excluded: chain 7 residue 322 SER Chi-restraints excluded: chain 7 residue 352 LEU Chi-restraints excluded: chain 7 residue 360 THR Chi-restraints excluded: chain 7 residue 361 GLN Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 452 LEU Chi-restraints excluded: chain 7 residue 500 ARG Chi-restraints excluded: chain 7 residue 522 ASP Chi-restraints excluded: chain 7 residue 527 LEU Chi-restraints excluded: chain 7 residue 572 GLU Chi-restraints excluded: chain 7 residue 576 LYS Chi-restraints excluded: chain 7 residue 584 ASN Chi-restraints excluded: chain 7 residue 613 TYR Chi-restraints excluded: chain 7 residue 656 LYS Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 712 ASP Chi-restraints excluded: chain 7 residue 717 TYR Chi-restraints excluded: chain 7 residue 735 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 679 optimal weight: 0.7980 chunk 715 optimal weight: 50.0000 chunk 652 optimal weight: 6.9990 chunk 696 optimal weight: 1.9990 chunk 418 optimal weight: 20.0000 chunk 303 optimal weight: 10.0000 chunk 546 optimal weight: 7.9990 chunk 213 optimal weight: 3.9990 chunk 629 optimal weight: 10.0000 chunk 658 optimal weight: 30.0000 chunk 693 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 ASN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS C 203 GLN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 117 ASN ** M 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 251 ASN O 68 GLN ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 164 ASN ** 6 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 729 GLN 7 767 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5913 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 65568 Z= 0.364 Angle : 0.744 15.048 89081 Z= 0.373 Chirality : 0.045 0.402 10021 Planarity : 0.005 0.076 11132 Dihedral : 14.920 88.552 10450 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.49 % Favored : 91.32 % Rotamer: Outliers : 5.15 % Allowed : 26.74 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.59 % Twisted General : 0.11 % 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: -1.35 (0.10), residues: 7844 helix: 0.23 (0.10), residues: 2982 sheet: -0.97 (0.17), residues: 952 loop : -1.80 (0.10), residues: 3910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP X 263 HIS 0.013 0.001 HIS B 363 PHE 0.043 0.002 PHE 2 504 TYR 0.046 0.002 TYR 1 630 ARG 0.008 0.000 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 7137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 327 poor density : 254 time to evaluate : 5.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.5536 (OUTLIER) cc_final: 0.5276 (pt0) REVERT: A 465 TYR cc_start: 0.7640 (OUTLIER) cc_final: 0.6605 (p90) REVERT: A 845 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8213 (mp) REVERT: A 1269 GLU cc_start: 0.4942 (OUTLIER) cc_final: 0.4602 (pm20) REVERT: F 148 VAL cc_start: 0.8267 (OUTLIER) cc_final: 0.8048 (m) REVERT: G 122 ASN cc_start: 0.2531 (OUTLIER) cc_final: 0.2136 (m110) REVERT: J 49 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.6875 (mmm) REVERT: K 10 PHE cc_start: 0.4654 (OUTLIER) cc_final: 0.4410 (m-80) REVERT: M 96 ILE cc_start: 0.3526 (OUTLIER) cc_final: 0.3090 (pp) REVERT: M 317 TYR cc_start: 0.1922 (OUTLIER) cc_final: 0.1638 (t80) REVERT: 0 221 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7687 (pmt-80) REVERT: 0 498 THR cc_start: 0.7745 (OUTLIER) cc_final: 0.6972 (p) REVERT: 6 118 TYR cc_start: 0.5148 (OUTLIER) cc_final: 0.4349 (m-80) REVERT: 7 309 ASP cc_start: 0.3594 (OUTLIER) cc_final: 0.2258 (m-30) REVERT: 7 311 ASP cc_start: 0.8465 (p0) cc_final: 0.8229 (m-30) REVERT: 7 326 VAL cc_start: 0.5130 (t) cc_final: 0.3881 (p) REVERT: 7 365 TYR cc_start: 0.1301 (OUTLIER) cc_final: -0.0816 (m-80) REVERT: 7 452 LEU cc_start: 0.5668 (OUTLIER) cc_final: 0.5090 (tt) REVERT: 7 676 HIS cc_start: 0.1569 (OUTLIER) cc_final: 0.0807 (p-80) REVERT: 7 695 ARG cc_start: 0.0880 (OUTLIER) cc_final: -0.0313 (ppt170) REVERT: 7 716 MET cc_start: 0.2852 (mpp) cc_final: 0.2359 (mtm) outliers start: 327 outliers final: 256 residues processed: 561 average time/residue: 1.1681 time to fit residues: 903.4174 Evaluate side-chains 523 residues out of total 7137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 249 time to evaluate : 5.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1130 GLN Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1220 PHE Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1269 GLU Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1404 GLU Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 959 ASP Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1201 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 106 MET Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 117 ASN Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 234 GLN Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 317 TYR Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 358 TYR Chi-restraints excluded: chain Q residue 359 ASN Chi-restraints excluded: chain R residue 98 ASN Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 269 SER Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 103 HIS Chi-restraints excluded: chain W residue 120 ASN Chi-restraints excluded: chain X residue 217 CYS Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 73 SER Chi-restraints excluded: chain 0 residue 80 GLU Chi-restraints excluded: chain 0 residue 109 THR Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 137 THR Chi-restraints excluded: chain 0 residue 162 LEU Chi-restraints excluded: chain 0 residue 204 ASN Chi-restraints excluded: chain 0 residue 209 SER Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 249 SER Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 318 THR Chi-restraints excluded: chain 0 residue 321 ILE Chi-restraints excluded: chain 0 residue 324 ASN Chi-restraints excluded: chain 0 residue 361 GLN Chi-restraints excluded: chain 0 residue 402 ILE Chi-restraints excluded: chain 0 residue 407 THR Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 462 THR Chi-restraints excluded: chain 0 residue 498 THR Chi-restraints excluded: chain 0 residue 515 ASP Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 651 ASN Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 683 ASP Chi-restraints excluded: chain 0 residue 706 LEU Chi-restraints excluded: chain 0 residue 741 TYR Chi-restraints excluded: chain 0 residue 743 ASP Chi-restraints excluded: chain 1 residue 213 ARG Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 4 residue 227 THR Chi-restraints excluded: chain 4 residue 234 VAL Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 274 THR Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 128 LEU Chi-restraints excluded: chain 6 residue 145 ARG Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 6 residue 191 ASP Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 238 SER Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 282 TYR Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 297 LEU Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 317 PHE Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 406 CYS Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 53 ASN Chi-restraints excluded: chain 2 residue 57 VAL Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 343 THR Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 350 TYR Chi-restraints excluded: chain 2 residue 351 SER Chi-restraints excluded: chain 2 residue 366 LEU Chi-restraints excluded: chain 2 residue 373 MET Chi-restraints excluded: chain 2 residue 389 ASN Chi-restraints excluded: chain 2 residue 391 ILE Chi-restraints excluded: chain 2 residue 462 PHE Chi-restraints excluded: chain 2 residue 486 ASP Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 5 residue 47 VAL Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 60 ASP Chi-restraints excluded: chain 7 residue 309 ASP Chi-restraints excluded: chain 7 residue 316 PHE Chi-restraints excluded: chain 7 residue 322 SER Chi-restraints excluded: chain 7 residue 352 LEU Chi-restraints excluded: chain 7 residue 360 THR Chi-restraints excluded: chain 7 residue 361 GLN Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 452 LEU Chi-restraints excluded: chain 7 residue 500 ARG Chi-restraints excluded: chain 7 residue 522 ASP Chi-restraints excluded: chain 7 residue 527 LEU Chi-restraints excluded: chain 7 residue 576 LYS Chi-restraints excluded: chain 7 residue 613 TYR Chi-restraints excluded: chain 7 residue 656 LYS Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 695 ARG Chi-restraints excluded: chain 7 residue 712 ASP Chi-restraints excluded: chain 7 residue 717 TYR Chi-restraints excluded: chain 7 residue 735 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 457 optimal weight: 5.9990 chunk 736 optimal weight: 40.0000 chunk 449 optimal weight: 10.0000 chunk 349 optimal weight: 5.9990 chunk 511 optimal weight: 9.9990 chunk 772 optimal weight: 0.9980 chunk 710 optimal weight: 40.0000 chunk 614 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 474 optimal weight: 40.0000 chunk 376 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 ASN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS C 203 GLN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 251 ASN ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5902 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 65568 Z= 0.323 Angle : 0.748 19.918 89081 Z= 0.373 Chirality : 0.045 0.308 10021 Planarity : 0.004 0.076 11132 Dihedral : 14.878 88.416 10447 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.39 % Favored : 91.43 % Rotamer: Outliers : 4.74 % Allowed : 27.15 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.59 % Twisted General : 0.11 % 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: -1.31 (0.10), residues: 7844 helix: 0.27 (0.10), residues: 2973 sheet: -0.91 (0.17), residues: 934 loop : -1.78 (0.10), residues: 3937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP X 263 HIS 0.012 0.001 HIS B 363 PHE 0.044 0.001 PHE 2 504 TYR 0.036 0.001 TYR 2 13 ARG 0.008 0.000 ARG B 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15688 Ramachandran restraints generated. 7844 Oldfield, 0 Emsley, 7844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 7137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 251 time to evaluate : 5.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.5581 (OUTLIER) cc_final: 0.5333 (pt0) REVERT: A 465 TYR cc_start: 0.7611 (OUTLIER) cc_final: 0.6548 (p90) REVERT: A 845 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8149 (mp) REVERT: A 1417 GLU cc_start: 0.6408 (OUTLIER) cc_final: 0.5940 (tm-30) REVERT: G 122 ASN cc_start: 0.2799 (OUTLIER) cc_final: 0.2366 (m110) REVERT: J 49 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.6858 (mmm) REVERT: K 10 PHE cc_start: 0.4582 (OUTLIER) cc_final: 0.4265 (m-80) REVERT: M 96 ILE cc_start: 0.3536 (OUTLIER) cc_final: 0.3108 (pp) REVERT: M 237 THR cc_start: 0.4727 (OUTLIER) cc_final: 0.4087 (p) REVERT: M 317 TYR cc_start: 0.1857 (OUTLIER) cc_final: 0.1585 (t80) REVERT: Q 386 MET cc_start: 0.1607 (mpt) cc_final: 0.1144 (pmm) REVERT: 0 498 THR cc_start: 0.7938 (OUTLIER) cc_final: 0.7248 (p) REVERT: 6 118 TYR cc_start: 0.5196 (OUTLIER) cc_final: 0.4430 (m-80) REVERT: 7 309 ASP cc_start: 0.3427 (OUTLIER) cc_final: 0.2260 (m-30) REVERT: 7 311 ASP cc_start: 0.8436 (p0) cc_final: 0.8205 (m-30) REVERT: 7 365 TYR cc_start: 0.1277 (OUTLIER) cc_final: -0.0879 (m-80) REVERT: 7 452 LEU cc_start: 0.5784 (OUTLIER) cc_final: 0.5197 (tt) REVERT: 7 695 ARG cc_start: 0.0766 (OUTLIER) cc_final: -0.0202 (ppt170) outliers start: 301 outliers final: 253 residues processed: 540 average time/residue: 1.1542 time to fit residues: 859.8067 Evaluate side-chains 518 residues out of total 7137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 249 time to evaluate : 5.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1130 GLN Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1220 PHE Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1201 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 106 MET Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 8 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain M residue 234 GLN Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 317 TYR Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 358 TYR Chi-restraints excluded: chain Q residue 359 ASN Chi-restraints excluded: chain R residue 98 ASN Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 103 HIS Chi-restraints excluded: chain W residue 120 ASN Chi-restraints excluded: chain X residue 217 CYS Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 73 SER Chi-restraints excluded: chain 0 residue 80 GLU Chi-restraints excluded: chain 0 residue 109 THR Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 137 THR Chi-restraints excluded: chain 0 residue 162 LEU Chi-restraints excluded: chain 0 residue 204 ASN Chi-restraints excluded: chain 0 residue 209 SER Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 249 SER Chi-restraints excluded: chain 0 residue 318 THR Chi-restraints excluded: chain 0 residue 321 ILE Chi-restraints excluded: chain 0 residue 324 ASN Chi-restraints excluded: chain 0 residue 361 GLN Chi-restraints excluded: chain 0 residue 407 THR Chi-restraints excluded: chain 0 residue 453 PHE Chi-restraints excluded: chain 0 residue 462 THR Chi-restraints excluded: chain 0 residue 498 THR Chi-restraints excluded: chain 0 residue 515 ASP Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 673 LYS Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 683 ASP Chi-restraints excluded: chain 0 residue 706 LEU Chi-restraints excluded: chain 0 residue 741 TYR Chi-restraints excluded: chain 0 residue 743 ASP Chi-restraints excluded: chain 1 residue 213 ARG Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 227 THR Chi-restraints excluded: chain 4 residue 234 VAL Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 274 THR Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 128 LEU Chi-restraints excluded: chain 6 residue 145 ARG Chi-restraints excluded: chain 6 residue 155 ASP Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 238 SER Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 282 TYR Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 297 LEU Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 317 PHE Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 406 CYS Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 53 ASN Chi-restraints excluded: chain 2 residue 57 VAL Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 343 THR Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 350 TYR Chi-restraints excluded: chain 2 residue 351 SER Chi-restraints excluded: chain 2 residue 366 LEU Chi-restraints excluded: chain 2 residue 389 ASN Chi-restraints excluded: chain 2 residue 391 ILE Chi-restraints excluded: chain 2 residue 462 PHE Chi-restraints excluded: chain 2 residue 470 LEU Chi-restraints excluded: chain 2 residue 486 ASP Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 5 residue 47 VAL Chi-restraints excluded: chain 5 residue 49 PHE Chi-restraints excluded: chain 5 residue 52 HIS Chi-restraints excluded: chain 3 residue 25 ASP Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 7 residue 309 ASP Chi-restraints excluded: chain 7 residue 316 PHE Chi-restraints excluded: chain 7 residue 322 SER Chi-restraints excluded: chain 7 residue 352 LEU Chi-restraints excluded: chain 7 residue 360 THR Chi-restraints excluded: chain 7 residue 361 GLN Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 452 LEU Chi-restraints excluded: chain 7 residue 500 ARG Chi-restraints excluded: chain 7 residue 522 ASP Chi-restraints excluded: chain 7 residue 527 LEU Chi-restraints excluded: chain 7 residue 565 PHE Chi-restraints excluded: chain 7 residue 576 LYS Chi-restraints excluded: chain 7 residue 613 TYR Chi-restraints excluded: chain 7 residue 656 LYS Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 695 ARG Chi-restraints excluded: chain 7 residue 712 ASP Chi-restraints excluded: chain 7 residue 717 TYR Chi-restraints excluded: chain 7 residue 735 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 488 optimal weight: 50.0000 chunk 654 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 566 optimal weight: 0.5980 chunk 90 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 615 optimal weight: 7.9990 chunk 257 optimal weight: 0.7980 chunk 632 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 ASN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS C 203 GLN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 117 ASN ** M 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 251 ASN ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 382 HIS ** 5 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 729 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.070517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.049818 restraints weight = 469756.421| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.74 r_work: 0.3071 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 633 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 634 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 65568 Z= 0.221 Angle : 0.724 18.612 89081 Z= 0.360 Chirality : 0.044 0.510 10021 Planarity : 0.004 0.077 11132 Dihedral : 14.762 88.483 10437 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.94 % Favored : 91.89 % Rotamer: Outliers : 4.64 % Allowed : 27.36 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.03 % Twisted Proline : 0.59 % Twisted General : 0.11 % 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: -1.18 (0.10), residues: 7844 helix: 0.39 (0.10), residues: 2950 sheet: -0.78 (0.17), residues: 926 loop : -1.72 (0.10), residues: 3968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP X 263 HIS 0.012 0.001 HIS B 363 PHE 0.060 0.001 PHE 5 49 TYR 0.051 0.001 TYR 1 630 ARG 0.006 0.000 ARG 7 344 =============================================================================== Job complete usr+sys time: 20607.78 seconds wall clock time: 360 minutes 25.15 seconds (21625.15 seconds total)