Starting phenix.real_space_refine on Fri Apr 12 11:04:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6po2_20407/04_2024/6po2_20407.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6po2_20407/04_2024/6po2_20407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6po2_20407/04_2024/6po2_20407.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6po2_20407/04_2024/6po2_20407.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6po2_20407/04_2024/6po2_20407.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6po2_20407/04_2024/6po2_20407.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 468 5.16 5 C 51589 2.51 5 N 13993 2.21 5 O 14823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A GLU 426": "OE1" <-> "OE2" Residue "A ARG 427": "NH1" <-> "NH2" Residue "A ARG 443": "NH1" <-> "NH2" Residue "A GLU 504": "OE1" <-> "OE2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A GLU 542": "OE1" <-> "OE2" Residue "A GLU 568": "OE1" <-> "OE2" Residue "A GLU 598": "OE1" <-> "OE2" Residue "A GLU 634": "OE1" <-> "OE2" Residue "A ARG 645": "NH1" <-> "NH2" Residue "A ARG 655": "NH1" <-> "NH2" Residue "A ARG 695": "NH1" <-> "NH2" Residue "A GLU 745": "OE1" <-> "OE2" Residue "A ARG 827": "NH1" <-> "NH2" Residue "A ARG 884": "NH1" <-> "NH2" Residue "A GLU 888": "OE1" <-> "OE2" Residue "A ARG 893": "NH1" <-> "NH2" Residue "A ARG 895": "NH1" <-> "NH2" Residue "A GLU 1010": "OE1" <-> "OE2" Residue "A ARG 1023": "NH1" <-> "NH2" Residue "A GLU 1083": "OE1" <-> "OE2" Residue "A PHE 1093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1118": "NH1" <-> "NH2" Residue "A GLU 1202": "OE1" <-> "OE2" Residue "A ARG 1274": "NH1" <-> "NH2" Residue "A ARG 1291": "NH1" <-> "NH2" Residue "A GLU 1298": "OE1" <-> "OE2" Residue "B GLU 38": "OE1" <-> "OE2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B GLU 178": "OE1" <-> "OE2" Residue "B ARG 200": "NH1" <-> "NH2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B ARG 413": "NH1" <-> "NH2" Residue "B ARG 431": "NH1" <-> "NH2" Residue "B ARG 502": "NH1" <-> "NH2" Residue "B ARG 529": "NH1" <-> "NH2" Residue "B PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 646": "OE1" <-> "OE2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "B GLU 695": "OE1" <-> "OE2" Residue "B ARG 722": "NH1" <-> "NH2" Residue "B GLU 733": "OE1" <-> "OE2" Residue "B GLU 737": "OE1" <-> "OE2" Residue "B ARG 740": "NH1" <-> "NH2" Residue "B GLU 747": "OE1" <-> "OE2" Residue "B ARG 789": "NH1" <-> "NH2" Residue "B GLU 820": "OE1" <-> "OE2" Residue "B ARG 860": "NH1" <-> "NH2" Residue "B ARG 882": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C GLU 10": "OE1" <-> "OE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C ARG 151": "NH1" <-> "NH2" Residue "C GLU 157": "OE1" <-> "OE2" Residue "C GLU 160": "OE1" <-> "OE2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C ARG 241": "NH1" <-> "NH2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "C ARG 317": "NH1" <-> "NH2" Residue "C PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 413": "NH1" <-> "NH2" Residue "C ARG 431": "NH1" <-> "NH2" Residue "C GLU 461": "OE1" <-> "OE2" Residue "C ARG 529": "NH1" <-> "NH2" Residue "C ARG 615": "NH1" <-> "NH2" Residue "C ARG 632": "NH1" <-> "NH2" Residue "C GLU 695": "OE1" <-> "OE2" Residue "C GLU 719": "OE1" <-> "OE2" Residue "C GLU 724": "OE1" <-> "OE2" Residue "C ARG 862": "NH1" <-> "NH2" Residue "C ARG 873": "NH1" <-> "NH2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D ARG 103": "NH1" <-> "NH2" Residue "D GLU 120": "OE1" <-> "OE2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 413": "NH1" <-> "NH2" Residue "D ARG 431": "NH1" <-> "NH2" Residue "D ARG 502": "NH1" <-> "NH2" Residue "D ARG 529": "NH1" <-> "NH2" Residue "D GLU 646": "OE1" <-> "OE2" Residue "D GLU 686": "OE1" <-> "OE2" Residue "D GLU 719": "OE1" <-> "OE2" Residue "D ARG 722": "NH1" <-> "NH2" Residue "D GLU 733": "OE1" <-> "OE2" Residue "D GLU 737": "OE1" <-> "OE2" Residue "D ARG 740": "NH1" <-> "NH2" Residue "D ARG 759": "NH1" <-> "NH2" Residue "D ARG 789": "NH1" <-> "NH2" Residue "D ARG 860": "NH1" <-> "NH2" Residue "D ARG 882": "NH1" <-> "NH2" Residue "E ARG 8": "NH1" <-> "NH2" Residue "E GLU 10": "OE1" <-> "OE2" Residue "E GLU 38": "OE1" <-> "OE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E ARG 151": "NH1" <-> "NH2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 193": "OE1" <-> "OE2" Residue "E GLU 231": "OE1" <-> "OE2" Residue "E ARG 241": "NH1" <-> "NH2" Residue "E ARG 283": "NH1" <-> "NH2" Residue "E ARG 317": "NH1" <-> "NH2" Residue "E PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 413": "NH1" <-> "NH2" Residue "E ARG 431": "NH1" <-> "NH2" Residue "E GLU 481": "OE1" <-> "OE2" Residue "E ARG 529": "NH1" <-> "NH2" Residue "E GLU 600": "OE1" <-> "OE2" Residue "E ARG 615": "NH1" <-> "NH2" Residue "E GLU 646": "OE1" <-> "OE2" Residue "E GLU 712": "OE1" <-> "OE2" Residue "E GLU 719": "OE1" <-> "OE2" Residue "E GLU 724": "OE1" <-> "OE2" Residue "E GLU 737": "OE1" <-> "OE2" Residue "E GLU 820": "OE1" <-> "OE2" Residue "E ASP 837": "OD1" <-> "OD2" Residue "E ARG 862": "NH1" <-> "NH2" Residue "E ARG 873": "NH1" <-> "NH2" Residue "F ARG 100": "NH1" <-> "NH2" Residue "F ARG 103": "NH1" <-> "NH2" Residue "F TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 120": "OE1" <-> "OE2" Residue "F GLU 122": "OE1" <-> "OE2" Residue "F ARG 154": "NH1" <-> "NH2" Residue "F ARG 200": "NH1" <-> "NH2" Residue "F GLU 225": "OE1" <-> "OE2" Residue "F ARG 413": "NH1" <-> "NH2" Residue "F ARG 431": "NH1" <-> "NH2" Residue "F GLU 458": "OE1" <-> "OE2" Residue "F ARG 460": "NH1" <-> "NH2" Residue "F GLU 461": "OE1" <-> "OE2" Residue "F TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 502": "NH1" <-> "NH2" Residue "F ARG 529": "NH1" <-> "NH2" Residue "F GLU 719": "OE1" <-> "OE2" Residue "F ARG 722": "NH1" <-> "NH2" Residue "F GLU 737": "OE1" <-> "OE2" Residue "F ARG 740": "NH1" <-> "NH2" Residue "F ARG 789": "NH1" <-> "NH2" Residue "F GLU 806": "OE1" <-> "OE2" Residue "F GLU 859": "OE1" <-> "OE2" Residue "F ARG 860": "NH1" <-> "NH2" Residue "F ARG 882": "NH1" <-> "NH2" Residue "G ARG 8": "NH1" <-> "NH2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G GLU 120": "OE1" <-> "OE2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G ARG 151": "NH1" <-> "NH2" Residue "G GLU 160": "OE1" <-> "OE2" Residue "G GLU 178": "OE1" <-> "OE2" Residue "G GLU 211": "OE1" <-> "OE2" Residue "G GLU 231": "OE1" <-> "OE2" Residue "G ARG 241": "NH1" <-> "NH2" Residue "G ARG 283": "NH1" <-> "NH2" Residue "G ARG 317": "NH1" <-> "NH2" Residue "G GLU 363": "OE1" <-> "OE2" Residue "G ARG 413": "NH1" <-> "NH2" Residue "G ARG 431": "NH1" <-> "NH2" Residue "G ARG 460": "NH1" <-> "NH2" Residue "G ARG 529": "NH1" <-> "NH2" Residue "G GLU 606": "OE1" <-> "OE2" Residue "G ARG 615": "NH1" <-> "NH2" Residue "G GLU 646": "OE1" <-> "OE2" Residue "G GLU 686": "OE1" <-> "OE2" Residue "G GLU 695": "OE1" <-> "OE2" Residue "G GLU 719": "OE1" <-> "OE2" Residue "G GLU 724": "OE1" <-> "OE2" Residue "G GLU 733": "OE1" <-> "OE2" Residue "G GLU 747": "OE1" <-> "OE2" Residue "G ARG 862": "NH1" <-> "NH2" Residue "G ARG 873": "NH1" <-> "NH2" Residue "H GLU 38": "OE1" <-> "OE2" Residue "H ARG 100": "NH1" <-> "NH2" Residue "H ARG 103": "NH1" <-> "NH2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "H ARG 154": "NH1" <-> "NH2" Residue "H GLU 157": "OE1" <-> "OE2" Residue "H GLU 162": "OE1" <-> "OE2" Residue "H GLU 167": "OE1" <-> "OE2" Residue "H GLU 178": "OE1" <-> "OE2" Residue "H GLU 193": "OE1" <-> "OE2" Residue "H ARG 200": "NH1" <-> "NH2" Residue "H GLU 225": "OE1" <-> "OE2" Residue "H ARG 241": "NH1" <-> "NH2" Residue "H ARG 317": "NH1" <-> "NH2" Residue "H PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 413": "NH1" <-> "NH2" Residue "H ARG 431": "NH1" <-> "NH2" Residue "H ARG 502": "NH1" <-> "NH2" Residue "H GLU 512": "OE1" <-> "OE2" Residue "H ARG 529": "NH1" <-> "NH2" Residue "H PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 646": "OE1" <-> "OE2" Residue "H ARG 722": "NH1" <-> "NH2" Residue "H ARG 740": "NH1" <-> "NH2" Residue "H GLU 747": "OE1" <-> "OE2" Residue "H ARG 789": "NH1" <-> "NH2" Residue "H GLU 831": "OE1" <-> "OE2" Residue "H ARG 860": "NH1" <-> "NH2" Residue "H ARG 862": "NH1" <-> "NH2" Residue "H ARG 882": "NH1" <-> "NH2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ARG 151": "NH1" <-> "NH2" Residue "I GLU 157": "OE1" <-> "OE2" Residue "I GLU 193": "OE1" <-> "OE2" Residue "I GLU 231": "OE1" <-> "OE2" Residue "I ARG 241": "NH1" <-> "NH2" Residue "I ARG 283": "NH1" <-> "NH2" Residue "I ARG 317": "NH1" <-> "NH2" Residue "I GLU 363": "OE1" <-> "OE2" Residue "I ARG 364": "NH1" <-> "NH2" Residue "I ARG 413": "NH1" <-> "NH2" Residue "I ARG 431": "NH1" <-> "NH2" Residue "I ARG 529": "NH1" <-> "NH2" Residue "I ARG 615": "NH1" <-> "NH2" Residue "I GLU 646": "OE1" <-> "OE2" Residue "I GLU 695": "OE1" <-> "OE2" Residue "I GLU 712": "OE1" <-> "OE2" Residue "I GLU 724": "OE1" <-> "OE2" Residue "I GLU 737": "OE1" <-> "OE2" Residue "I GLU 747": "OE1" <-> "OE2" Residue "I TYR 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 831": "OE1" <-> "OE2" Residue "I ARG 862": "NH1" <-> "NH2" Residue "I ARG 873": "NH1" <-> "NH2" Residue "J ARG 55": "NH1" <-> "NH2" Residue "J ARG 100": "NH1" <-> "NH2" Residue "J ARG 103": "NH1" <-> "NH2" Residue "J GLU 110": "OE1" <-> "OE2" Residue "J ARG 154": "NH1" <-> "NH2" Residue "J GLU 160": "OE1" <-> "OE2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J GLU 167": "OE1" <-> "OE2" Residue "J GLU 193": "OE1" <-> "OE2" Residue "J ARG 200": "NH1" <-> "NH2" Residue "J GLU 253": "OE1" <-> "OE2" Residue "J TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 413": "NH1" <-> "NH2" Residue "J ARG 431": "NH1" <-> "NH2" Residue "J ARG 460": "NH1" <-> "NH2" Residue "J TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 502": "NH1" <-> "NH2" Residue "J GLU 512": "OE1" <-> "OE2" Residue "J ARG 529": "NH1" <-> "NH2" Residue "J GLU 591": "OE1" <-> "OE2" Residue "J GLU 719": "OE1" <-> "OE2" Residue "J ARG 722": "NH1" <-> "NH2" Residue "J GLU 733": "OE1" <-> "OE2" Residue "J GLU 737": "OE1" <-> "OE2" Residue "J ARG 740": "NH1" <-> "NH2" Residue "J GLU 747": "OE1" <-> "OE2" Residue "J ARG 789": "NH1" <-> "NH2" Residue "J GLU 831": "OE1" <-> "OE2" Residue "J GLU 859": "OE1" <-> "OE2" Residue "J ARG 860": "NH1" <-> "NH2" Residue "J ARG 862": "NH1" <-> "NH2" Residue "J ARG 882": "NH1" <-> "NH2" Residue "K ARG 8": "NH1" <-> "NH2" Residue "K GLU 10": "OE1" <-> "OE2" Residue "K TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 120": "OE1" <-> "OE2" Residue "K ARG 151": "NH1" <-> "NH2" Residue "K GLU 160": "OE1" <-> "OE2" Residue "K GLU 240": "OE1" <-> "OE2" Residue "K ARG 241": "NH1" <-> "NH2" Residue "K ARG 283": "NH1" <-> "NH2" Residue "K ARG 317": "NH1" <-> "NH2" Residue "K PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 413": "NH1" <-> "NH2" Residue "K ARG 431": "NH1" <-> "NH2" Residue "K GLU 461": "OE1" <-> "OE2" Residue "K ARG 529": "NH1" <-> "NH2" Residue "K GLU 606": "OE1" <-> "OE2" Residue "K ARG 615": "NH1" <-> "NH2" Residue "K PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 646": "OE1" <-> "OE2" Residue "K GLU 719": "OE1" <-> "OE2" Residue "K GLU 737": "OE1" <-> "OE2" Residue "K GLU 747": "OE1" <-> "OE2" Residue "K GLU 831": "OE1" <-> "OE2" Residue "K ARG 862": "NH1" <-> "NH2" Residue "K ARG 873": "NH1" <-> "NH2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 80873 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 10062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1244, 10062 Classifications: {'peptide': 1244} Link IDs: {'PTRANS': 49, 'TRANS': 1194} Chain breaks: 2 Chain: "B" Number of atoms: 7046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 872, 7046 Classifications: {'peptide': 872} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 44, 'TRANS': 827} Chain: "C" Number of atoms: 7151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7151 Classifications: {'peptide': 885} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 47, 'TRANS': 837} Chain breaks: 1 Chain: "D" Number of atoms: 6968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 863, 6968 Classifications: {'peptide': 863} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 45, 'TRANS': 817} Chain breaks: 1 Chain: "E" Number of atoms: 7151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7151 Classifications: {'peptide': 885} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 47, 'TRANS': 837} Chain breaks: 1 Chain: "F" Number of atoms: 6995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 6995 Classifications: {'peptide': 868} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 45, 'TRANS': 822} Chain breaks: 1 Chain: "G" Number of atoms: 7151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7151 Classifications: {'peptide': 885} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 47, 'TRANS': 837} Chain breaks: 1 Chain: "H" Number of atoms: 7017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 7017 Classifications: {'peptide': 868} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 44, 'TRANS': 823} Chain: "I" Number of atoms: 7151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7151 Classifications: {'peptide': 885} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 47, 'TRANS': 837} Chain breaks: 1 Chain: "J" Number of atoms: 7030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 870, 7030 Classifications: {'peptide': 870} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 44, 'TRANS': 825} Chain: "K" Number of atoms: 7151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7151 Classifications: {'peptide': 885} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 47, 'TRANS': 837} Chain breaks: 1 Time building chain proxies: 30.88, per 1000 atoms: 0.38 Number of scatterers: 80873 At special positions: 0 Unit cell: (330.48, 326.4, 129.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 468 16.00 O 14823 8.00 N 13993 7.00 C 51589 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: 23.68 Conformation dependent library (CDL) restraints added in 11.0 seconds 19940 Ramachandran restraints generated. 9970 Oldfield, 0 Emsley, 9970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19068 Finding SS restraints... Secondary structure from input PDB file: 418 helices and 129 sheets defined 42.1% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.49 Creating SS restraints... Processing helix chain 'A' and resid 3 through 20 removed outlier: 3.971A pdb=" N ALA A 9 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN A 10 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 11 " --> pdb=" O GLN A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 48 removed outlier: 3.537A pdb=" N LYS A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS A 48 " --> pdb=" O ILE A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 48' Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.663A pdb=" N TYR A 83 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 84 " --> pdb=" O TRP A 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 80 through 84' Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.607A pdb=" N ASN A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 139 removed outlier: 3.587A pdb=" N ASN A 137 " --> pdb=" O PHE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 162 removed outlier: 3.690A pdb=" N TRP A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN A 155 " --> pdb=" O CYS A 151 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 177 removed outlier: 3.522A pdb=" N MET A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A 174 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 210 removed outlier: 3.519A pdb=" N CYS A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 225 removed outlier: 3.906A pdb=" N GLU A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A 223 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 removed outlier: 3.690A pdb=" N PHE A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 271 removed outlier: 3.703A pdb=" N ASN A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ALA A 263 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Proline residue: A 264 - end of helix removed outlier: 3.840A pdb=" N VAL A 269 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 removed outlier: 3.805A pdb=" N PHE A 311 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 312 " --> pdb=" O ALA A 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 308 through 312' Processing helix chain 'A' and resid 313 through 338 removed outlier: 3.744A pdb=" N ASN A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG A 321 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 337 " --> pdb=" O TYR A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 352 removed outlier: 3.500A pdb=" N LEU A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 347 through 352' Processing helix chain 'A' and resid 363 through 375 removed outlier: 3.860A pdb=" N MET A 367 " --> pdb=" O LYS A 363 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 370 " --> pdb=" O ASN A 366 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 379 removed outlier: 3.862A pdb=" N ILE A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 379' Processing helix chain 'A' and resid 405 through 413 Processing helix chain 'A' and resid 413 through 426 removed outlier: 3.607A pdb=" N PHE A 417 " --> pdb=" O THR A 413 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 422 " --> pdb=" O LYS A 418 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 442 removed outlier: 3.656A pdb=" N LEU A 442 " --> pdb=" O THR A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 535 Processing helix chain 'A' and resid 537 through 542 removed outlier: 3.527A pdb=" N GLU A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 546 removed outlier: 4.013A pdb=" N ARG A 546 " --> pdb=" O TYR A 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 543 through 546' Processing helix chain 'A' and resid 577 through 582 removed outlier: 3.623A pdb=" N PHE A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 604 removed outlier: 3.714A pdb=" N HIS A 602 " --> pdb=" O GLU A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 620 removed outlier: 3.518A pdb=" N GLY A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 615 " --> pdb=" O GLY A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 624 removed outlier: 3.562A pdb=" N ARG A 624 " --> pdb=" O ALA A 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 621 through 624' Processing helix chain 'A' and resid 632 through 637 removed outlier: 3.625A pdb=" N ILE A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 662 through 670 removed outlier: 3.661A pdb=" N ARG A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 668 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 750 removed outlier: 3.526A pdb=" N ALA A 730 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 731 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 732 " --> pdb=" O LEU A 728 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 741 " --> pdb=" O ALA A 737 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN A 743 " --> pdb=" O GLY A 739 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 745 " --> pdb=" O LEU A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 793 removed outlier: 3.547A pdb=" N ALA A 785 " --> pdb=" O ASP A 781 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 787 " --> pdb=" O VAL A 783 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N PHE A 788 " --> pdb=" O ALA A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 850 removed outlier: 3.811A pdb=" N VAL A 846 " --> pdb=" O VAL A 842 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 847 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 859 removed outlier: 4.090A pdb=" N LYS A 856 " --> pdb=" O THR A 852 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 857 " --> pdb=" O MET A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 873 removed outlier: 3.874A pdb=" N LEU A 870 " --> pdb=" O ALA A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 881 removed outlier: 4.593A pdb=" N TRP A 880 " --> pdb=" O ILE A 877 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS A 881 " --> pdb=" O GLY A 878 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 877 through 881' Processing helix chain 'A' and resid 913 through 917 removed outlier: 3.853A pdb=" N LEU A 916 " --> pdb=" O PRO A 913 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR A 917 " --> pdb=" O LEU A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 917' Processing helix chain 'A' and resid 937 through 945 removed outlier: 3.746A pdb=" N VAL A 942 " --> pdb=" O GLU A 938 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 945 " --> pdb=" O TYR A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 951 removed outlier: 3.588A pdb=" N ASP A 951 " --> pdb=" O SER A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1000 removed outlier: 3.655A pdb=" N ALA A 998 " --> pdb=" O ALA A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1007 Processing helix chain 'A' and resid 1008 through 1010 No H-bonds generated for 'chain 'A' and resid 1008 through 1010' Processing helix chain 'A' and resid 1019 through 1031 removed outlier: 3.712A pdb=" N LEU A1031 " --> pdb=" O HIS A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1054 removed outlier: 3.675A pdb=" N THR A1038 " --> pdb=" O SER A1034 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A1043 " --> pdb=" O LEU A1039 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU A1046 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1077 removed outlier: 3.500A pdb=" N LYS A1076 " --> pdb=" O SER A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1109 removed outlier: 3.598A pdb=" N ILE A1104 " --> pdb=" O PRO A1100 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLN A1105 " --> pdb=" O GLN A1101 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A1106 " --> pdb=" O PHE A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1132 removed outlier: 3.688A pdb=" N ASP A1126 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A1128 " --> pdb=" O ARG A1124 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP A1132 " --> pdb=" O ILE A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1137 removed outlier: 3.841A pdb=" N GLY A1137 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1151 removed outlier: 3.951A pdb=" N ASN A1146 " --> pdb=" O ASN A1142 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A1147 " --> pdb=" O THR A1143 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A1151 " --> pdb=" O VAL A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1165 removed outlier: 4.345A pdb=" N VAL A1161 " --> pdb=" O GLY A1158 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR A1162 " --> pdb=" O ASP A1159 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE A1164 " --> pdb=" O VAL A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1174 removed outlier: 3.638A pdb=" N ALA A1174 " --> pdb=" O THR A1171 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1171 through 1174' Processing helix chain 'A' and resid 1175 through 1187 removed outlier: 3.948A pdb=" N MET A1181 " --> pdb=" O LEU A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1218 removed outlier: 3.632A pdb=" N ILE A1215 " --> pdb=" O THR A1211 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP A1216 " --> pdb=" O GLN A1212 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR A1217 " --> pdb=" O ASP A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1246 removed outlier: 3.897A pdb=" N GLN A1239 " --> pdb=" O LEU A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1275 removed outlier: 3.563A pdb=" N ILE A1268 " --> pdb=" O LYS A1264 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A1273 " --> pdb=" O ARG A1269 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG A1274 " --> pdb=" O LEU A1270 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR A1275 " --> pdb=" O GLN A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1286 Processing helix chain 'A' and resid 1291 through 1296 Processing helix chain 'A' and resid 1297 through 1299 No H-bonds generated for 'chain 'A' and resid 1297 through 1299' Processing helix chain 'B' and resid 41 through 54 removed outlier: 4.001A pdb=" N GLN B 47 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR B 52 " --> pdb=" O ALA B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 112 removed outlier: 3.627A pdb=" N SER B 112 " --> pdb=" O TYR B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 141 removed outlier: 3.628A pdb=" N ILE B 131 " --> pdb=" O TYR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 185 removed outlier: 3.533A pdb=" N ASN B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 190 removed outlier: 3.971A pdb=" N SER B 190 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 230 removed outlier: 4.108A pdb=" N ILE B 216 " --> pdb=" O PRO B 212 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 247 removed outlier: 4.137A pdb=" N ARG B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS B 244 " --> pdb=" O GLU B 240 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ARG B 245 " --> pdb=" O ARG B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 297 removed outlier: 3.519A pdb=" N THR B 295 " --> pdb=" O MET B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 312 removed outlier: 3.828A pdb=" N SER B 311 " --> pdb=" O PRO B 307 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 312 " --> pdb=" O ARG B 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 307 through 312' Processing helix chain 'B' and resid 323 through 328 removed outlier: 3.786A pdb=" N LEU B 327 " --> pdb=" O PRO B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 349 removed outlier: 3.562A pdb=" N ASP B 339 " --> pdb=" O GLN B 335 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B 340 " --> pdb=" O GLN B 336 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B 346 " --> pdb=" O LYS B 342 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 381 removed outlier: 4.064A pdb=" N VAL B 372 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL B 375 " --> pdb=" O MET B 371 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS B 378 " --> pdb=" O GLY B 374 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU B 379 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 407 removed outlier: 3.726A pdb=" N ASP B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 407 " --> pdb=" O ASN B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 440 Processing helix chain 'B' and resid 474 through 477 Processing helix chain 'B' and resid 494 through 507 removed outlier: 3.502A pdb=" N ARG B 502 " --> pdb=" O ASN B 498 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 519 removed outlier: 3.871A pdb=" N PHE B 516 " --> pdb=" O GLU B 512 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 518 " --> pdb=" O ALA B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 535 removed outlier: 3.578A pdb=" N ARG B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE B 533 " --> pdb=" O ARG B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 550 Processing helix chain 'B' and resid 552 through 558 Processing helix chain 'B' and resid 574 through 581 removed outlier: 3.563A pdb=" N PHE B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN B 581 " --> pdb=" O TRP B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 618 removed outlier: 3.590A pdb=" N ILE B 599 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER B 601 " --> pdb=" O PRO B 597 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 604 " --> pdb=" O GLU B 600 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 605 " --> pdb=" O SER B 601 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET B 610 " --> pdb=" O GLU B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 632 through 642 removed outlier: 4.343A pdb=" N PHE B 636 " --> pdb=" O ARG B 632 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TRP B 637 " --> pdb=" O PRO B 633 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS B 638 " --> pdb=" O SER B 634 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN B 642 " --> pdb=" O LYS B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 656 removed outlier: 4.148A pdb=" N LEU B 654 " --> pdb=" O ALA B 650 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER B 655 " --> pdb=" O VAL B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 672 removed outlier: 3.582A pdb=" N ARG B 668 " --> pdb=" O ARG B 664 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL B 670 " --> pdb=" O MET B 666 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET B 671 " --> pdb=" O MET B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 691 removed outlier: 3.878A pdb=" N GLU B 686 " --> pdb=" O ALA B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 724 removed outlier: 3.747A pdb=" N GLU B 724 " --> pdb=" O ARG B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 753 removed outlier: 3.634A pdb=" N ALA B 749 " --> pdb=" O THR B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 768 removed outlier: 3.672A pdb=" N ARG B 764 " --> pdb=" O ALA B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 870 removed outlier: 3.726A pdb=" N ALA B 868 " --> pdb=" O GLN B 865 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL B 869 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU B 870 " --> pdb=" O LEU B 867 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 865 through 870' Processing helix chain 'B' and resid 887 through 890 removed outlier: 3.932A pdb=" N LEU B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 887 through 890' Processing helix chain 'C' and resid 27 through 47 removed outlier: 3.594A pdb=" N LEU C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 43 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG C 44 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 46 " --> pdb=" O LYS C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 74 removed outlier: 3.581A pdb=" N ILE C 67 " --> pdb=" O ASP C 63 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing helix chain 'C' and resid 106 through 111 Processing helix chain 'C' and resid 123 through 142 removed outlier: 4.001A pdb=" N TYR C 127 " --> pdb=" O PRO C 123 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE C 136 " --> pdb=" O LYS C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 176 through 188 removed outlier: 3.813A pdb=" N ASN C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA C 186 " --> pdb=" O MET C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 227 removed outlier: 3.931A pdb=" N ILE C 216 " --> pdb=" O PRO C 212 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN C 221 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 246 removed outlier: 3.642A pdb=" N LEU C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG C 245 " --> pdb=" O ARG C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 removed outlier: 3.879A pdb=" N ASP C 280 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 281 " --> pdb=" O VAL C 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 277 through 281' Processing helix chain 'C' and resid 286 through 297 removed outlier: 3.814A pdb=" N MET C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASN C 292 " --> pdb=" O ASN C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 310 removed outlier: 3.745A pdb=" N SER C 310 " --> pdb=" O PRO C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 329 removed outlier: 3.648A pdb=" N GLY C 329 " --> pdb=" O ALA C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 347 removed outlier: 3.781A pdb=" N ASP C 339 " --> pdb=" O GLN C 335 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL C 340 " --> pdb=" O GLN C 336 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 343 " --> pdb=" O ASP C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 381 removed outlier: 4.219A pdb=" N ARG C 370 " --> pdb=" O ASP C 366 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET C 371 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL C 375 " --> pdb=" O MET C 371 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS C 378 " --> pdb=" O GLY C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 408 removed outlier: 3.729A pdb=" N ASP C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU C 402 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR C 405 " --> pdb=" O ALA C 401 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 407 " --> pdb=" O ASN C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 440 removed outlier: 3.596A pdb=" N ARG C 440 " --> pdb=" O ASN C 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 437 through 440' Processing helix chain 'C' and resid 474 through 477 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 494 through 505 removed outlier: 3.634A pdb=" N GLU C 499 " --> pdb=" O HIS C 495 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N MET C 500 " --> pdb=" O CYS C 496 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET C 503 " --> pdb=" O GLU C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 519 removed outlier: 3.595A pdb=" N PHE C 516 " --> pdb=" O GLU C 512 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER C 518 " --> pdb=" O ALA C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 535 removed outlier: 3.584A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN C 535 " --> pdb=" O ASN C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 550 Processing helix chain 'C' and resid 553 through 559 removed outlier: 3.647A pdb=" N ALA C 558 " --> pdb=" O PRO C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 579 Processing helix chain 'C' and resid 595 through 619 removed outlier: 3.505A pdb=" N SER C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET C 614 " --> pdb=" O MET C 610 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS C 616 " --> pdb=" O VAL C 612 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU C 619 " --> pdb=" O ARG C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 634 through 643 removed outlier: 3.528A pdb=" N LYS C 638 " --> pdb=" O SER C 634 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP C 643 " --> pdb=" O ALA C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 653 removed outlier: 3.625A pdb=" N VAL C 651 " --> pdb=" O ALA C 647 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET C 652 " --> pdb=" O VAL C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 671 removed outlier: 3.679A pdb=" N ARG C 668 " --> pdb=" O ARG C 664 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL C 670 " --> pdb=" O MET C 666 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET C 671 " --> pdb=" O MET C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 691 removed outlier: 3.588A pdb=" N GLU C 686 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA C 691 " --> pdb=" O ALA C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 697 Processing helix chain 'C' and resid 717 through 723 Processing helix chain 'C' and resid 745 through 756 Processing helix chain 'C' and resid 758 through 768 removed outlier: 3.646A pdb=" N ARG C 763 " --> pdb=" O ARG C 759 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG C 764 " --> pdb=" O ALA C 760 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP C 768 " --> pdb=" O ARG C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 791 through 796 Processing helix chain 'C' and resid 864 through 866 No H-bonds generated for 'chain 'C' and resid 864 through 866' Processing helix chain 'C' and resid 887 through 890 Processing helix chain 'D' and resid 32 through 42 removed outlier: 3.592A pdb=" N GLU D 38 " --> pdb=" O PHE D 34 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 76 removed outlier: 3.713A pdb=" N ALA D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 111 removed outlier: 3.833A pdb=" N GLU D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 141 removed outlier: 3.634A pdb=" N PHE D 126 " --> pdb=" O GLU D 122 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG D 138 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 175 removed outlier: 4.463A pdb=" N VAL D 174 " --> pdb=" O ASN D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 188 removed outlier: 3.859A pdb=" N ALA D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N MET D 182 " --> pdb=" O GLU D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.695A pdb=" N ARG D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU D 225 " --> pdb=" O GLN D 221 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA D 226 " --> pdb=" O GLY D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 244 removed outlier: 3.578A pdb=" N TRP D 238 " --> pdb=" O ASN D 234 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 297 removed outlier: 3.709A pdb=" N LEU D 289 " --> pdb=" O SER D 285 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR D 295 " --> pdb=" O MET D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 314 removed outlier: 3.592A pdb=" N THR D 313 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 328 removed outlier: 3.563A pdb=" N ILE D 326 " --> pdb=" O GLY D 322 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU D 327 " --> pdb=" O PRO D 323 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR D 328 " --> pdb=" O PHE D 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 322 through 328' Processing helix chain 'D' and resid 335 through 349 removed outlier: 3.758A pdb=" N VAL D 340 " --> pdb=" O GLN D 336 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 345 " --> pdb=" O ARG D 341 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA D 346 " --> pdb=" O LYS D 342 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET D 348 " --> pdb=" O TYR D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 376 removed outlier: 3.539A pdb=" N VAL D 372 " --> pdb=" O ALA D 368 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL D 375 " --> pdb=" O MET D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 380 removed outlier: 3.634A pdb=" N LEU D 380 " --> pdb=" O GLY D 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 377 through 380' Processing helix chain 'D' and resid 393 through 407 removed outlier: 3.640A pdb=" N ASP D 399 " --> pdb=" O ALA D 395 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE D 400 " --> pdb=" O ARG D 396 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU D 402 " --> pdb=" O LEU D 398 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU D 407 " --> pdb=" O ASN D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 477 removed outlier: 3.620A pdb=" N ILE D 477 " --> pdb=" O TYR D 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 474 through 477' Processing helix chain 'D' and resid 494 through 505 removed outlier: 3.552A pdb=" N VAL D 505 " --> pdb=" O LEU D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 514 removed outlier: 3.531A pdb=" N ALA D 514 " --> pdb=" O ASP D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 527 removed outlier: 3.682A pdb=" N VAL D 525 " --> pdb=" O PRO D 521 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG D 526 " --> pdb=" O PHE D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 537 removed outlier: 4.014A pdb=" N ILE D 533 " --> pdb=" O ARG D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 550 Processing helix chain 'D' and resid 553 through 558 Processing helix chain 'D' and resid 573 through 575 No H-bonds generated for 'chain 'D' and resid 573 through 575' Processing helix chain 'D' and resid 576 through 581 removed outlier: 3.670A pdb=" N ASN D 581 " --> pdb=" O TRP D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 618 removed outlier: 3.547A pdb=" N SER D 601 " --> pdb=" O PRO D 597 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS D 616 " --> pdb=" O VAL D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 642 Processing helix chain 'D' and resid 645 through 653 removed outlier: 3.634A pdb=" N MET D 652 " --> pdb=" O VAL D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 672 removed outlier: 3.587A pdb=" N MET D 666 " --> pdb=" O ASN D 662 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG D 668 " --> pdb=" O ARG D 664 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET D 671 " --> pdb=" O MET D 667 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 672 " --> pdb=" O ARG D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 691 removed outlier: 3.584A pdb=" N LEU D 683 " --> pdb=" O LEU D 679 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLU D 686 " --> pdb=" O ALA D 682 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 689 " --> pdb=" O GLU D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 697 Processing helix chain 'D' and resid 717 through 724 Processing helix chain 'D' and resid 746 through 755 removed outlier: 3.515A pdb=" N GLN D 752 " --> pdb=" O ILE D 748 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET D 755 " --> pdb=" O LEU D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 791 through 796 Processing helix chain 'D' and resid 864 through 868 removed outlier: 4.352A pdb=" N LEU D 867 " --> pdb=" O GLY D 864 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA D 868 " --> pdb=" O GLN D 865 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 864 through 868' Processing helix chain 'E' and resid 27 through 44 removed outlier: 3.604A pdb=" N LEU E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL E 33 " --> pdb=" O PRO E 29 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU E 36 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE E 39 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN E 41 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS E 42 " --> pdb=" O GLU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 74 removed outlier: 3.925A pdb=" N LYS E 72 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU E 74 " --> pdb=" O ASP E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 115 removed outlier: 3.665A pdb=" N SER E 112 " --> pdb=" O TYR E 108 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN E 113 " --> pdb=" O GLU E 109 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY E 115 " --> pdb=" O MET E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 141 removed outlier: 3.702A pdb=" N ILE E 131 " --> pdb=" O TYR E 127 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG E 138 " --> pdb=" O VAL E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 164 Processing helix chain 'E' and resid 170 through 175 removed outlier: 4.258A pdb=" N VAL E 174 " --> pdb=" O ASN E 170 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU E 175 " --> pdb=" O VAL E 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 170 through 175' Processing helix chain 'E' and resid 178 through 188 removed outlier: 3.561A pdb=" N MET E 182 " --> pdb=" O GLU E 178 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN E 185 " --> pdb=" O ALA E 181 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA E 186 " --> pdb=" O MET E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 227 removed outlier: 3.747A pdb=" N ILE E 216 " --> pdb=" O PRO E 212 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG E 219 " --> pdb=" O ARG E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 247 removed outlier: 3.570A pdb=" N LEU E 239 " --> pdb=" O SER E 235 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG E 241 " --> pdb=" O GLY E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 281 removed outlier: 3.698A pdb=" N ASP E 280 " --> pdb=" O VAL E 277 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL E 281 " --> pdb=" O VAL E 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 277 through 281' Processing helix chain 'E' and resid 286 through 297 removed outlier: 3.501A pdb=" N MET E 291 " --> pdb=" O ALA E 287 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR E 295 " --> pdb=" O MET E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 329 removed outlier: 3.716A pdb=" N GLY E 329 " --> pdb=" O ALA E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 348 removed outlier: 3.501A pdb=" N ARG E 341 " --> pdb=" O LEU E 337 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS E 342 " --> pdb=" O ASN E 338 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE E 343 " --> pdb=" O ASP E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 376 removed outlier: 4.196A pdb=" N MET E 371 " --> pdb=" O PRO E 367 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL E 372 " --> pdb=" O ALA E 368 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA E 373 " --> pdb=" O VAL E 369 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL E 375 " --> pdb=" O MET E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 380 removed outlier: 3.671A pdb=" N LEU E 380 " --> pdb=" O GLY E 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 377 through 380' Processing helix chain 'E' and resid 393 through 404 removed outlier: 4.188A pdb=" N ASP E 399 " --> pdb=" O ALA E 395 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU E 402 " --> pdb=" O LEU E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 440 Processing helix chain 'E' and resid 474 through 477 Processing helix chain 'E' and resid 494 through 505 removed outlier: 3.679A pdb=" N GLU E 499 " --> pdb=" O HIS E 495 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N MET E 500 " --> pdb=" O CYS E 496 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU E 501 " --> pdb=" O TYR E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 519 removed outlier: 3.531A pdb=" N TYR E 515 " --> pdb=" O SER E 511 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 535 removed outlier: 4.143A pdb=" N GLN E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN E 535 " --> pdb=" O ASN E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 550 Processing helix chain 'E' and resid 552 through 557 Processing helix chain 'E' and resid 574 through 579 Processing helix chain 'E' and resid 595 through 618 removed outlier: 3.554A pdb=" N LEU E 607 " --> pdb=" O TYR E 603 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER E 608 " --> pdb=" O ALA E 604 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL E 612 " --> pdb=" O SER E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 624 Processing helix chain 'E' and resid 633 through 643 removed outlier: 3.891A pdb=" N TRP E 637 " --> pdb=" O PRO E 633 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS E 638 " --> pdb=" O SER E 634 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA E 639 " --> pdb=" O HIS E 635 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU E 641 " --> pdb=" O TRP E 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 645 through 653 removed outlier: 3.617A pdb=" N VAL E 651 " --> pdb=" O ALA E 647 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET E 652 " --> pdb=" O VAL E 648 " (cutoff:3.500A) Processing helix chain 'E' and resid 665 through 670 removed outlier: 3.716A pdb=" N VAL E 670 " --> pdb=" O MET E 666 " (cutoff:3.500A) Processing helix chain 'E' and resid 678 through 690 removed outlier: 4.211A pdb=" N GLU E 686 " --> pdb=" O ALA E 682 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA E 687 " --> pdb=" O LEU E 683 " (cutoff:3.500A) Processing helix chain 'E' and resid 694 through 697 Processing helix chain 'E' and resid 719 through 724 removed outlier: 3.724A pdb=" N GLU E 724 " --> pdb=" O ARG E 720 " (cutoff:3.500A) Processing helix chain 'E' and resid 745 through 755 Processing helix chain 'E' and resid 757 through 768 removed outlier: 3.600A pdb=" N ARG E 763 " --> pdb=" O ARG E 759 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG E 764 " --> pdb=" O ALA E 760 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE E 765 " --> pdb=" O ALA E 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 791 through 796 Processing helix chain 'E' and resid 864 through 866 No H-bonds generated for 'chain 'E' and resid 864 through 866' Processing helix chain 'F' and resid 36 through 41 removed outlier: 3.504A pdb=" N MET F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 75 removed outlier: 3.589A pdb=" N ILE F 67 " --> pdb=" O ASP F 63 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS F 72 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA F 73 " --> pdb=" O ASP F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 112 Processing helix chain 'F' and resid 122 through 141 removed outlier: 3.597A pdb=" N ILE F 130 " --> pdb=" O PHE F 126 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE F 131 " --> pdb=" O TYR F 127 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS F 132 " --> pdb=" O SER F 128 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE F 137 " --> pdb=" O LYS F 133 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG F 138 " --> pdb=" O VAL F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 188 removed outlier: 3.638A pdb=" N ILE F 183 " --> pdb=" O HIS F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 231 removed outlier: 3.794A pdb=" N ARG F 215 " --> pdb=" O GLU F 211 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE F 216 " --> pdb=" O PRO F 212 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA F 226 " --> pdb=" O GLY F 222 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN F 228 " --> pdb=" O ILE F 224 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU F 231 " --> pdb=" O VAL F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 246 removed outlier: 3.674A pdb=" N ARG F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG F 245 " --> pdb=" O ARG F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 297 Processing helix chain 'F' and resid 323 through 328 removed outlier: 3.616A pdb=" N LEU F 327 " --> pdb=" O PRO F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 347 removed outlier: 3.652A pdb=" N ARG F 341 " --> pdb=" O LEU F 337 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 376 removed outlier: 4.096A pdb=" N GLY F 374 " --> pdb=" O ARG F 370 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL F 375 " --> pdb=" O MET F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 407 removed outlier: 3.743A pdb=" N GLN F 397 " --> pdb=" O ASN F 393 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP F 399 " --> pdb=" O ALA F 395 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE F 400 " --> pdb=" O ARG F 396 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU F 402 " --> pdb=" O LEU F 398 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR F 405 " --> pdb=" O ALA F 401 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU F 407 " --> pdb=" O ASN F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 440 removed outlier: 3.815A pdb=" N ARG F 440 " --> pdb=" O ASN F 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 437 through 440' Processing helix chain 'F' and resid 474 through 477 Processing helix chain 'F' and resid 494 through 505 removed outlier: 4.029A pdb=" N MET F 503 " --> pdb=" O GLU F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 517 removed outlier: 3.782A pdb=" N TYR F 515 " --> pdb=" O SER F 511 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE F 516 " --> pdb=" O GLU F 512 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG F 517 " --> pdb=" O ALA F 513 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 537 removed outlier: 3.581A pdb=" N ASN F 531 " --> pdb=" O PHE F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 550 Processing helix chain 'F' and resid 552 through 558 removed outlier: 3.554A pdb=" N ALA F 558 " --> pdb=" O PRO F 554 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 575 No H-bonds generated for 'chain 'F' and resid 573 through 575' Processing helix chain 'F' and resid 576 through 581 removed outlier: 3.542A pdb=" N PHE F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN F 581 " --> pdb=" O TRP F 577 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 576 through 581' Processing helix chain 'F' and resid 595 through 618 removed outlier: 3.571A pdb=" N SER F 601 " --> pdb=" O PRO F 597 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER F 605 " --> pdb=" O SER F 601 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER F 608 " --> pdb=" O ALA F 604 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET F 614 " --> pdb=" O MET F 610 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS F 616 " --> pdb=" O VAL F 612 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER F 618 " --> pdb=" O MET F 614 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 634 through 642 Processing helix chain 'F' and resid 645 through 657 removed outlier: 3.613A pdb=" N MET F 652 " --> pdb=" O VAL F 648 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU F 654 " --> pdb=" O ALA F 650 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER F 655 " --> pdb=" O VAL F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 671 removed outlier: 3.540A pdb=" N MET F 666 " --> pdb=" O ASN F 662 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG F 668 " --> pdb=" O ARG F 664 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET F 671 " --> pdb=" O MET F 667 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 691 removed outlier: 3.718A pdb=" N LEU F 683 " --> pdb=" O LEU F 679 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU F 686 " --> pdb=" O ALA F 682 " (cutoff:3.500A) Processing helix chain 'F' and resid 693 through 698 removed outlier: 3.508A pdb=" N ASP F 696 " --> pdb=" O ASP F 693 " (cutoff:3.500A) Processing helix chain 'F' and resid 719 through 724 removed outlier: 3.738A pdb=" N GLU F 724 " --> pdb=" O ARG F 720 " (cutoff:3.500A) Processing helix chain 'F' and resid 745 through 755 removed outlier: 3.607A pdb=" N ALA F 749 " --> pdb=" O THR F 745 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET F 755 " --> pdb=" O LEU F 751 " (cutoff:3.500A) Processing helix chain 'F' and resid 757 through 768 removed outlier: 3.502A pdb=" N ARG F 764 " --> pdb=" O ALA F 760 " (cutoff:3.500A) Processing helix chain 'F' and resid 835 through 840 removed outlier: 4.316A pdb=" N LEU F 839 " --> pdb=" O THR F 835 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL F 840 " --> pdb=" O PRO F 836 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 835 through 840' Processing helix chain 'F' and resid 887 through 891 removed outlier: 3.502A pdb=" N LEU F 890 " --> pdb=" O THR F 887 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS F 891 " --> pdb=" O GLN F 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 887 through 891' Processing helix chain 'G' and resid 27 through 37 removed outlier: 3.866A pdb=" N VAL G 33 " --> pdb=" O PRO G 29 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU G 36 " --> pdb=" O SER G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 47 removed outlier: 3.540A pdb=" N VAL G 43 " --> pdb=" O ILE G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 74 removed outlier: 3.699A pdb=" N LYS G 72 " --> pdb=" O LEU G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 113 removed outlier: 3.842A pdb=" N SER G 112 " --> pdb=" O TYR G 108 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN G 113 " --> pdb=" O GLU G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 141 removed outlier: 3.693A pdb=" N PHE G 126 " --> pdb=" O GLU G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 175 removed outlier: 3.556A pdb=" N LEU G 175 " --> pdb=" O LEU G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 188 removed outlier: 4.072A pdb=" N ALA G 181 " --> pdb=" O ALA G 177 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA G 186 " --> pdb=" O MET G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 227 removed outlier: 3.693A pdb=" N ILE G 216 " --> pdb=" O PRO G 212 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR G 217 " --> pdb=" O VAL G 213 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE G 224 " --> pdb=" O LEU G 220 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA G 226 " --> pdb=" O GLY G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 246 removed outlier: 3.523A pdb=" N GLY G 237 " --> pdb=" O ARG G 233 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP G 238 " --> pdb=" O ASN G 234 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG G 241 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG G 245 " --> pdb=" O ARG G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 281 removed outlier: 3.645A pdb=" N ASP G 280 " --> pdb=" O VAL G 277 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL G 281 " --> pdb=" O VAL G 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 277 through 281' Processing helix chain 'G' and resid 286 through 297 removed outlier: 3.968A pdb=" N ASN G 292 " --> pdb=" O ASN G 288 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR G 295 " --> pdb=" O MET G 291 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU G 297 " --> pdb=" O ILE G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 329 Processing helix chain 'G' and resid 333 through 349 removed outlier: 3.702A pdb=" N ARG G 341 " --> pdb=" O LEU G 337 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET G 348 " --> pdb=" O TYR G 344 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE G 349 " --> pdb=" O LEU G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 378 removed outlier: 4.409A pdb=" N ARG G 370 " --> pdb=" O ASP G 366 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET G 371 " --> pdb=" O PRO G 367 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL G 375 " --> pdb=" O MET G 371 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS G 378 " --> pdb=" O GLY G 374 " (cutoff:3.500A) Processing helix chain 'G' and resid 393 through 407 removed outlier: 3.963A pdb=" N ASP G 399 " --> pdb=" O ALA G 395 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE G 400 " --> pdb=" O ARG G 396 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA G 401 " --> pdb=" O GLN G 397 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU G 402 " --> pdb=" O LEU G 398 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU G 407 " --> pdb=" O ASN G 403 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 440 Processing helix chain 'G' and resid 474 through 477 Processing helix chain 'G' and resid 478 through 483 removed outlier: 3.981A pdb=" N LEU G 482 " --> pdb=" O SER G 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 494 through 505 removed outlier: 3.658A pdb=" N GLU G 499 " --> pdb=" O HIS G 495 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N MET G 500 " --> pdb=" O CYS G 496 " (cutoff:3.500A) Processing helix chain 'G' and resid 512 through 518 removed outlier: 3.535A pdb=" N SER G 518 " --> pdb=" O ALA G 514 " (cutoff:3.500A) Processing helix chain 'G' and resid 519 through 535 removed outlier: 3.734A pdb=" N GLN G 532 " --> pdb=" O ALA G 528 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN G 535 " --> pdb=" O ASN G 531 " (cutoff:3.500A) Processing helix chain 'G' and resid 545 through 550 removed outlier: 3.531A pdb=" N ASN G 550 " --> pdb=" O ASP G 546 " (cutoff:3.500A) Processing helix chain 'G' and resid 552 through 559 removed outlier: 3.927A pdb=" N ALA G 558 " --> pdb=" O PRO G 554 " (cutoff:3.500A) Processing helix chain 'G' and resid 574 through 579 Processing helix chain 'G' and resid 595 through 618 removed outlier: 3.857A pdb=" N MET G 610 " --> pdb=" O GLU G 606 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP G 613 " --> pdb=" O VAL G 609 " (cutoff:3.500A) Processing helix chain 'G' and resid 619 through 624 removed outlier: 3.575A pdb=" N PHE G 624 " --> pdb=" O MET G 620 " (cutoff:3.500A) Processing helix chain 'G' and resid 633 through 643 removed outlier: 3.792A pdb=" N TRP G 637 " --> pdb=" O PRO G 633 " (cutoff:3.500A) Processing helix chain 'G' and resid 645 through 653 removed outlier: 3.648A pdb=" N LYS G 649 " --> pdb=" O PRO G 645 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL G 651 " --> pdb=" O ALA G 647 " (cutoff:3.500A) Processing helix chain 'G' and resid 662 through 671 removed outlier: 3.620A pdb=" N MET G 666 " --> pdb=" O ASN G 662 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG G 668 " --> pdb=" O ARG G 664 " (cutoff:3.500A) Processing helix chain 'G' and resid 678 through 688 removed outlier: 3.540A pdb=" N ALA G 682 " --> pdb=" O SER G 678 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU G 686 " --> pdb=" O ALA G 682 " (cutoff:3.500A) Processing helix chain 'G' and resid 694 through 697 Processing helix chain 'G' and resid 717 through 724 removed outlier: 3.501A pdb=" N GLU G 724 " --> pdb=" O ARG G 720 " (cutoff:3.500A) Processing helix chain 'G' and resid 745 through 756 removed outlier: 3.617A pdb=" N ASN G 754 " --> pdb=" O ARG G 750 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET G 755 " --> pdb=" O LEU G 751 " (cutoff:3.500A) Processing helix chain 'G' and resid 757 through 768 removed outlier: 3.583A pdb=" N ARG G 763 " --> pdb=" O ARG G 759 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG G 764 " --> pdb=" O ALA G 760 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE G 765 " --> pdb=" O ALA G 761 " (cutoff:3.500A) Processing helix chain 'G' and resid 791 through 796 Processing helix chain 'G' and resid 887 through 890 removed outlier: 3.841A pdb=" N LEU G 890 " --> pdb=" O THR G 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 887 through 890' Processing helix chain 'H' and resid 35 through 47 removed outlier: 3.947A pdb=" N MET H 40 " --> pdb=" O LEU H 36 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN H 41 " --> pdb=" O GLN H 37 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN H 45 " --> pdb=" O GLN H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 75 removed outlier: 4.328A pdb=" N ILE H 67 " --> pdb=" O ASP H 63 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP H 70 " --> pdb=" O LYS H 66 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE H 71 " --> pdb=" O ILE H 67 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS H 72 " --> pdb=" O LEU H 68 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA H 73 " --> pdb=" O ASP H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 Processing helix chain 'H' and resid 123 through 141 removed outlier: 3.765A pdb=" N THR H 129 " --> pdb=" O LYS H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 175 removed outlier: 4.713A pdb=" N VAL H 174 " --> pdb=" O ASN H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 186 removed outlier: 3.511A pdb=" N ALA H 186 " --> pdb=" O MET H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 190 removed outlier: 3.725A pdb=" N SER H 190 " --> pdb=" O LEU H 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 187 through 190' Processing helix chain 'H' and resid 210 through 230 removed outlier: 3.707A pdb=" N ARG H 215 " --> pdb=" O GLU H 211 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE H 216 " --> pdb=" O PRO H 212 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA H 226 " --> pdb=" O GLY H 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 243 removed outlier: 3.512A pdb=" N LEU H 239 " --> pdb=" O SER H 235 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 297 removed outlier: 4.375A pdb=" N ASN H 292 " --> pdb=" O ASN H 288 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR H 295 " --> pdb=" O MET H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 309 through 314 removed outlier: 3.756A pdb=" N THR H 313 " --> pdb=" O ILE H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 322 through 328 removed outlier: 3.678A pdb=" N LEU H 327 " --> pdb=" O PRO H 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 347 removed outlier: 3.698A pdb=" N LYS H 342 " --> pdb=" O ASN H 338 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU H 345 " --> pdb=" O ARG H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 368 through 381 removed outlier: 3.793A pdb=" N GLY H 374 " --> pdb=" O ARG H 370 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL H 375 " --> pdb=" O MET H 371 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU H 379 " --> pdb=" O VAL H 375 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE H 381 " --> pdb=" O GLY H 377 " (cutoff:3.500A) Processing helix chain 'H' and resid 393 through 406 removed outlier: 3.855A pdb=" N ASP H 399 " --> pdb=" O ALA H 395 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU H 402 " --> pdb=" O LEU H 398 " (cutoff:3.500A) Processing helix chain 'H' and resid 437 through 440 Processing helix chain 'H' and resid 474 through 477 Processing helix chain 'H' and resid 494 through 507 Processing helix chain 'H' and resid 509 through 519 removed outlier: 4.177A pdb=" N TYR H 515 " --> pdb=" O SER H 511 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE H 516 " --> pdb=" O GLU H 512 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER H 518 " --> pdb=" O ALA H 514 " (cutoff:3.500A) Processing helix chain 'H' and resid 519 through 537 removed outlier: 3.552A pdb=" N PHE H 527 " --> pdb=" O HIS H 523 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLN H 532 " --> pdb=" O ALA H 528 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN H 535 " --> pdb=" O ASN H 531 " (cutoff:3.500A) Processing helix chain 'H' and resid 545 through 550 removed outlier: 3.631A pdb=" N ASN H 550 " --> pdb=" O ASP H 546 " (cutoff:3.500A) Processing helix chain 'H' and resid 553 through 558 removed outlier: 3.673A pdb=" N ALA H 558 " --> pdb=" O PRO H 554 " (cutoff:3.500A) Processing helix chain 'H' and resid 574 through 581 removed outlier: 3.607A pdb=" N PHE H 580 " --> pdb=" O LEU H 576 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN H 581 " --> pdb=" O TRP H 577 " (cutoff:3.500A) Processing helix chain 'H' and resid 595 through 618 removed outlier: 3.545A pdb=" N SER H 601 " --> pdb=" O PRO H 597 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER H 605 " --> pdb=" O SER H 601 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER H 608 " --> pdb=" O ALA H 604 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL H 609 " --> pdb=" O SER H 605 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL H 612 " --> pdb=" O SER H 608 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER H 618 " --> pdb=" O MET H 614 " (cutoff:3.500A) Processing helix chain 'H' and resid 619 through 624 Processing helix chain 'H' and resid 634 through 642 removed outlier: 3.616A pdb=" N LYS H 638 " --> pdb=" O SER H 634 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU H 641 " --> pdb=" O TRP H 637 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN H 642 " --> pdb=" O LYS H 638 " (cutoff:3.500A) Processing helix chain 'H' and resid 645 through 656 removed outlier: 4.383A pdb=" N SER H 655 " --> pdb=" O VAL H 651 " (cutoff:3.500A) Processing helix chain 'H' and resid 662 through 672 removed outlier: 3.511A pdb=" N MET H 666 " --> pdb=" O ASN H 662 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG H 668 " --> pdb=" O ARG H 664 " (cutoff:3.500A) Processing helix chain 'H' and resid 678 through 691 removed outlier: 3.684A pdb=" N LEU H 683 " --> pdb=" O LEU H 679 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU H 686 " --> pdb=" O ALA H 682 " (cutoff:3.500A) Processing helix chain 'H' and resid 717 through 723 Processing helix chain 'H' and resid 737 through 739 No H-bonds generated for 'chain 'H' and resid 737 through 739' Processing helix chain 'H' and resid 745 through 755 removed outlier: 3.570A pdb=" N MET H 755 " --> pdb=" O LEU H 751 " (cutoff:3.500A) Processing helix chain 'H' and resid 757 through 769 removed outlier: 3.541A pdb=" N ILE H 765 " --> pdb=" O ALA H 761 " (cutoff:3.500A) Processing helix chain 'H' and resid 864 through 866 No H-bonds generated for 'chain 'H' and resid 864 through 866' Processing helix chain 'H' and resid 887 through 891 removed outlier: 3.899A pdb=" N LYS H 891 " --> pdb=" O GLN H 888 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 44 removed outlier: 4.318A pdb=" N VAL I 33 " --> pdb=" O PRO I 29 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU I 36 " --> pdb=" O SER I 32 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS I 42 " --> pdb=" O GLU I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 50 removed outlier: 3.845A pdb=" N TYR I 50 " --> pdb=" O VAL I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 75 removed outlier: 3.506A pdb=" N LYS I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA I 75 " --> pdb=" O ILE I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 111 removed outlier: 3.842A pdb=" N GLU I 109 " --> pdb=" O ASP I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 141 Processing helix chain 'I' and resid 161 through 164 Processing helix chain 'I' and resid 176 through 188 removed outlier: 4.194A pdb=" N ALA I 181 " --> pdb=" O ALA I 177 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA I 186 " --> pdb=" O MET I 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 227 removed outlier: 4.248A pdb=" N ILE I 216 " --> pdb=" O PRO I 212 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG I 219 " --> pdb=" O ARG I 215 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE I 224 " --> pdb=" O LEU I 220 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU I 225 " --> pdb=" O GLN I 221 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA I 226 " --> pdb=" O GLY I 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 247 removed outlier: 3.745A pdb=" N ARG I 241 " --> pdb=" O GLY I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 277 through 281 removed outlier: 3.830A pdb=" N ASP I 280 " --> pdb=" O VAL I 277 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL I 281 " --> pdb=" O VAL I 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 277 through 281' Processing helix chain 'I' and resid 284 through 297 removed outlier: 3.587A pdb=" N LEU I 289 " --> pdb=" O SER I 285 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR I 295 " --> pdb=" O MET I 291 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS I 296 " --> pdb=" O ASN I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 306 through 310 removed outlier: 3.766A pdb=" N SER I 310 " --> pdb=" O PRO I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 324 through 329 removed outlier: 3.732A pdb=" N GLY I 329 " --> pdb=" O ALA I 325 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 349 removed outlier: 3.767A pdb=" N LYS I 342 " --> pdb=" O ASN I 338 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU I 345 " --> pdb=" O ARG I 341 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE I 349 " --> pdb=" O LEU I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 367 through 373 removed outlier: 3.869A pdb=" N MET I 371 " --> pdb=" O PRO I 367 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 380 removed outlier: 4.206A pdb=" N GLY I 377 " --> pdb=" O GLY I 374 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU I 380 " --> pdb=" O GLY I 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 393 through 406 removed outlier: 3.823A pdb=" N ASP I 399 " --> pdb=" O ALA I 395 " (cutoff:3.500A) Processing helix chain 'I' and resid 437 through 440 removed outlier: 3.756A pdb=" N ARG I 440 " --> pdb=" O ASN I 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 437 through 440' Processing helix chain 'I' and resid 474 through 477 Processing helix chain 'I' and resid 494 through 505 removed outlier: 4.188A pdb=" N MET I 500 " --> pdb=" O CYS I 496 " (cutoff:3.500A) Processing helix chain 'I' and resid 511 through 518 removed outlier: 3.539A pdb=" N TYR I 515 " --> pdb=" O SER I 511 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 535 removed outlier: 3.989A pdb=" N GLN I 532 " --> pdb=" O ALA I 528 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN I 535 " --> pdb=" O ASN I 531 " (cutoff:3.500A) Processing helix chain 'I' and resid 545 through 550 Processing helix chain 'I' and resid 553 through 558 removed outlier: 4.153A pdb=" N ALA I 558 " --> pdb=" O PRO I 554 " (cutoff:3.500A) Processing helix chain 'I' and resid 574 through 579 Processing helix chain 'I' and resid 595 through 618 removed outlier: 3.780A pdb=" N LEU I 617 " --> pdb=" O ASP I 613 " (cutoff:3.500A) Processing helix chain 'I' and resid 619 through 624 Processing helix chain 'I' and resid 633 through 641 removed outlier: 3.711A pdb=" N TRP I 637 " --> pdb=" O PRO I 633 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU I 641 " --> pdb=" O TRP I 637 " (cutoff:3.500A) Processing helix chain 'I' and resid 645 through 653 Processing helix chain 'I' and resid 656 through 660 removed outlier: 3.848A pdb=" N ASN I 659 " --> pdb=" O HIS I 656 " (cutoff:3.500A) Processing helix chain 'I' and resid 662 through 670 removed outlier: 3.669A pdb=" N MET I 666 " --> pdb=" O ASN I 662 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET I 667 " --> pdb=" O ILE I 663 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG I 668 " --> pdb=" O ARG I 664 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL I 670 " --> pdb=" O MET I 666 " (cutoff:3.500A) Processing helix chain 'I' and resid 678 through 690 removed outlier: 4.275A pdb=" N GLU I 686 " --> pdb=" O ALA I 682 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA I 687 " --> pdb=" O LEU I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 694 through 697 Processing helix chain 'I' and resid 717 through 724 Processing helix chain 'I' and resid 745 through 755 removed outlier: 3.784A pdb=" N LEU I 751 " --> pdb=" O GLU I 747 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA I 753 " --> pdb=" O ALA I 749 " (cutoff:3.500A) Processing helix chain 'I' and resid 757 through 768 removed outlier: 3.719A pdb=" N ILE I 765 " --> pdb=" O ALA I 761 " (cutoff:3.500A) Processing helix chain 'I' and resid 791 through 797 Processing helix chain 'I' and resid 864 through 866 No H-bonds generated for 'chain 'I' and resid 864 through 866' Processing helix chain 'I' and resid 887 through 890 removed outlier: 3.601A pdb=" N LEU I 890 " --> pdb=" O THR I 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 887 through 890' Processing helix chain 'J' and resid 38 through 43 Processing helix chain 'J' and resid 43 through 52 removed outlier: 4.324A pdb=" N ASP J 49 " --> pdb=" O GLN J 45 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR J 50 " --> pdb=" O VAL J 46 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET J 51 " --> pdb=" O GLN J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 75 removed outlier: 3.763A pdb=" N ILE J 67 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE J 71 " --> pdb=" O ILE J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 112 Processing helix chain 'J' and resid 122 through 141 removed outlier: 3.567A pdb=" N PHE J 126 " --> pdb=" O GLU J 122 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE J 137 " --> pdb=" O LYS J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 188 removed outlier: 3.570A pdb=" N ALA J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET J 182 " --> pdb=" O GLU J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 230 removed outlier: 3.705A pdb=" N ARG J 215 " --> pdb=" O GLU J 211 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE J 216 " --> pdb=" O PRO J 212 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA J 226 " --> pdb=" O GLY J 222 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU J 229 " --> pdb=" O GLU J 225 " (cutoff:3.500A) Processing helix chain 'J' and resid 230 through 246 removed outlier: 3.568A pdb=" N GLU J 240 " --> pdb=" O ILE J 236 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG J 241 " --> pdb=" O GLY J 237 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG J 245 " --> pdb=" O ARG J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 261 No H-bonds generated for 'chain 'J' and resid 259 through 261' Processing helix chain 'J' and resid 275 through 280 removed outlier: 3.636A pdb=" N TRP J 279 " --> pdb=" O PRO J 275 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 297 removed outlier: 3.585A pdb=" N THR J 295 " --> pdb=" O MET J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 312 Processing helix chain 'J' and resid 322 through 328 removed outlier: 3.582A pdb=" N ILE J 326 " --> pdb=" O GLY J 322 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU J 327 " --> pdb=" O PRO J 323 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR J 328 " --> pdb=" O PHE J 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 322 through 328' Processing helix chain 'J' and resid 336 through 349 removed outlier: 3.625A pdb=" N LEU J 345 " --> pdb=" O ARG J 341 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA J 346 " --> pdb=" O LYS J 342 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET J 348 " --> pdb=" O TYR J 344 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE J 349 " --> pdb=" O LEU J 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 366 through 371 Processing helix chain 'J' and resid 371 through 381 removed outlier: 3.560A pdb=" N VAL J 375 " --> pdb=" O MET J 371 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY J 377 " --> pdb=" O ALA J 373 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HIS J 378 " --> pdb=" O GLY J 374 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU J 379 " --> pdb=" O VAL J 375 " (cutoff:3.500A) Processing helix chain 'J' and resid 393 through 407 removed outlier: 3.753A pdb=" N GLN J 397 " --> pdb=" O ASN J 393 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP J 399 " --> pdb=" O ALA J 395 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU J 402 " --> pdb=" O LEU J 398 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR J 405 " --> pdb=" O ALA J 401 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU J 407 " --> pdb=" O ASN J 403 " (cutoff:3.500A) Processing helix chain 'J' and resid 437 through 440 removed outlier: 3.538A pdb=" N ARG J 440 " --> pdb=" O ASN J 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 437 through 440' Processing helix chain 'J' and resid 473 through 477 removed outlier: 3.739A pdb=" N GLY J 476 " --> pdb=" O ARG J 473 " (cutoff:3.500A) Processing helix chain 'J' and resid 494 through 507 removed outlier: 3.632A pdb=" N LEU J 501 " --> pdb=" O TYR J 497 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG J 502 " --> pdb=" O ASN J 498 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET J 503 " --> pdb=" O GLU J 499 " (cutoff:3.500A) Processing helix chain 'J' and resid 509 through 514 Processing helix chain 'J' and resid 519 through 537 removed outlier: 3.534A pdb=" N VAL J 525 " --> pdb=" O PRO J 521 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG J 529 " --> pdb=" O VAL J 525 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN J 532 " --> pdb=" O ALA J 528 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN J 535 " --> pdb=" O ASN J 531 " (cutoff:3.500A) Processing helix chain 'J' and resid 545 through 550 Processing helix chain 'J' and resid 552 through 558 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.686A pdb=" N PHE J 580 " --> pdb=" O LEU J 576 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN J 581 " --> pdb=" O TRP J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 595 through 618 removed outlier: 3.892A pdb=" N SER J 601 " --> pdb=" O PRO J 597 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER J 605 " --> pdb=" O SER J 601 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER J 608 " --> pdb=" O ALA J 604 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL J 609 " --> pdb=" O SER J 605 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS J 616 " --> pdb=" O VAL J 612 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER J 618 " --> pdb=" O MET J 614 " (cutoff:3.500A) Processing helix chain 'J' and resid 619 through 624 Processing helix chain 'J' and resid 632 through 642 removed outlier: 4.209A pdb=" N PHE J 636 " --> pdb=" O ARG J 632 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TRP J 637 " --> pdb=" O PRO J 633 " (cutoff:3.500A) Processing helix chain 'J' and resid 645 through 653 Processing helix chain 'J' and resid 662 through 672 removed outlier: 3.630A pdb=" N MET J 666 " --> pdb=" O ASN J 662 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG J 668 " --> pdb=" O ARG J 664 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET J 671 " --> pdb=" O MET J 667 " (cutoff:3.500A) Processing helix chain 'J' and resid 678 through 683 removed outlier: 3.560A pdb=" N LEU J 683 " --> pdb=" O LEU J 679 " (cutoff:3.500A) Processing helix chain 'J' and resid 683 through 691 Processing helix chain 'J' and resid 693 through 698 removed outlier: 3.551A pdb=" N ASP J 696 " --> pdb=" O ASP J 693 " (cutoff:3.500A) Processing helix chain 'J' and resid 718 through 723 Processing helix chain 'J' and resid 737 through 739 No H-bonds generated for 'chain 'J' and resid 737 through 739' Processing helix chain 'J' and resid 745 through 755 removed outlier: 3.565A pdb=" N ALA J 749 " --> pdb=" O THR J 745 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET J 755 " --> pdb=" O LEU J 751 " (cutoff:3.500A) Processing helix chain 'J' and resid 758 through 768 removed outlier: 3.734A pdb=" N ARG J 764 " --> pdb=" O ALA J 760 " (cutoff:3.500A) Processing helix chain 'J' and resid 864 through 869 removed outlier: 4.252A pdb=" N LEU J 867 " --> pdb=" O GLY J 864 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL J 869 " --> pdb=" O ILE J 866 " (cutoff:3.500A) Processing helix chain 'J' and resid 887 through 891 removed outlier: 3.503A pdb=" N LEU J 890 " --> pdb=" O THR J 887 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS J 891 " --> pdb=" O GLN J 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 887 through 891' Processing helix chain 'K' and resid 8 through 12 removed outlier: 3.570A pdb=" N ARG K 11 " --> pdb=" O ARG K 8 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE K 12 " --> pdb=" O PRO K 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 8 through 12' Processing helix chain 'K' and resid 27 through 50 removed outlier: 3.900A pdb=" N VAL K 33 " --> pdb=" O PRO K 29 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE K 39 " --> pdb=" O ALA K 35 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS K 42 " --> pdb=" O GLU K 38 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN K 45 " --> pdb=" O GLN K 41 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA K 48 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR K 50 " --> pdb=" O VAL K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 73 Processing helix chain 'K' and resid 74 through 77 Processing helix chain 'K' and resid 106 through 111 Processing helix chain 'K' and resid 122 through 141 removed outlier: 3.682A pdb=" N PHE K 126 " --> pdb=" O GLU K 122 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR K 127 " --> pdb=" O PRO K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 175 removed outlier: 3.555A pdb=" N LEU K 175 " --> pdb=" O LEU K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 188 removed outlier: 3.676A pdb=" N ALA K 181 " --> pdb=" O ALA K 177 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA K 186 " --> pdb=" O MET K 182 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP K 188 " --> pdb=" O GLN K 184 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 227 removed outlier: 3.741A pdb=" N ILE K 216 " --> pdb=" O PRO K 212 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE K 224 " --> pdb=" O LEU K 220 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA K 226 " --> pdb=" O GLY K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 247 removed outlier: 3.850A pdb=" N SER K 235 " --> pdb=" O GLU K 231 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TRP K 238 " --> pdb=" O ASN K 234 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG K 241 " --> pdb=" O GLY K 237 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG K 245 " --> pdb=" O ARG K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 277 through 281 removed outlier: 3.711A pdb=" N ASP K 280 " --> pdb=" O VAL K 277 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL K 281 " --> pdb=" O VAL K 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 277 through 281' Processing helix chain 'K' and resid 284 through 297 removed outlier: 3.584A pdb=" N ASN K 288 " --> pdb=" O SER K 284 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS K 296 " --> pdb=" O ASN K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 329 removed outlier: 3.805A pdb=" N GLY K 329 " --> pdb=" O ALA K 325 " (cutoff:3.500A) Processing helix chain 'K' and resid 333 through 347 removed outlier: 3.664A pdb=" N ASN K 338 " --> pdb=" O ALA K 334 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL K 340 " --> pdb=" O GLN K 336 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE K 343 " --> pdb=" O ASP K 339 " (cutoff:3.500A) Processing helix chain 'K' and resid 366 through 373 removed outlier: 4.308A pdb=" N ARG K 370 " --> pdb=" O ASP K 366 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET K 371 " --> pdb=" O PRO K 367 " (cutoff:3.500A) Processing helix chain 'K' and resid 374 through 379 Processing helix chain 'K' and resid 393 through 406 removed outlier: 3.525A pdb=" N ASP K 399 " --> pdb=" O ALA K 395 " (cutoff:3.500A) Processing helix chain 'K' and resid 437 through 440 removed outlier: 3.704A pdb=" N ARG K 440 " --> pdb=" O ASN K 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 437 through 440' Processing helix chain 'K' and resid 474 through 477 Processing helix chain 'K' and resid 494 through 505 removed outlier: 3.693A pdb=" N GLU K 499 " --> pdb=" O HIS K 495 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N MET K 500 " --> pdb=" O CYS K 496 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG K 502 " --> pdb=" O ASN K 498 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU K 504 " --> pdb=" O MET K 500 " (cutoff:3.500A) Processing helix chain 'K' and resid 509 through 519 removed outlier: 3.638A pdb=" N TYR K 515 " --> pdb=" O SER K 511 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE K 516 " --> pdb=" O GLU K 512 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER K 518 " --> pdb=" O ALA K 514 " (cutoff:3.500A) Processing helix chain 'K' and resid 519 through 534 removed outlier: 3.510A pdb=" N PHE K 527 " --> pdb=" O HIS K 523 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA K 528 " --> pdb=" O MET K 524 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN K 532 " --> pdb=" O ALA K 528 " (cutoff:3.500A) Processing helix chain 'K' and resid 545 through 550 Processing helix chain 'K' and resid 552 through 559 removed outlier: 4.020A pdb=" N ALA K 558 " --> pdb=" O PRO K 554 " (cutoff:3.500A) Processing helix chain 'K' and resid 574 through 579 Processing helix chain 'K' and resid 595 through 616 Processing helix chain 'K' and resid 619 through 624 Processing helix chain 'K' and resid 633 through 643 removed outlier: 3.932A pdb=" N TRP K 637 " --> pdb=" O PRO K 633 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS K 638 " --> pdb=" O SER K 634 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU K 641 " --> pdb=" O TRP K 637 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP K 643 " --> pdb=" O ALA K 639 " (cutoff:3.500A) Processing helix chain 'K' and resid 645 through 653 removed outlier: 3.587A pdb=" N VAL K 651 " --> pdb=" O ALA K 647 " (cutoff:3.500A) Processing helix chain 'K' and resid 662 through 671 removed outlier: 3.510A pdb=" N MET K 666 " --> pdb=" O ASN K 662 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG K 668 " --> pdb=" O ARG K 664 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP K 669 " --> pdb=" O ASP K 665 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL K 670 " --> pdb=" O MET K 666 " (cutoff:3.500A) Processing helix chain 'K' and resid 678 through 690 removed outlier: 4.137A pdb=" N GLU K 686 " --> pdb=" O ALA K 682 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA K 687 " --> pdb=" O LEU K 683 " (cutoff:3.500A) Processing helix chain 'K' and resid 717 through 723 Processing helix chain 'K' and resid 745 through 755 removed outlier: 3.504A pdb=" N ALA K 749 " --> pdb=" O THR K 745 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA K 753 " --> pdb=" O ALA K 749 " (cutoff:3.500A) Processing helix chain 'K' and resid 757 through 768 removed outlier: 3.579A pdb=" N ARG K 763 " --> pdb=" O ARG K 759 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG K 764 " --> pdb=" O ALA K 760 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE K 765 " --> pdb=" O ALA K 761 " (cutoff:3.500A) Processing helix chain 'K' and resid 791 through 796 removed outlier: 3.531A pdb=" N LEU K 795 " --> pdb=" O PRO K 791 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN K 796 " --> pdb=" O ASP K 792 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 791 through 796' Processing helix chain 'K' and resid 864 through 866 No H-bonds generated for 'chain 'K' and resid 864 through 866' Processing helix chain 'K' and resid 887 through 890 removed outlier: 3.705A pdb=" N LEU K 890 " --> pdb=" O THR K 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 887 through 890' Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=AA3, first strand: chain 'A' and resid 230 through 231 Processing sheet with id=AA4, first strand: chain 'A' and resid 278 through 285 removed outlier: 3.703A pdb=" N GLN A 283 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LYS A 299 " --> pdb=" O GLN A 283 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR A 285 " --> pdb=" O TYR A 297 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TYR A 297 " --> pdb=" O THR A 285 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 521 through 524 removed outlier: 3.897A pdb=" N SER A 524 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR A 508 " --> pdb=" O SER A 524 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A 509 " --> pdb=" O ASN A 652 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR A 649 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 717 " --> pdb=" O THR A 649 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 755 through 762 removed outlier: 3.550A pdb=" N THR A 755 " --> pdb=" O LYS A 771 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TYR A 769 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU A 759 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU A 767 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TYR A 761 " --> pdb=" O ASP A 765 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ASP A 765 " --> pdb=" O TYR A 761 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 657 through 660 removed outlier: 3.635A pdb=" N PHE A 658 " --> pdb=" O ILE A 706 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N SER A 689 " --> pdb=" O THR A 709 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLY A 711 " --> pdb=" O SER A 689 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 809 through 811 removed outlier: 4.092A pdb=" N HIS A 816 " --> pdb=" O VAL A 823 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1069 through 1071 removed outlier: 6.707A pdb=" N ILE A1070 " --> pdb=" O LYS A1195 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id=AB2, first strand: chain 'B' and resid 82 through 83 removed outlier: 7.221A pdb=" N LEU B 145 " --> pdb=" O TYR B 877 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 90 through 93 removed outlier: 4.044A pdb=" N LEU B 102 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 861 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU B 859 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 150 through 152 Processing sheet with id=AB5, first strand: chain 'B' and resid 248 through 250 Processing sheet with id=AB6, first strand: chain 'B' and resid 263 through 266 Processing sheet with id=AB7, first strand: chain 'B' and resid 299 through 303 removed outlier: 6.792A pdb=" N GLU B 301 " --> pdb=" O PRO B 586 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE B 303 " --> pdb=" O PHE B 584 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N PHE B 584 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 353 through 357 Processing sheet with id=AB9, first strand: chain 'B' and resid 383 through 384 removed outlier: 4.231A pdb=" N PHE B 387 " --> pdb=" O GLY B 384 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 416 through 418 Processing sheet with id=AC2, first strand: chain 'B' and resid 457 through 459 Processing sheet with id=AC3, first strand: chain 'B' and resid 699 through 700 Processing sheet with id=AC4, first strand: chain 'B' and resid 741 through 744 removed outlier: 3.649A pdb=" N VAL B 772 " --> pdb=" O MET B 705 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE B 774 " --> pdb=" O VAL B 703 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL B 703 " --> pdb=" O PHE B 774 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 708 through 709 Processing sheet with id=AC6, first strand: chain 'B' and resid 800 through 807 removed outlier: 4.823A pdb=" N LYS C 895 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 22 through 26 removed outlier: 4.388A pdb=" N SER C 24 " --> pdb=" O TYR C 302 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR C 299 " --> pdb=" O THR C 587 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 52 through 53 Processing sheet with id=AC9, first strand: chain 'C' and resid 81 through 83 Processing sheet with id=AD1, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.901A pdb=" N LEU C 102 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 859 " --> pdb=" O ARG C 103 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 150 through 153 Processing sheet with id=AD3, first strand: chain 'C' and resid 206 through 207 removed outlier: 3.586A pdb=" N ARG C 872 " --> pdb=" O GLY C 207 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 264 through 266 removed outlier: 6.074A pdb=" N ILE C 264 " --> pdb=" O MET C 884 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 313 through 315 removed outlier: 6.841A pdb=" N ILE C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AD7, first strand: chain 'C' and resid 416 through 418 removed outlier: 3.667A pdb=" N ASN C 417 " --> pdb=" O GLN C 428 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 457 through 458 Processing sheet with id=AD9, first strand: chain 'C' and resid 699 through 700 removed outlier: 3.555A pdb=" N ARG C 782 " --> pdb=" O THR C 821 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 741 through 743 removed outlier: 6.571A pdb=" N VAL C 742 " --> pdb=" O ARG C 773 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C 772 " --> pdb=" O MET C 705 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AE3, first strand: chain 'D' and resid 81 through 83 removed outlier: 6.996A pdb=" N LYS D 81 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N HIS D 146 " --> pdb=" O LYS D 81 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N VAL D 83 " --> pdb=" O HIS D 146 " (cutoff:3.500A) removed outlier: 9.501A pdb=" N PHE D 143 " --> pdb=" O VAL D 875 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N TYR D 877 " --> pdb=" O PHE D 143 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU D 145 " --> pdb=" O TYR D 877 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 166 through 167 removed outlier: 6.878A pdb=" N PHE D 90 " --> pdb=" O GLU D 167 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU D 859 " --> pdb=" O ARG D 103 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 150 through 153 Processing sheet with id=AE6, first strand: chain 'D' and resid 299 through 303 removed outlier: 6.923A pdb=" N GLU D 301 " --> pdb=" O PRO D 586 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE D 303 " --> pdb=" O PHE D 584 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N PHE D 584 " --> pdb=" O ILE D 303 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 353 through 357 Processing sheet with id=AE8, first strand: chain 'D' and resid 383 through 384 removed outlier: 3.535A pdb=" N GLY D 384 " --> pdb=" O PHE D 387 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE D 387 " --> pdb=" O GLY D 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 416 through 418 removed outlier: 3.670A pdb=" N ASN D 417 " --> pdb=" O GLN D 428 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 457 through 459 Processing sheet with id=AF2, first strand: chain 'D' and resid 699 through 700 removed outlier: 6.241A pdb=" N THR D 780 " --> pdb=" O THR D 821 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ILE D 823 " --> pdb=" O THR D 780 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ARG D 782 " --> pdb=" O ILE D 823 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N TYR D 825 " --> pdb=" O ARG D 782 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LYS D 784 " --> pdb=" O TYR D 825 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ILE D 827 " --> pdb=" O LYS D 784 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N TYR D 786 " --> pdb=" O ILE D 827 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 703 through 709 removed outlier: 7.273A pdb=" N TYR D 704 " --> pdb=" O VAL D 851 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL D 851 " --> pdb=" O TYR D 704 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N HIS D 706 " --> pdb=" O THR D 849 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N THR D 849 " --> pdb=" O HIS D 706 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 741 through 744 Processing sheet with id=AF5, first strand: chain 'D' and resid 800 through 805 removed outlier: 4.517A pdb=" N LYS E 895 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 22 through 26 removed outlier: 4.076A pdb=" N SER E 24 " --> pdb=" O TYR E 302 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU E 301 " --> pdb=" O PRO E 586 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 52 through 53 removed outlier: 3.575A pdb=" N ILE F 883 " --> pdb=" O ALA E 53 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 90 through 93 removed outlier: 3.561A pdb=" N ILE E 93 " --> pdb=" O LEU E 102 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU E 102 " --> pdb=" O ILE E 93 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 150 through 153 Processing sheet with id=AG1, first strand: chain 'E' and resid 202 through 207 Processing sheet with id=AG2, first strand: chain 'E' and resid 263 through 266 removed outlier: 3.685A pdb=" N VAL E 266 " --> pdb=" O MET E 884 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 353 through 356 removed outlier: 6.266A pdb=" N ILE E 354 " --> pdb=" O LEU E 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'E' and resid 416 through 418 Processing sheet with id=AG5, first strand: chain 'E' and resid 457 through 458 Processing sheet with id=AG6, first strand: chain 'E' and resid 699 through 700 Processing sheet with id=AG7, first strand: chain 'E' and resid 741 through 743 removed outlier: 6.625A pdb=" N VAL E 742 " --> pdb=" O ARG E 773 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N MET E 848 " --> pdb=" O HIS E 706 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASP E 708 " --> pdb=" O TYR E 846 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR E 846 " --> pdb=" O ASP E 708 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 82 through 83 removed outlier: 7.531A pdb=" N LEU F 145 " --> pdb=" O TYR F 877 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL F 197 " --> pdb=" O ARG F 200 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 91 through 93 removed outlier: 3.589A pdb=" N GLU F 859 " --> pdb=" O ARG F 103 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 150 through 153 Processing sheet with id=AH2, first strand: chain 'F' and resid 248 through 250 Processing sheet with id=AH3, first strand: chain 'F' and resid 299 through 303 removed outlier: 7.171A pdb=" N THR F 299 " --> pdb=" O THR F 587 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR F 587 " --> pdb=" O THR F 299 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 353 through 357 removed outlier: 6.989A pdb=" N ILE F 354 " --> pdb=" O LEU F 569 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N VAL F 571 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASP F 356 " --> pdb=" O VAL F 571 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'F' and resid 417 through 418 Processing sheet with id=AH6, first strand: chain 'F' and resid 457 through 459 Processing sheet with id=AH7, first strand: chain 'F' and resid 731 through 732 removed outlier: 6.814A pdb=" N VAL F 703 " --> pdb=" O PHE F 774 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE F 774 " --> pdb=" O VAL F 703 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL F 772 " --> pdb=" O MET F 705 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'F' and resid 708 through 709 Processing sheet with id=AH9, first strand: chain 'F' and resid 727 through 729 removed outlier: 6.496A pdb=" N ARG F 782 " --> pdb=" O ILE F 823 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N TYR F 825 " --> pdb=" O ARG F 782 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LYS F 784 " --> pdb=" O TYR F 825 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ILE F 827 " --> pdb=" O LYS F 784 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TYR F 786 " --> pdb=" O ILE F 827 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'F' and resid 800 through 805 removed outlier: 4.826A pdb=" N LYS G 895 " --> pdb=" O GLU G 253 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 22 through 26 removed outlier: 4.231A pdb=" N SER G 24 " --> pdb=" O TYR G 302 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR G 299 " --> pdb=" O THR G 587 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AI4, first strand: chain 'G' and resid 91 through 93 removed outlier: 3.627A pdb=" N LEU G 102 " --> pdb=" O ILE G 93 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU G 859 " --> pdb=" O ARG G 103 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'G' and resid 150 through 153 Processing sheet with id=AI6, first strand: chain 'G' and resid 203 through 207 Processing sheet with id=AI7, first strand: chain 'G' and resid 263 through 266 Processing sheet with id=AI8, first strand: chain 'G' and resid 353 through 354 Processing sheet with id=AI9, first strand: chain 'G' and resid 416 through 418 removed outlier: 3.603A pdb=" N ASN G 417 " --> pdb=" O GLN G 428 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'G' and resid 457 through 458 Processing sheet with id=AJ2, first strand: chain 'G' and resid 699 through 700 removed outlier: 3.518A pdb=" N THR G 700 " --> pdb=" O ARG G 779 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'G' and resid 741 through 743 removed outlier: 6.782A pdb=" N VAL G 742 " --> pdb=" O ARG G 773 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR G 704 " --> pdb=" O VAL G 851 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL G 851 " --> pdb=" O TYR G 704 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N HIS G 706 " --> pdb=" O THR G 849 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N THR G 849 " --> pdb=" O HIS G 706 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'H' and resid 82 through 83 removed outlier: 7.271A pdb=" N LEU H 145 " --> pdb=" O TYR H 877 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'H' and resid 91 through 93 removed outlier: 3.621A pdb=" N LEU H 102 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU H 859 " --> pdb=" O ARG H 103 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'H' and resid 150 through 152 Processing sheet with id=AJ7, first strand: chain 'H' and resid 248 through 250 Processing sheet with id=AJ8, first strand: chain 'H' and resid 299 through 303 removed outlier: 6.666A pdb=" N THR H 299 " --> pdb=" O THR H 587 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'H' and resid 353 through 357 removed outlier: 6.985A pdb=" N ILE H 354 " --> pdb=" O LEU H 569 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL H 571 " --> pdb=" O ILE H 354 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASP H 356 " --> pdb=" O VAL H 571 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ9 Processing sheet with id=AK1, first strand: chain 'H' and resid 416 through 418 Processing sheet with id=AK2, first strand: chain 'H' and resid 457 through 459 Processing sheet with id=AK3, first strand: chain 'H' and resid 731 through 732 removed outlier: 6.632A pdb=" N VAL H 703 " --> pdb=" O PHE H 774 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE H 774 " --> pdb=" O VAL H 703 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL H 772 " --> pdb=" O MET H 705 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'H' and resid 708 through 709 removed outlier: 3.519A pdb=" N ASP H 708 " --> pdb=" O THR H 847 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'H' and resid 727 through 729 Processing sheet with id=AK6, first strand: chain 'H' and resid 800 through 804 Processing sheet with id=AK7, first strand: chain 'I' and resid 22 through 26 removed outlier: 6.794A pdb=" N TYR I 302 " --> pdb=" O LEU I 23 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N SER I 25 " --> pdb=" O GLY I 300 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY I 300 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR I 299 " --> pdb=" O THR I 587 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'I' and resid 51 through 53 removed outlier: 4.331A pdb=" N MET I 51 " --> pdb=" O ASP J 885 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE J 883 " --> pdb=" O ALA I 53 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL J 266 " --> pdb=" O MET J 884 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'I' and resid 91 through 93 removed outlier: 3.789A pdb=" N LEU I 102 " --> pdb=" O ILE I 93 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL I 101 " --> pdb=" O VAL I 861 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU I 859 " --> pdb=" O ARG I 103 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'I' and resid 150 through 153 Processing sheet with id=AL2, first strand: chain 'I' and resid 202 through 207 Processing sheet with id=AL3, first strand: chain 'I' and resid 263 through 266 removed outlier: 3.613A pdb=" N VAL I 266 " --> pdb=" O MET I 884 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'I' and resid 353 through 356 removed outlier: 6.224A pdb=" N ILE I 354 " --> pdb=" O LEU I 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL4 Processing sheet with id=AL5, first strand: chain 'I' and resid 428 through 429 Processing sheet with id=AL6, first strand: chain 'I' and resid 457 through 458 Processing sheet with id=AL7, first strand: chain 'I' and resid 699 through 700 removed outlier: 3.812A pdb=" N THR I 700 " --> pdb=" O ARG I 779 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG I 782 " --> pdb=" O THR I 821 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'I' and resid 741 through 743 removed outlier: 6.798A pdb=" N TYR I 704 " --> pdb=" O VAL I 851 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL I 851 " --> pdb=" O TYR I 704 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N HIS I 706 " --> pdb=" O THR I 849 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N THR I 849 " --> pdb=" O HIS I 706 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'J' and resid 82 through 83 removed outlier: 7.126A pdb=" N LEU J 145 " --> pdb=" O TYR J 877 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL J 202 " --> pdb=" O GLY J 195 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'J' and resid 166 through 167 removed outlier: 7.048A pdb=" N PHE J 90 " --> pdb=" O GLU J 167 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'J' and resid 150 through 153 Processing sheet with id=AM3, first strand: chain 'J' and resid 248 through 250 Processing sheet with id=AM4, first strand: chain 'J' and resid 299 through 303 removed outlier: 7.362A pdb=" N THR J 299 " --> pdb=" O THR J 587 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR J 587 " --> pdb=" O THR J 299 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'J' and resid 353 through 357 Processing sheet with id=AM6, first strand: chain 'J' and resid 428 through 429 Processing sheet with id=AM7, first strand: chain 'J' and resid 703 through 704 removed outlier: 3.528A pdb=" N LYS J 850 " --> pdb=" O TYR J 704 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'J' and resid 708 through 709 Processing sheet with id=AM9, first strand: chain 'J' and resid 727 through 729 removed outlier: 3.582A pdb=" N TYR J 825 " --> pdb=" O LYS J 784 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'J' and resid 741 through 744 Processing sheet with id=AN2, first strand: chain 'J' and resid 800 through 805 removed outlier: 3.637A pdb=" N LYS J 816 " --> pdb=" O SER J 801 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR J 814 " --> pdb=" O ASP J 803 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'K' and resid 25 through 26 removed outlier: 5.752A pdb=" N GLU K 301 " --> pdb=" O PRO K 586 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'K' and resid 90 through 93 removed outlier: 3.997A pdb=" N LEU K 102 " --> pdb=" O ILE K 93 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'K' and resid 150 through 153 Processing sheet with id=AN6, first strand: chain 'K' and resid 202 through 207 Processing sheet with id=AN7, first strand: chain 'K' and resid 263 through 266 Processing sheet with id=AN8, first strand: chain 'K' and resid 353 through 354 Processing sheet with id=AN9, first strand: chain 'K' and resid 416 through 418 Processing sheet with id=AO1, first strand: chain 'K' and resid 457 through 459 Processing sheet with id=AO2, first strand: chain 'K' and resid 699 through 700 Processing sheet with id=AO3, first strand: chain 'K' and resid 741 through 743 removed outlier: 4.120A pdb=" N MET K 848 " --> pdb=" O HIS K 706 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASP K 708 " --> pdb=" O TYR K 846 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N TYR K 846 " --> pdb=" O ASP K 708 " (cutoff:3.500A) 2484 hydrogen bonds defined for protein. 7035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 38.38 Time building geometry restraints manager: 26.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 25773 1.34 - 1.45: 13024 1.45 - 1.57: 42986 1.57 - 1.69: 0 1.69 - 1.81: 874 Bond restraints: 82657 Sorted by residual: bond pdb=" C LEU A 538 " pdb=" N PRO A 539 " ideal model delta sigma weight residual 1.334 1.374 -0.041 8.40e-03 1.42e+04 2.33e+01 bond pdb=" N GLU G 461 " pdb=" CA GLU G 461 " ideal model delta sigma weight residual 1.453 1.489 -0.036 9.20e-03 1.18e+04 1.51e+01 bond pdb=" N GLU H 461 " pdb=" CA GLU H 461 " ideal model delta sigma weight residual 1.462 1.495 -0.033 8.50e-03 1.38e+04 1.49e+01 bond pdb=" N VAL H 794 " pdb=" CA VAL H 794 " ideal model delta sigma weight residual 1.460 1.505 -0.045 1.19e-02 7.06e+03 1.45e+01 bond pdb=" N VAL F 794 " pdb=" CA VAL F 794 " ideal model delta sigma weight residual 1.460 1.505 -0.045 1.19e-02 7.06e+03 1.43e+01 ... (remaining 82652 not shown) Histogram of bond angle deviations from ideal: 97.19 - 104.66: 1790 104.66 - 112.12: 38724 112.12 - 119.59: 30544 119.59 - 127.06: 40207 127.06 - 134.53: 921 Bond angle restraints: 112186 Sorted by residual: angle pdb=" N VAL J 369 " pdb=" CA VAL J 369 " pdb=" C VAL J 369 " ideal model delta sigma weight residual 112.96 107.15 5.81 1.00e+00 1.00e+00 3.38e+01 angle pdb=" C GLU G 193 " pdb=" N ASN G 194 " pdb=" CA ASN G 194 " ideal model delta sigma weight residual 122.46 130.36 -7.90 1.41e+00 5.03e-01 3.14e+01 angle pdb=" C ASP D 105 " pdb=" N THR D 106 " pdb=" CA THR D 106 " ideal model delta sigma weight residual 121.54 132.24 -10.70 1.91e+00 2.74e-01 3.14e+01 angle pdb=" N PRO G 464 " pdb=" CA PRO G 464 " pdb=" C PRO G 464 " ideal model delta sigma weight residual 113.53 105.77 7.76 1.39e+00 5.18e-01 3.12e+01 angle pdb=" C LEU A 530 " pdb=" N VAL A 531 " pdb=" CA VAL A 531 " ideal model delta sigma weight residual 120.24 123.66 -3.42 6.30e-01 2.52e+00 2.94e+01 ... (remaining 112181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.11: 45039 18.11 - 36.21: 4170 36.21 - 54.32: 705 54.32 - 72.43: 137 72.43 - 90.54: 69 Dihedral angle restraints: 50120 sinusoidal: 20620 harmonic: 29500 Sorted by residual: dihedral pdb=" CA ASP E 356 " pdb=" C ASP E 356 " pdb=" N LEU E 357 " pdb=" CA LEU E 357 " ideal model delta harmonic sigma weight residual 180.00 -151.68 -28.32 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA ILE H 359 " pdb=" C ILE H 359 " pdb=" N ASP H 360 " pdb=" CA ASP H 360 " ideal model delta harmonic sigma weight residual 180.00 -153.33 -26.67 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA HIS B 656 " pdb=" C HIS B 656 " pdb=" N SER B 657 " pdb=" CA SER B 657 " ideal model delta harmonic sigma weight residual 180.00 153.61 26.39 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 50117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 10854 0.079 - 0.158: 1554 0.158 - 0.236: 115 0.236 - 0.315: 16 0.315 - 0.394: 1 Chirality restraints: 12540 Sorted by residual: chirality pdb=" CB VAL D 266 " pdb=" CA VAL D 266 " pdb=" CG1 VAL D 266 " pdb=" CG2 VAL D 266 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CB VAL B 57 " pdb=" CA VAL B 57 " pdb=" CG1 VAL B 57 " pdb=" CG2 VAL B 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA ASP G 201 " pdb=" N ASP G 201 " pdb=" C ASP G 201 " pdb=" CB ASP G 201 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 12537 not shown) Planarity restraints: 14541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 460 " -0.022 2.00e-02 2.50e+03 4.45e-02 1.98e+01 pdb=" C ARG C 460 " 0.077 2.00e-02 2.50e+03 pdb=" O ARG C 460 " -0.029 2.00e-02 2.50e+03 pdb=" N GLU C 461 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 423 " 0.052 5.00e-02 4.00e+02 7.82e-02 9.78e+00 pdb=" N PRO B 424 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 424 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 424 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 251 " 0.047 5.00e-02 4.00e+02 7.11e-02 8.08e+00 pdb=" N PRO A 252 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 252 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 252 " 0.040 5.00e-02 4.00e+02 ... (remaining 14538 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 4506 2.72 - 3.27: 74863 3.27 - 3.81: 125548 3.81 - 4.36: 153600 4.36 - 4.90: 264010 Nonbonded interactions: 622527 Sorted by model distance: nonbonded pdb=" O ASP A 764 " pdb=" OD1 ASP A 765 " model vdw 2.178 3.040 nonbonded pdb=" N ASP E 793 " pdb=" OD1 ASP E 793 " model vdw 2.197 2.520 nonbonded pdb=" CG2 VAL G 595 " pdb=" NZ LYS G 891 " model vdw 2.217 3.540 nonbonded pdb=" CG1 VAL K 438 " pdb=" CZ2 TRP K 452 " model vdw 2.226 3.760 nonbonded pdb=" OH TYR I 410 " pdb=" OE2 GLU I 512 " model vdw 2.231 2.440 ... (remaining 622522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 36 or resid 59 through 804 or resid 815 through 901)) selection = (chain 'C' and (resid 36 or resid 59 through 901)) selection = (chain 'D' and (resid 36 or resid 59 through 804 or resid 815 through 901)) selection = (chain 'E' and (resid 36 or resid 59 through 901)) selection = (chain 'F' and (resid 23 or resid 59 through 804 or resid 815 through 901)) selection = (chain 'G' and (resid 36 or resid 59 through 901)) selection = (chain 'H' and (resid 36 or resid 59 through 804 or resid 815 through 901)) selection = (chain 'I' and (resid 36 or resid 59 through 901)) selection = (chain 'J' and (resid 36 or resid 59 through 804 or resid 815 through 901)) selection = (chain 'K' and (resid 36 or resid 59 through 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 7.080 Check model and map are aligned: 0.910 Set scattering table: 0.550 Process input model: 171.040 Find NCS groups from input model: 5.500 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 189.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 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 : 0.006 0.065 82657 Z= 0.413 Angle : 0.819 11.519 112186 Z= 0.456 Chirality : 0.055 0.394 12540 Planarity : 0.006 0.078 14541 Dihedral : 14.433 90.536 31052 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.68 % Allowed : 9.10 % Favored : 90.22 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.37 (0.06), residues: 9970 helix: -4.70 (0.03), residues: 4026 sheet: -2.18 (0.14), residues: 1221 loop : -2.76 (0.07), residues: 4723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 386 HIS 0.014 0.001 HIS F 656 PHE 0.032 0.002 PHE H 59 TYR 0.026 0.002 TYR H 471 ARG 0.013 0.001 ARG J 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19940 Ramachandran restraints generated. 9970 Oldfield, 0 Emsley, 9970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19940 Ramachandran restraints generated. 9970 Oldfield, 0 Emsley, 9970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1563 residues out of total 8837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1503 time to evaluate : 6.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 TYR cc_start: 0.7852 (t80) cc_final: 0.7611 (t80) REVERT: A 206 GLU cc_start: 0.7470 (tm-30) cc_final: 0.6844 (tm-30) REVERT: A 210 MET cc_start: 0.8226 (tpp) cc_final: 0.7979 (tpp) REVERT: A 222 MET cc_start: 0.8772 (mmp) cc_final: 0.8306 (mmm) REVERT: A 299 LYS cc_start: 0.8761 (pttm) cc_final: 0.8450 (tptt) REVERT: A 322 MET cc_start: 0.8165 (mtp) cc_final: 0.7948 (mtp) REVERT: A 367 MET cc_start: 0.9159 (mmm) cc_final: 0.8865 (mmm) REVERT: A 412 LEU cc_start: 0.8825 (mm) cc_final: 0.8592 (mm) REVERT: A 441 MET cc_start: 0.8762 (ttm) cc_final: 0.8001 (mtp) REVERT: A 500 TYR cc_start: 0.8517 (m-80) cc_final: 0.7954 (m-80) REVERT: A 614 GLN cc_start: 0.8158 (mt0) cc_final: 0.7829 (mt0) REVERT: A 760 GLN cc_start: 0.8621 (mt0) cc_final: 0.8209 (tt0) REVERT: A 864 ASP cc_start: 0.8052 (m-30) cc_final: 0.7666 (p0) REVERT: A 963 ASP cc_start: 0.7613 (t0) cc_final: 0.7245 (t0) REVERT: A 996 GLN cc_start: 0.7738 (mm-40) cc_final: 0.6721 (mp10) REVERT: A 1074 TYR cc_start: 0.8719 (t80) cc_final: 0.8424 (t80) REVERT: A 1081 TYR cc_start: 0.8976 (m-10) cc_final: 0.8752 (m-10) REVERT: A 1083 GLU cc_start: 0.7899 (pt0) cc_final: 0.7338 (pt0) REVERT: A 1087 ASP cc_start: 0.8740 (m-30) cc_final: 0.8086 (p0) REVERT: A 1260 ASP cc_start: 0.7276 (p0) cc_final: 0.7026 (p0) REVERT: A 1285 LYS cc_start: 0.6072 (mttm) cc_final: 0.5328 (mtpp) REVERT: B 84 LYS cc_start: 0.8982 (mttp) cc_final: 0.8466 (mmtt) REVERT: B 503 MET cc_start: 0.9139 (ttp) cc_final: 0.8899 (ttm) REVERT: B 610 MET cc_start: 0.9188 (mtp) cc_final: 0.8927 (mtp) REVERT: B 638 LYS cc_start: 0.9173 (tptt) cc_final: 0.8672 (tptm) REVERT: B 693 ASP cc_start: 0.8646 (t70) cc_final: 0.8195 (t70) REVERT: B 695 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8371 (mt-10) REVERT: B 698 MET cc_start: 0.9026 (mmm) cc_final: 0.8585 (tpp) REVERT: B 714 ARG cc_start: 0.8361 (ttm170) cc_final: 0.7898 (ptt180) REVERT: B 719 GLU cc_start: 0.8310 (tt0) cc_final: 0.8002 (tp30) REVERT: B 784 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8419 (mmtt) REVERT: B 816 LYS cc_start: 0.9308 (mttt) cc_final: 0.9050 (mttm) REVERT: B 856 ARG cc_start: 0.8481 (ptt180) cc_final: 0.7866 (mmt-90) REVERT: C 13 LYS cc_start: 0.8276 (mmtp) cc_final: 0.8029 (mmtp) REVERT: C 66 LYS cc_start: 0.8950 (ttmt) cc_final: 0.8691 (tptp) REVERT: C 187 LEU cc_start: 0.9376 (mm) cc_final: 0.9116 (mm) REVERT: C 484 ASN cc_start: 0.8555 (m110) cc_final: 0.8271 (m-40) REVERT: C 592 MET cc_start: 0.8983 (ptp) cc_final: 0.8718 (ptp) REVERT: C 698 MET cc_start: 0.8708 (mmm) cc_final: 0.8389 (mmm) REVERT: C 705 MET cc_start: 0.9027 (ttt) cc_final: 0.8633 (tpp) REVERT: C 709 MET cc_start: 0.8942 (ptp) cc_final: 0.8534 (pmm) REVERT: C 884 MET cc_start: 0.7955 (mtt) cc_final: 0.7696 (mmm) REVERT: D 71 ILE cc_start: 0.9346 (mm) cc_final: 0.9043 (mt) REVERT: D 98 ARG cc_start: 0.9040 (mmm-85) cc_final: 0.8723 (ttm170) REVERT: D 167 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7526 (tm-30) REVERT: D 270 GLN cc_start: 0.8651 (mt0) cc_final: 0.8383 (mt0) REVERT: D 371 MET cc_start: 0.9089 (mtt) cc_final: 0.8317 (mtt) REVERT: D 413 ARG cc_start: 0.8263 (ttm170) cc_final: 0.7860 (ttt-90) REVERT: D 537 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.7714 (t70) REVERT: D 548 MET cc_start: 0.9040 (mtt) cc_final: 0.8837 (mtp) REVERT: D 695 GLU cc_start: 0.8528 (tt0) cc_final: 0.8327 (tt0) REVERT: D 698 MET cc_start: 0.9423 (mmm) cc_final: 0.9169 (mmm) REVERT: D 731 MET cc_start: 0.9503 (ttt) cc_final: 0.8928 (ttt) REVERT: D 856 ARG cc_start: 0.7429 (ttp-170) cc_final: 0.7110 (mmt180) REVERT: E 120 GLU cc_start: 0.8693 (pm20) cc_final: 0.8317 (pm20) REVERT: E 218 ASN cc_start: 0.8698 (m-40) cc_final: 0.8493 (m110) REVERT: E 610 MET cc_start: 0.9277 (mtt) cc_final: 0.8959 (mtt) REVERT: E 667 MET cc_start: 0.8079 (tpp) cc_final: 0.7639 (tpt) REVERT: E 740 ARG cc_start: 0.6671 (ttt-90) cc_final: 0.6349 (tpt-90) REVERT: E 848 MET cc_start: 0.8029 (mmm) cc_final: 0.7072 (mmm) REVERT: E 881 MET cc_start: 0.8467 (mmm) cc_final: 0.7936 (mmm) REVERT: F 98 ARG cc_start: 0.8558 (mtm-85) cc_final: 0.8013 (mtp-110) REVERT: F 121 ASP cc_start: 0.8577 (p0) cc_final: 0.8034 (p0) REVERT: F 156 MET cc_start: 0.7572 (ptt) cc_final: 0.7111 (ptt) REVERT: F 185 ASN cc_start: 0.9236 (m110) cc_final: 0.8983 (m110) REVERT: F 193 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7673 (tm-30) REVERT: F 276 GLN cc_start: 0.8561 (tp-100) cc_final: 0.8251 (tp40) REVERT: F 365 MET cc_start: 0.8725 (mtp) cc_final: 0.8484 (mtm) REVERT: F 393 ASN cc_start: 0.9086 (t0) cc_final: 0.8877 (t0) REVERT: F 432 ASN cc_start: 0.8597 (t0) cc_final: 0.8384 (t0) REVERT: F 460 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7093 (mmt-90) REVERT: F 471 TYR cc_start: 0.7798 (OUTLIER) cc_final: 0.7104 (m-80) REVERT: F 626 ASP cc_start: 0.8302 (t0) cc_final: 0.8085 (t0) REVERT: F 662 ASN cc_start: 0.8464 (p0) cc_final: 0.8122 (p0) REVERT: F 685 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7531 (tm-30) REVERT: F 733 GLU cc_start: 0.6392 (tm-30) cc_final: 0.6150 (tm-30) REVERT: F 740 ARG cc_start: 0.8636 (mtp85) cc_final: 0.8409 (mmm160) REVERT: F 747 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8528 (mp0) REVERT: G 111 MET cc_start: 0.9191 (tpp) cc_final: 0.8662 (tpp) REVERT: G 182 MET cc_start: 0.7119 (mmm) cc_final: 0.6913 (ttt) REVERT: G 241 ARG cc_start: 0.8809 (mtm-85) cc_final: 0.8590 (mtm-85) REVERT: G 250 TYR cc_start: 0.8274 (m-10) cc_final: 0.8003 (m-10) REVERT: G 460 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6566 (ttp80) REVERT: G 622 ARG cc_start: 0.8628 (mmm160) cc_final: 0.8303 (ttt180) REVERT: G 694 PHE cc_start: 0.9041 (m-80) cc_final: 0.8775 (m-80) REVERT: G 726 PHE cc_start: 0.8630 (t80) cc_final: 0.8333 (t80) REVERT: G 881 MET cc_start: 0.8751 (mmp) cc_final: 0.8519 (mmm) REVERT: H 40 MET cc_start: 0.6937 (ttt) cc_final: 0.6695 (ttt) REVERT: H 66 LYS cc_start: 0.8548 (tmtt) cc_final: 0.8314 (ttmt) REVERT: H 98 ARG cc_start: 0.8628 (mtm-85) cc_final: 0.8166 (mtt-85) REVERT: H 100 ARG cc_start: 0.8129 (mtt180) cc_final: 0.7857 (mtm180) REVERT: H 152 ASP cc_start: 0.8163 (p0) cc_final: 0.7899 (p0) REVERT: H 169 LYS cc_start: 0.9466 (mtpp) cc_final: 0.9257 (mtpp) REVERT: H 664 ARG cc_start: 0.8756 (ttm-80) cc_final: 0.8553 (mtp85) REVERT: H 698 MET cc_start: 0.9069 (mmm) cc_final: 0.8305 (mtp) REVERT: H 737 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7212 (tm-30) REVERT: H 766 MET cc_start: 0.8521 (mmm) cc_final: 0.7902 (mtm) REVERT: H 848 MET cc_start: 0.8657 (mmt) cc_final: 0.8329 (mmp) REVERT: I 40 MET cc_start: 0.8841 (mmt) cc_final: 0.8334 (mmm) REVERT: I 51 MET cc_start: 0.8319 (tmm) cc_final: 0.7697 (tmm) REVERT: I 308 ARG cc_start: 0.8608 (mtp180) cc_final: 0.8396 (mtp85) REVERT: I 394 MET cc_start: 0.9125 (tpt) cc_final: 0.8796 (tpp) REVERT: I 622 ARG cc_start: 0.8649 (mmm160) cc_final: 0.8187 (ttp-170) REVERT: I 735 PRO cc_start: 0.9297 (Cg_endo) cc_final: 0.9092 (Cg_exo) REVERT: J 81 LYS cc_start: 0.8932 (ttmt) cc_final: 0.8686 (ttpt) REVERT: J 95 MET cc_start: 0.8583 (mtm) cc_final: 0.7629 (ptp) REVERT: J 592 MET cc_start: 0.7625 (mmt) cc_final: 0.7169 (mmt) REVERT: J 600 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8043 (mt-10) REVERT: J 620 MET cc_start: 0.9252 (mmt) cc_final: 0.9033 (mmm) REVERT: J 626 ASP cc_start: 0.8533 (p0) cc_final: 0.8263 (p0) REVERT: J 643 ASP cc_start: 0.7772 (t70) cc_final: 0.7359 (t70) REVERT: J 709 MET cc_start: 0.8666 (ptm) cc_final: 0.8062 (ptm) REVERT: J 720 ARG cc_start: 0.9183 (mmm-85) cc_final: 0.7988 (ptm160) REVERT: J 721 PHE cc_start: 0.9449 (t80) cc_final: 0.9205 (t80) REVERT: J 755 MET cc_start: 0.8699 (mtt) cc_final: 0.8351 (mtm) REVERT: K 182 MET cc_start: 0.6639 (mmm) cc_final: 0.5738 (mtp) REVERT: K 259 ARG cc_start: 0.8749 (ttt-90) cc_final: 0.8506 (tpt-90) REVERT: K 316 GLN cc_start: 0.7659 (mp10) cc_final: 0.7409 (tm-30) REVERT: K 348 MET cc_start: 0.8601 (mtt) cc_final: 0.8379 (mtt) REVERT: K 622 ARG cc_start: 0.9007 (mmm160) cc_final: 0.8275 (tpt90) REVERT: K 764 ARG cc_start: 0.8725 (ttt-90) cc_final: 0.8507 (tpt-90) REVERT: K 766 MET cc_start: 0.8971 (mmp) cc_final: 0.8224 (mmp) REVERT: K 878 LYS cc_start: 0.8638 (mmmt) cc_final: 0.8257 (mmmt) outliers start: 60 outliers final: 33 residues processed: 1546 average time/residue: 0.7969 time to fit residues: 2036.9188 Evaluate side-chains 1174 residues out of total 8837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1137 time to evaluate : 7.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 671 MET Chi-restraints excluded: chain E residue 793 ASP Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 460 ARG Chi-restraints excluded: chain F residue 471 TYR Chi-restraints excluded: chain F residue 671 MET Chi-restraints excluded: chain F residue 794 VAL Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 460 ARG Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 851 VAL Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 391 THR Chi-restraints excluded: chain I residue 477 ILE Chi-restraints excluded: chain I residue 671 MET Chi-restraints excluded: chain I residue 772 VAL Chi-restraints excluded: chain J residue 271 LEU Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain K residue 354 ILE Chi-restraints excluded: chain K residue 671 MET Chi-restraints excluded: chain K residue 794 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 996 random chunks: chunk 841 optimal weight: 3.9990 chunk 754 optimal weight: 7.9990 chunk 418 optimal weight: 0.9990 chunk 257 optimal weight: 2.9990 chunk 509 optimal weight: 0.8980 chunk 403 optimal weight: 30.0000 chunk 780 optimal weight: 9.9990 chunk 302 optimal weight: 7.9990 chunk 474 optimal weight: 8.9990 chunk 581 optimal weight: 5.9990 chunk 904 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN A 283 GLN A 335 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 507 GLN A 648 ASN A 843 GLN A 863 HIS A 867 GLN A 962 HIS A1239 GLN A1300 GLN B 45 GLN B 96 GLN B 389 ASN B 450 ASN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 535 ASN B 550 ASN B 635 HIS ** B 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 GLN B 702 GLN B 723 GLN B 743 GLN B 829 ASN C 92 HIS C 153 HIS C 221 GLN C 288 ASN C 378 HIS C 411 ASN C 531 ASN C 532 GLN C 539 HIS C 561 HIS C 621 GLN C 635 HIS C 642 ASN C 653 ASN C 796 GLN C 834 ASN D 41 GLN D 292 ASN ** D 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 ASN D 437 ASN D 531 ASN D 532 GLN D 535 ASN D 635 HIS D 659 ASN D 676 GLN D 723 GLN D 757 GLN E 389 ASN E 417 ASN E 433 GLN E 467 HIS E 531 ASN E 635 HIS E 653 ASN ** E 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 692 ASN E 706 HIS E 723 GLN E 754 ASN E 843 ASN F 78 GLN F 153 HIS F 185 ASN F 244 HIS F 288 ASN ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN ** F 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 532 GLN F 535 ASN F 550 ASN F 562 GLN F 635 HIS F 676 GLN F 702 GLN F 743 GLN F 829 ASN G 47 GLN G 218 ASN G 270 GLN G 288 ASN G 378 HIS G 467 HIS G 484 ASN G 531 ASN G 539 HIS G 550 ASN G 621 GLN G 635 HIS G 642 ASN ** G 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 706 HIS H 47 GLN H 179 HIS ** H 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 437 ASN H 450 ASN H 535 ASN H 550 ASN H 635 HIS H 642 ASN H 659 ASN H 702 GLN H 743 GLN ** H 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 829 ASN I 47 GLN ** I 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 ASN I 389 ASN I 393 ASN I 415 GLN I 531 ASN I 550 ASN I 635 HIS I 653 ASN ** I 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 179 HIS J 244 HIS J 288 ASN J 292 ASN J 352 GLN J 389 ASN J 417 ASN J 433 GLN ** J 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 535 ASN J 635 HIS J 659 ASN J 743 GLN J 754 ASN J 834 ASN K 47 GLN K 65 GLN K 276 GLN K 378 HIS K 389 ASN K 433 GLN K 635 HIS K 653 ASN ** K 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 723 GLN K 834 ASN Total number of N/Q/H flips: 139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 82657 Z= 0.199 Angle : 0.578 10.479 112186 Z= 0.300 Chirality : 0.044 0.224 12540 Planarity : 0.005 0.060 14541 Dihedral : 5.348 59.355 11265 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.74 % Allowed : 13.53 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.07), residues: 9970 helix: -2.90 (0.06), residues: 4098 sheet: -1.83 (0.14), residues: 1145 loop : -2.20 (0.08), residues: 4727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 105 HIS 0.010 0.001 HIS D 244 PHE 0.028 0.001 PHE A 662 TYR 0.022 0.001 TYR C 786 ARG 0.009 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19940 Ramachandran restraints generated. 9970 Oldfield, 0 Emsley, 9970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19940 Ramachandran restraints generated. 9970 Oldfield, 0 Emsley, 9970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1407 residues out of total 8837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1253 time to evaluate : 7.568 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: A 95 PHE cc_start: 0.8378 (t80) cc_final: 0.8063 (t80) REVERT: A 96 GLU cc_start: 0.7776 (pm20) cc_final: 0.7559 (pm20) REVERT: A 124 MET cc_start: 0.6534 (pmm) cc_final: 0.6333 (pmm) REVERT: A 206 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7289 (tm-30) REVERT: A 207 MET cc_start: 0.8779 (ttp) cc_final: 0.8350 (ttp) REVERT: A 210 MET cc_start: 0.8195 (tpp) cc_final: 0.7821 (tpp) REVERT: A 329 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8194 (tp30) REVERT: A 412 LEU cc_start: 0.8814 (mm) cc_final: 0.8594 (mm) REVERT: A 441 MET cc_start: 0.8923 (ttm) cc_final: 0.7988 (mtp) REVERT: A 500 TYR cc_start: 0.8568 (m-80) cc_final: 0.8249 (m-80) REVERT: A 614 GLN cc_start: 0.7972 (mt0) cc_final: 0.7584 (mt0) REVERT: A 760 GLN cc_start: 0.8565 (mt0) cc_final: 0.8144 (tt0) REVERT: A 829 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7069 (mtm) REVERT: A 987 PHE cc_start: 0.6870 (OUTLIER) cc_final: 0.6596 (m-80) REVERT: A 1074 TYR cc_start: 0.8545 (t80) cc_final: 0.8288 (t80) REVERT: A 1081 TYR cc_start: 0.8766 (m-10) cc_final: 0.8459 (m-10) REVERT: A 1087 ASP cc_start: 0.8726 (m-30) cc_final: 0.8098 (p0) REVERT: A 1260 ASP cc_start: 0.7427 (p0) cc_final: 0.7180 (p0) REVERT: A 1285 LYS cc_start: 0.6457 (mttm) cc_final: 0.6157 (mmtt) REVERT: B 84 LYS cc_start: 0.8893 (mttp) cc_final: 0.8308 (mmtt) REVERT: B 638 LYS cc_start: 0.9046 (tptt) cc_final: 0.8716 (tptm) REVERT: B 693 ASP cc_start: 0.8607 (t70) cc_final: 0.8160 (t70) REVERT: B 698 MET cc_start: 0.9090 (mmm) cc_final: 0.8709 (tpp) REVERT: B 705 MET cc_start: 0.8784 (ttm) cc_final: 0.8420 (ttm) REVERT: B 714 ARG cc_start: 0.8418 (ttm170) cc_final: 0.7995 (ptt180) REVERT: B 816 LYS cc_start: 0.9249 (mttt) cc_final: 0.8913 (mtpp) REVERT: B 856 ARG cc_start: 0.8456 (ptt180) cc_final: 0.7842 (mmt-90) REVERT: C 187 LEU cc_start: 0.9097 (mm) cc_final: 0.8269 (mt) REVERT: C 253 GLU cc_start: 0.7654 (tt0) cc_final: 0.7207 (tt0) REVERT: C 291 MET cc_start: 0.8685 (mmm) cc_final: 0.8241 (mmm) REVERT: C 396 ARG cc_start: 0.8360 (tpt170) cc_final: 0.8044 (tpp-160) REVERT: C 484 ASN cc_start: 0.8519 (m110) cc_final: 0.8300 (m-40) REVERT: C 548 MET cc_start: 0.9239 (mtt) cc_final: 0.9029 (mtp) REVERT: C 592 MET cc_start: 0.9131 (ptp) cc_final: 0.8928 (ptp) REVERT: C 620 MET cc_start: 0.8800 (mmt) cc_final: 0.8211 (mmt) REVERT: C 698 MET cc_start: 0.8803 (mmm) cc_final: 0.8299 (mmm) REVERT: C 705 MET cc_start: 0.9204 (ttt) cc_final: 0.8875 (tpp) REVERT: C 709 MET cc_start: 0.9084 (ptp) cc_final: 0.8717 (pmm) REVERT: C 731 MET cc_start: 0.8997 (ttm) cc_final: 0.8335 (tmm) REVERT: C 786 TYR cc_start: 0.4497 (m-80) cc_final: 0.4212 (m-80) REVERT: C 884 MET cc_start: 0.7927 (mtt) cc_final: 0.7665 (mmm) REVERT: D 71 ILE cc_start: 0.9137 (mm) cc_final: 0.8764 (mt) REVERT: D 98 ARG cc_start: 0.9062 (mmm-85) cc_final: 0.8704 (ttm170) REVERT: D 167 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7558 (pp20) REVERT: D 270 GLN cc_start: 0.8541 (mt0) cc_final: 0.8277 (mt0) REVERT: D 371 MET cc_start: 0.9076 (mtt) cc_final: 0.8303 (mtt) REVERT: D 407 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.8786 (pp) REVERT: D 413 ARG cc_start: 0.8205 (ttm170) cc_final: 0.7855 (ttt-90) REVERT: D 537 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.7746 (t70) REVERT: D 667 MET cc_start: 0.9106 (tpt) cc_final: 0.8625 (tpt) REVERT: D 693 ASP cc_start: 0.8313 (t0) cc_final: 0.7860 (t0) REVERT: D 695 GLU cc_start: 0.8511 (tt0) cc_final: 0.8269 (tt0) REVERT: D 726 PHE cc_start: 0.8059 (t80) cc_final: 0.7652 (t80) REVERT: D 731 MET cc_start: 0.9364 (ttt) cc_final: 0.8873 (ttt) REVERT: E 120 GLU cc_start: 0.8667 (pm20) cc_final: 0.8260 (pm20) REVERT: E 276 GLN cc_start: 0.8650 (tp-100) cc_final: 0.8344 (mm-40) REVERT: E 610 MET cc_start: 0.9255 (mtt) cc_final: 0.8984 (mtt) REVERT: E 617 LEU cc_start: 0.9527 (mt) cc_final: 0.9310 (mm) REVERT: E 667 MET cc_start: 0.8192 (tpp) cc_final: 0.7844 (tpt) REVERT: E 699 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8690 (pp) REVERT: E 709 MET cc_start: 0.8150 (mmm) cc_final: 0.7746 (mmm) REVERT: E 754 ASN cc_start: 0.8999 (m-40) cc_final: 0.8598 (m-40) REVERT: E 848 MET cc_start: 0.7947 (mmm) cc_final: 0.7376 (mmm) REVERT: E 881 MET cc_start: 0.8464 (mmm) cc_final: 0.8016 (mmm) REVERT: F 98 ARG cc_start: 0.8550 (mtm-85) cc_final: 0.7971 (mtp-110) REVERT: F 121 ASP cc_start: 0.8367 (p0) cc_final: 0.7893 (p0) REVERT: F 156 MET cc_start: 0.7643 (ptt) cc_final: 0.7245 (ptt) REVERT: F 169 LYS cc_start: 0.8990 (mmmt) cc_final: 0.8707 (mmmt) REVERT: F 185 ASN cc_start: 0.9235 (m-40) cc_final: 0.9016 (m110) REVERT: F 193 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7212 (tm-30) REVERT: F 276 GLN cc_start: 0.8506 (tp-100) cc_final: 0.8183 (tp40) REVERT: F 365 MET cc_start: 0.8781 (mtp) cc_final: 0.8569 (mtm) REVERT: F 471 TYR cc_start: 0.7712 (OUTLIER) cc_final: 0.6860 (m-80) REVERT: F 499 GLU cc_start: 0.8468 (mm-30) cc_final: 0.7596 (mm-30) REVERT: F 524 MET cc_start: 0.8845 (mmm) cc_final: 0.8219 (mmt) REVERT: F 547 ASP cc_start: 0.8760 (p0) cc_final: 0.8514 (p0) REVERT: F 626 ASP cc_start: 0.8290 (t0) cc_final: 0.8079 (t0) REVERT: F 638 LYS cc_start: 0.8819 (tptt) cc_final: 0.8513 (mmtt) REVERT: F 662 ASN cc_start: 0.8445 (p0) cc_final: 0.8104 (p0) REVERT: F 685 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7410 (tm-30) REVERT: F 698 MET cc_start: 0.9201 (mmm) cc_final: 0.8890 (mmm) REVERT: F 714 ARG cc_start: 0.7115 (ttp80) cc_final: 0.6637 (ptt-90) REVERT: F 733 GLU cc_start: 0.6382 (tm-30) cc_final: 0.6133 (tm-30) REVERT: F 747 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8598 (mp0) REVERT: F 848 MET cc_start: 0.8401 (mmt) cc_final: 0.8184 (mmt) REVERT: G 10 GLU cc_start: 0.6188 (pp20) cc_final: 0.5919 (pp20) REVERT: G 111 MET cc_start: 0.9136 (tpp) cc_final: 0.8643 (tpp) REVERT: G 182 MET cc_start: 0.7256 (mmm) cc_final: 0.6945 (ttt) REVERT: G 250 TYR cc_start: 0.8258 (m-10) cc_final: 0.7997 (m-10) REVERT: G 492 MET cc_start: 0.8023 (ttm) cc_final: 0.7793 (ttm) REVERT: G 668 ARG cc_start: 0.8768 (ttp-170) cc_final: 0.8092 (ttm110) REVERT: G 848 MET cc_start: 0.8189 (mmm) cc_final: 0.7763 (mmm) REVERT: G 873 ARG cc_start: 0.6574 (tmm160) cc_final: 0.6361 (tmm160) REVERT: G 881 MET cc_start: 0.8830 (mmp) cc_final: 0.8450 (mmm) REVERT: H 40 MET cc_start: 0.6842 (ttt) cc_final: 0.6474 (ttt) REVERT: H 66 LYS cc_start: 0.8538 (tmtt) cc_final: 0.8331 (ttmt) REVERT: H 95 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8229 (ptt) REVERT: H 98 ARG cc_start: 0.8578 (mtm-85) cc_final: 0.8094 (mtt-85) REVERT: H 100 ARG cc_start: 0.8101 (mtt180) cc_final: 0.7576 (mtm110) REVERT: H 412 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8325 (m) REVERT: H 519 MET cc_start: 0.9308 (tpt) cc_final: 0.8726 (mmt) REVERT: H 695 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8156 (mt-10) REVERT: H 698 MET cc_start: 0.9145 (mmm) cc_final: 0.8706 (mmm) REVERT: H 766 MET cc_start: 0.8185 (mmm) cc_final: 0.7578 (mtm) REVERT: H 786 TYR cc_start: 0.5970 (m-80) cc_final: 0.5433 (m-80) REVERT: H 848 MET cc_start: 0.8675 (mmt) cc_final: 0.8252 (mmp) REVERT: I 40 MET cc_start: 0.8696 (mmt) cc_final: 0.8178 (mmm) REVERT: I 51 MET cc_start: 0.8496 (tmm) cc_final: 0.8118 (tmm) REVERT: I 182 MET cc_start: 0.7055 (ttt) cc_final: 0.6804 (ttm) REVERT: I 227 VAL cc_start: 0.9116 (t) cc_final: 0.8777 (m) REVERT: I 308 ARG cc_start: 0.8670 (mtp180) cc_final: 0.8451 (mtp85) REVERT: I 394 MET cc_start: 0.8756 (tpt) cc_final: 0.8512 (tpp) REVERT: I 622 ARG cc_start: 0.8680 (mmm160) cc_final: 0.8228 (ttp-170) REVERT: I 694 PHE cc_start: 0.9266 (m-80) cc_final: 0.9007 (m-80) REVERT: I 856 ARG cc_start: 0.8790 (mmt180) cc_final: 0.8243 (ttm-80) REVERT: J 81 LYS cc_start: 0.8799 (ttmt) cc_final: 0.8542 (ttpt) REVERT: J 95 MET cc_start: 0.8506 (mtm) cc_final: 0.7940 (ptp) REVERT: J 394 MET cc_start: 0.9153 (ttt) cc_final: 0.8865 (ttt) REVERT: J 407 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8685 (pp) REVERT: J 532 GLN cc_start: 0.8687 (mt0) cc_final: 0.8471 (mt0) REVERT: J 709 MET cc_start: 0.8678 (ptm) cc_final: 0.8210 (ptm) REVERT: J 720 ARG cc_start: 0.9170 (mmm-85) cc_final: 0.8073 (ptm160) REVERT: J 755 MET cc_start: 0.8932 (mtt) cc_final: 0.8615 (mtm) REVERT: K 172 LEU cc_start: 0.8477 (mt) cc_final: 0.8239 (mp) REVERT: K 182 MET cc_start: 0.6203 (mmm) cc_final: 0.5571 (ptp) REVERT: K 259 ARG cc_start: 0.8746 (ttt-90) cc_final: 0.8522 (tpt-90) REVERT: K 348 MET cc_start: 0.8519 (mtt) cc_final: 0.8310 (mtp) REVERT: K 396 ARG cc_start: 0.8266 (tpt170) cc_final: 0.7980 (tpp80) REVERT: K 495 HIS cc_start: 0.8484 (t-90) cc_final: 0.8171 (t70) REVERT: K 622 ARG cc_start: 0.9059 (mmm160) cc_final: 0.8388 (tpt90) REVERT: K 764 ARG cc_start: 0.8731 (ttt-90) cc_final: 0.8528 (tpt-90) REVERT: K 766 MET cc_start: 0.8675 (mmp) cc_final: 0.8405 (mmp) REVERT: K 769 ASP cc_start: 0.7752 (t0) cc_final: 0.7469 (t0) REVERT: K 774 PHE cc_start: 0.8604 (m-10) cc_final: 0.8213 (m-10) REVERT: K 800 PHE cc_start: 0.8834 (p90) cc_final: 0.8626 (p90) REVERT: K 878 LYS cc_start: 0.8405 (mmmt) cc_final: 0.8118 (mmmt) outliers start: 154 outliers final: 95 residues processed: 1360 average time/residue: 0.7657 time to fit residues: 1759.6093 Evaluate side-chains 1205 residues out of total 8837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1101 time to evaluate : 6.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 829 MET Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 769 ASP Chi-restraints excluded: chain B residue 820 GLU Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 884 MET Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 718 ILE Chi-restraints excluded: chain D residue 840 VAL Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 455 ILE Chi-restraints excluded: chain E residue 698 MET Chi-restraints excluded: chain E residue 699 LEU Chi-restraints excluded: chain E residue 793 ASP Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 194 ASN Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 471 TYR Chi-restraints excluded: chain F residue 492 MET Chi-restraints excluded: chain F residue 794 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 321 THR Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 496 CYS Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 179 HIS Chi-restraints excluded: chain H residue 391 THR Chi-restraints excluded: chain H residue 412 THR Chi-restraints excluded: chain H residue 414 VAL Chi-restraints excluded: chain H residue 570 ASP Chi-restraints excluded: chain H residue 608 SER Chi-restraints excluded: chain H residue 614 MET Chi-restraints excluded: chain H residue 851 VAL Chi-restraints excluded: chain H residue 861 VAL Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 172 LEU Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 271 LEU Chi-restraints excluded: chain I residue 391 THR Chi-restraints excluded: chain I residue 671 MET Chi-restraints excluded: chain I residue 772 VAL Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain J residue 271 LEU Chi-restraints excluded: chain J residue 407 LEU Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 595 VAL Chi-restraints excluded: chain J residue 739 ASP Chi-restraints excluded: chain J residue 777 VAL Chi-restraints excluded: chain J residue 857 ILE Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 354 ILE Chi-restraints excluded: chain K residue 595 VAL Chi-restraints excluded: chain K residue 619 LEU Chi-restraints excluded: chain K residue 683 LEU Chi-restraints excluded: chain K residue 794 VAL Chi-restraints excluded: chain K residue 839 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 996 random chunks: chunk 502 optimal weight: 4.9990 chunk 280 optimal weight: 0.9990 chunk 752 optimal weight: 0.6980 chunk 615 optimal weight: 9.9990 chunk 249 optimal weight: 10.0000 chunk 906 optimal weight: 0.7980 chunk 978 optimal weight: 10.0000 chunk 806 optimal weight: 7.9990 chunk 898 optimal weight: 20.0000 chunk 308 optimal weight: 10.0000 chunk 726 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 GLN A1239 GLN B 378 HIS ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 HIS B 659 ASN C 676 GLN D 539 HIS E 230 GLN E 433 GLN ** E 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 HIS ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 389 ASN ** F 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 539 HIS G 433 GLN G 621 GLN ** G 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN H 179 HIS H 270 GLN ** H 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 754 ASN ** H 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 532 GLN I 706 HIS J 153 HIS J 179 HIS J 196 ASN ** J 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 539 HIS J 757 GLN K 47 GLN K 92 HIS ** K 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 82657 Z= 0.170 Angle : 0.530 12.104 112186 Z= 0.270 Chirality : 0.043 0.168 12540 Planarity : 0.004 0.052 14541 Dihedral : 4.872 57.685 11239 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.52 % Allowed : 15.31 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.08), residues: 9970 helix: -1.79 (0.07), residues: 4130 sheet: -1.45 (0.15), residues: 1137 loop : -1.97 (0.08), residues: 4703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 105 HIS 0.010 0.001 HIS H 179 PHE 0.025 0.001 PHE A 608 TYR 0.017 0.001 TYR B 50 ARG 0.007 0.000 ARG E 241 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19940 Ramachandran restraints generated. 9970 Oldfield, 0 Emsley, 9970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19940 Ramachandran restraints generated. 9970 Oldfield, 0 Emsley, 9970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1419 residues out of total 8837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1196 time to evaluate : 7.064 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: A 35 TYR cc_start: 0.5555 (OUTLIER) cc_final: 0.4743 (p90) REVERT: A 69 ARG cc_start: 0.7899 (mtm110) cc_final: 0.7632 (mtp85) REVERT: A 206 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7341 (tm-30) REVERT: A 207 MET cc_start: 0.8843 (ttp) cc_final: 0.8383 (ttp) REVERT: A 210 MET cc_start: 0.8194 (tpp) cc_final: 0.7894 (tpp) REVERT: A 242 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8675 (mp) REVERT: A 329 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8197 (tp30) REVERT: A 412 LEU cc_start: 0.8751 (mm) cc_final: 0.8520 (mm) REVERT: A 436 ASP cc_start: 0.8416 (p0) cc_final: 0.8180 (p0) REVERT: A 441 MET cc_start: 0.8981 (ttm) cc_final: 0.8006 (mtp) REVERT: A 500 TYR cc_start: 0.8561 (m-80) cc_final: 0.8240 (m-80) REVERT: A 614 GLN cc_start: 0.7979 (mt0) cc_final: 0.7725 (mt0) REVERT: A 635 GLN cc_start: 0.8055 (tt0) cc_final: 0.7744 (tm-30) REVERT: A 760 GLN cc_start: 0.8575 (mt0) cc_final: 0.8156 (tt0) REVERT: A 829 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7057 (mtm) REVERT: A 1087 ASP cc_start: 0.8748 (m-30) cc_final: 0.8107 (p0) REVERT: A 1195 LYS cc_start: 0.8595 (tmtt) cc_final: 0.8336 (tmtt) REVERT: A 1285 LYS cc_start: 0.6698 (mttm) cc_final: 0.6355 (mmtt) REVERT: B 84 LYS cc_start: 0.8870 (mttp) cc_final: 0.8282 (mmtt) REVERT: B 183 ILE cc_start: 0.8890 (mm) cc_final: 0.8686 (mm) REVERT: B 524 MET cc_start: 0.9080 (mmt) cc_final: 0.8733 (mmt) REVERT: B 547 ASP cc_start: 0.8002 (p0) cc_final: 0.7785 (p0) REVERT: B 638 LYS cc_start: 0.9051 (tptt) cc_final: 0.8733 (tptm) REVERT: B 698 MET cc_start: 0.9049 (mmm) cc_final: 0.8735 (tpp) REVERT: B 714 ARG cc_start: 0.8412 (ttm170) cc_final: 0.7996 (ptt180) REVERT: B 769 ASP cc_start: 0.9257 (OUTLIER) cc_final: 0.8800 (t70) REVERT: B 816 LYS cc_start: 0.9273 (mttt) cc_final: 0.8972 (mtpp) REVERT: B 856 ARG cc_start: 0.8402 (ptt180) cc_final: 0.7726 (mmt-90) REVERT: C 111 MET cc_start: 0.8871 (tpt) cc_final: 0.8454 (tpt) REVERT: C 187 LEU cc_start: 0.9070 (mm) cc_final: 0.8270 (mt) REVERT: C 253 GLU cc_start: 0.7699 (tt0) cc_final: 0.7165 (tt0) REVERT: C 291 MET cc_start: 0.8659 (mmm) cc_final: 0.8249 (mmm) REVERT: C 478 ASP cc_start: 0.7615 (t0) cc_final: 0.7174 (t0) REVERT: C 480 ARG cc_start: 0.8191 (ttp-110) cc_final: 0.7868 (ttp-110) REVERT: C 548 MET cc_start: 0.9255 (mtt) cc_final: 0.9043 (mtp) REVERT: C 592 MET cc_start: 0.9117 (ptp) cc_final: 0.8893 (ptp) REVERT: C 620 MET cc_start: 0.8776 (mmt) cc_final: 0.8570 (mmt) REVERT: C 698 MET cc_start: 0.8801 (mmm) cc_final: 0.8504 (mmm) REVERT: C 705 MET cc_start: 0.9209 (ttt) cc_final: 0.8877 (tpp) REVERT: C 721 PHE cc_start: 0.8044 (t80) cc_final: 0.7672 (t80) REVERT: C 754 ASN cc_start: 0.8319 (m110) cc_final: 0.8035 (m110) REVERT: C 786 TYR cc_start: 0.4550 (m-80) cc_final: 0.4270 (m-80) REVERT: C 884 MET cc_start: 0.7952 (mtt) cc_final: 0.7620 (mmm) REVERT: D 71 ILE cc_start: 0.9184 (mm) cc_final: 0.8827 (mt) REVERT: D 98 ARG cc_start: 0.9040 (mmm-85) cc_final: 0.8673 (ttm170) REVERT: D 111 MET cc_start: 0.9477 (tpp) cc_final: 0.9235 (tpt) REVERT: D 167 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7349 (pp20) REVERT: D 270 GLN cc_start: 0.8517 (mt0) cc_final: 0.8271 (mt0) REVERT: D 271 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8261 (tm) REVERT: D 371 MET cc_start: 0.9100 (mtt) cc_final: 0.8335 (mtt) REVERT: D 407 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.8769 (pp) REVERT: D 413 ARG cc_start: 0.8203 (ttm170) cc_final: 0.7846 (ttt-90) REVERT: D 537 ASP cc_start: 0.8710 (OUTLIER) cc_final: 0.7837 (t70) REVERT: D 562 GLN cc_start: 0.6859 (mp10) cc_final: 0.6616 (mp10) REVERT: D 667 MET cc_start: 0.9009 (tpt) cc_final: 0.8580 (tpt) REVERT: D 693 ASP cc_start: 0.8289 (t0) cc_final: 0.7757 (t0) REVERT: D 731 MET cc_start: 0.9408 (ttt) cc_final: 0.8823 (ttp) REVERT: D 759 ARG cc_start: 0.8074 (mtt180) cc_final: 0.7236 (tmt170) REVERT: E 120 GLU cc_start: 0.8572 (pm20) cc_final: 0.8164 (pm20) REVERT: E 218 ASN cc_start: 0.8341 (m110) cc_final: 0.8121 (m110) REVERT: E 276 GLN cc_start: 0.8645 (tp-100) cc_final: 0.8391 (mm-40) REVERT: E 610 MET cc_start: 0.9166 (mtt) cc_final: 0.8937 (mtt) REVERT: E 667 MET cc_start: 0.8096 (tpp) cc_final: 0.7795 (tpt) REVERT: E 699 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8712 (pp) REVERT: E 709 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7976 (mmm) REVERT: E 754 ASN cc_start: 0.9020 (m-40) cc_final: 0.8590 (m-40) REVERT: E 764 ARG cc_start: 0.8919 (mtp-110) cc_final: 0.8377 (tpt-90) REVERT: E 848 MET cc_start: 0.8006 (mmm) cc_final: 0.7325 (mmm) REVERT: F 98 ARG cc_start: 0.8521 (mtm-85) cc_final: 0.7956 (mtp-110) REVERT: F 121 ASP cc_start: 0.8403 (p0) cc_final: 0.7862 (p0) REVERT: F 156 MET cc_start: 0.7589 (ptt) cc_final: 0.7211 (ptt) REVERT: F 167 GLU cc_start: 0.8542 (tp30) cc_final: 0.7173 (tp30) REVERT: F 169 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8398 (ptpp) REVERT: F 187 LEU cc_start: 0.9520 (tt) cc_final: 0.9259 (tt) REVERT: F 193 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7188 (tm-30) REVERT: F 276 GLN cc_start: 0.8475 (tp-100) cc_final: 0.8270 (tp40) REVERT: F 471 TYR cc_start: 0.7733 (OUTLIER) cc_final: 0.6894 (m-80) REVERT: F 499 GLU cc_start: 0.8531 (mm-30) cc_final: 0.7738 (mm-30) REVERT: F 524 MET cc_start: 0.8925 (mmm) cc_final: 0.8227 (mmt) REVERT: F 638 LYS cc_start: 0.8800 (tptt) cc_final: 0.8502 (mmtt) REVERT: F 662 ASN cc_start: 0.8423 (p0) cc_final: 0.8095 (p0) REVERT: F 685 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7483 (tm-30) REVERT: F 698 MET cc_start: 0.9219 (mmm) cc_final: 0.8892 (mmm) REVERT: F 714 ARG cc_start: 0.7023 (ttp80) cc_final: 0.6543 (ptt-90) REVERT: F 733 GLU cc_start: 0.6357 (tm-30) cc_final: 0.6091 (tm-30) REVERT: G 10 GLU cc_start: 0.6164 (pp20) cc_final: 0.5855 (pp20) REVERT: G 111 MET cc_start: 0.9103 (tpp) cc_final: 0.8687 (tpp) REVERT: G 250 TYR cc_start: 0.8241 (m-10) cc_final: 0.7979 (m-10) REVERT: G 492 MET cc_start: 0.8056 (ttm) cc_final: 0.7589 (ttm) REVERT: G 503 MET cc_start: 0.9246 (ttt) cc_final: 0.9026 (ttt) REVERT: G 668 ARG cc_start: 0.8693 (ttp-170) cc_final: 0.8112 (ttm110) REVERT: G 727 TYR cc_start: 0.8241 (p90) cc_final: 0.7607 (p90) REVERT: G 848 MET cc_start: 0.8340 (mmm) cc_final: 0.7898 (mmm) REVERT: H 40 MET cc_start: 0.6832 (ttt) cc_final: 0.6472 (ttt) REVERT: H 51 MET cc_start: 0.5830 (tmm) cc_final: 0.5629 (tmm) REVERT: H 66 LYS cc_start: 0.8531 (tmtt) cc_final: 0.8326 (ttmt) REVERT: H 98 ARG cc_start: 0.8518 (mtm-85) cc_final: 0.8063 (mtt-85) REVERT: H 100 ARG cc_start: 0.8111 (mtt180) cc_final: 0.7599 (mtm110) REVERT: H 262 ASP cc_start: 0.8870 (p0) cc_final: 0.8316 (p0) REVERT: H 519 MET cc_start: 0.9225 (tpt) cc_final: 0.8615 (mmt) REVERT: H 535 ASN cc_start: 0.8827 (m-40) cc_final: 0.8372 (m-40) REVERT: H 664 ARG cc_start: 0.8444 (mtp85) cc_final: 0.8090 (mtp85) REVERT: H 695 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8155 (mt-10) REVERT: H 698 MET cc_start: 0.9161 (mmm) cc_final: 0.8681 (mmm) REVERT: H 731 MET cc_start: 0.9152 (tpp) cc_final: 0.8928 (tpp) REVERT: H 739 ASP cc_start: 0.8190 (m-30) cc_final: 0.7977 (m-30) REVERT: H 740 ARG cc_start: 0.8154 (mtp85) cc_final: 0.7875 (ttm-80) REVERT: H 747 GLU cc_start: 0.8573 (mp0) cc_final: 0.8227 (mp0) REVERT: H 766 MET cc_start: 0.8206 (mmm) cc_final: 0.7469 (mtm) REVERT: H 786 TYR cc_start: 0.6049 (m-80) cc_final: 0.5562 (m-80) REVERT: I 51 MET cc_start: 0.8542 (tmm) cc_final: 0.8194 (tmm) REVERT: I 58 ASP cc_start: 0.8336 (t0) cc_final: 0.7995 (t0) REVERT: I 182 MET cc_start: 0.6783 (ttt) cc_final: 0.6511 (ttm) REVERT: I 227 VAL cc_start: 0.9233 (t) cc_final: 0.9009 (m) REVERT: I 308 ARG cc_start: 0.8683 (mtp180) cc_final: 0.8443 (mtp85) REVERT: I 503 MET cc_start: 0.9116 (tmm) cc_final: 0.8796 (ttt) REVERT: I 622 ARG cc_start: 0.8686 (mmm160) cc_final: 0.8296 (ttp-170) REVERT: I 694 PHE cc_start: 0.9259 (m-80) cc_final: 0.9007 (m-80) REVERT: J 81 LYS cc_start: 0.8837 (ttmt) cc_final: 0.8603 (ttpt) REVERT: J 122 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7382 (mm-30) REVERT: J 407 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8698 (pp) REVERT: J 532 GLN cc_start: 0.8678 (mt0) cc_final: 0.8429 (mt0) REVERT: J 592 MET cc_start: 0.7748 (mmt) cc_final: 0.7300 (mmt) REVERT: J 709 MET cc_start: 0.8647 (ptm) cc_final: 0.8212 (ptm) REVERT: J 720 ARG cc_start: 0.9175 (mmm-85) cc_final: 0.7998 (ptm160) REVERT: J 755 MET cc_start: 0.8909 (mtt) cc_final: 0.8598 (mtm) REVERT: K 172 LEU cc_start: 0.8524 (mt) cc_final: 0.8290 (mp) REVERT: K 182 MET cc_start: 0.6270 (mmm) cc_final: 0.5730 (ptm) REVERT: K 348 MET cc_start: 0.8542 (mtt) cc_final: 0.8293 (mtp) REVERT: K 396 ARG cc_start: 0.8231 (tpt170) cc_final: 0.7995 (tpp80) REVERT: K 449 TYR cc_start: 0.9180 (m-80) cc_final: 0.8896 (m-80) REVERT: K 622 ARG cc_start: 0.9048 (mmm160) cc_final: 0.8378 (tpt90) REVERT: K 661 ILE cc_start: 0.8915 (mt) cc_final: 0.8703 (mm) REVERT: K 764 ARG cc_start: 0.8736 (ttt-90) cc_final: 0.8523 (tpt-90) REVERT: K 769 ASP cc_start: 0.7844 (t0) cc_final: 0.7500 (t0) REVERT: K 774 PHE cc_start: 0.8633 (m-10) cc_final: 0.8266 (m-10) REVERT: K 800 PHE cc_start: 0.8818 (p90) cc_final: 0.8614 (p90) REVERT: K 878 LYS cc_start: 0.8411 (mmmt) cc_final: 0.8098 (mmmt) REVERT: K 881 MET cc_start: 0.9069 (mmt) cc_final: 0.8804 (mmt) outliers start: 223 outliers final: 137 residues processed: 1362 average time/residue: 0.7515 time to fit residues: 1741.0803 Evaluate side-chains 1271 residues out of total 8837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1123 time to evaluate : 7.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 829 MET Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 769 ASP Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 884 MET Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 676 GLN Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 244 HIS Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 718 ILE Chi-restraints excluded: chain D residue 814 THR Chi-restraints excluded: chain D residue 840 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 699 LEU Chi-restraints excluded: chain E residue 709 MET Chi-restraints excluded: chain E residue 793 ASP Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 194 ASN Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain F residue 471 TYR Chi-restraints excluded: chain F residue 492 MET Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 794 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 321 THR Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 179 HIS Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 227 VAL Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 391 THR Chi-restraints excluded: chain H residue 412 THR Chi-restraints excluded: chain H residue 414 VAL Chi-restraints excluded: chain H residue 483 ILE Chi-restraints excluded: chain H residue 570 ASP Chi-restraints excluded: chain H residue 614 MET Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain H residue 851 VAL Chi-restraints excluded: chain H residue 861 VAL Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 271 LEU Chi-restraints excluded: chain I residue 391 THR Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 671 MET Chi-restraints excluded: chain I residue 772 VAL Chi-restraints excluded: chain I residue 792 ASP Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 191 ILE Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain J residue 271 LEU Chi-restraints excluded: chain J residue 388 THR Chi-restraints excluded: chain J residue 407 LEU Chi-restraints excluded: chain J residue 445 THR Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 652 MET Chi-restraints excluded: chain J residue 739 ASP Chi-restraints excluded: chain J residue 777 VAL Chi-restraints excluded: chain J residue 857 ILE Chi-restraints excluded: chain J residue 865 GLN Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 145 LEU Chi-restraints excluded: chain K residue 244 HIS Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 478 ASP Chi-restraints excluded: chain K residue 525 VAL Chi-restraints excluded: chain K residue 570 ASP Chi-restraints excluded: chain K residue 595 VAL Chi-restraints excluded: chain K residue 662 ASN Chi-restraints excluded: chain K residue 683 LEU Chi-restraints excluded: chain K residue 794 VAL Chi-restraints excluded: chain K residue 839 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 996 random chunks: chunk 895 optimal weight: 30.0000 chunk 681 optimal weight: 5.9990 chunk 470 optimal weight: 0.3980 chunk 100 optimal weight: 0.0270 chunk 432 optimal weight: 1.9990 chunk 608 optimal weight: 7.9990 chunk 909 optimal weight: 0.9980 chunk 962 optimal weight: 9.9990 chunk 475 optimal weight: 30.0000 chunk 861 optimal weight: 9.9990 chunk 259 optimal weight: 8.9990 overall best weight: 1.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 GLN A1053 ASN A1239 GLN B 467 HIS ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 ASN F 270 GLN F 276 GLN F 288 ASN ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 HIS ** H 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 378 HIS ** H 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 484 ASN I 659 ASN J 196 ASN J 288 ASN ** J 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 82657 Z= 0.147 Angle : 0.506 11.256 112186 Z= 0.256 Chirality : 0.042 0.243 12540 Planarity : 0.004 0.045 14541 Dihedral : 4.587 57.413 11234 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.51 % Allowed : 16.36 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.08), residues: 9970 helix: -1.11 (0.08), residues: 4093 sheet: -1.27 (0.15), residues: 1159 loop : -1.74 (0.09), residues: 4718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 771 HIS 0.005 0.001 HIS H 179 PHE 0.023 0.001 PHE A 114 TYR 0.022 0.001 TYR B 50 ARG 0.007 0.000 ARG I 664 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19940 Ramachandran restraints generated. 9970 Oldfield, 0 Emsley, 9970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19940 Ramachandran restraints generated. 9970 Oldfield, 0 Emsley, 9970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1403 residues out of total 8837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1181 time to evaluate : 7.072 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: A 35 TYR cc_start: 0.6509 (OUTLIER) cc_final: 0.5537 (p90) REVERT: A 206 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7238 (tm-30) REVERT: A 207 MET cc_start: 0.8846 (ttp) cc_final: 0.8422 (ttp) REVERT: A 210 MET cc_start: 0.8235 (tpp) cc_final: 0.7795 (tpp) REVERT: A 329 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8160 (tp30) REVERT: A 412 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8469 (mm) REVERT: A 441 MET cc_start: 0.8961 (ttm) cc_final: 0.7926 (mtp) REVERT: A 443 ARG cc_start: 0.6371 (mmt180) cc_final: 0.6004 (mmm160) REVERT: A 500 TYR cc_start: 0.8559 (m-80) cc_final: 0.8273 (m-80) REVERT: A 614 GLN cc_start: 0.7947 (mt0) cc_final: 0.7591 (mt0) REVERT: A 634 GLU cc_start: 0.7633 (mp0) cc_final: 0.7316 (mp0) REVERT: A 760 GLN cc_start: 0.8583 (mt0) cc_final: 0.8172 (tt0) REVERT: A 802 LYS cc_start: 0.9179 (mmmm) cc_final: 0.8455 (mttm) REVERT: A 829 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7441 (mtm) REVERT: A 940 MET cc_start: 0.9279 (tpp) cc_final: 0.8977 (tpp) REVERT: A 1087 ASP cc_start: 0.8731 (m-30) cc_final: 0.8113 (p0) REVERT: A 1285 LYS cc_start: 0.6667 (mttm) cc_final: 0.6331 (mmtt) REVERT: B 84 LYS cc_start: 0.8848 (mttp) cc_final: 0.8267 (mmtt) REVERT: B 524 MET cc_start: 0.9059 (mmt) cc_final: 0.8707 (mmt) REVERT: B 638 LYS cc_start: 0.8990 (tptt) cc_final: 0.8699 (tptm) REVERT: B 698 MET cc_start: 0.9032 (mmm) cc_final: 0.8741 (tpp) REVERT: B 714 ARG cc_start: 0.8410 (ttm170) cc_final: 0.7999 (ptt180) REVERT: B 769 ASP cc_start: 0.9159 (OUTLIER) cc_final: 0.8886 (t70) REVERT: B 816 LYS cc_start: 0.9282 (mttt) cc_final: 0.8979 (mtpp) REVERT: B 856 ARG cc_start: 0.8386 (ptt180) cc_final: 0.7699 (mmt-90) REVERT: C 187 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8310 (mt) REVERT: C 291 MET cc_start: 0.8591 (mmm) cc_final: 0.8157 (mmm) REVERT: C 478 ASP cc_start: 0.7698 (t0) cc_final: 0.7227 (t0) REVERT: C 480 ARG cc_start: 0.8202 (ttp-110) cc_final: 0.7897 (ttp-110) REVERT: C 498 ASN cc_start: 0.8717 (t0) cc_final: 0.8504 (t0) REVERT: C 510 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7540 (m-30) REVERT: C 548 MET cc_start: 0.9260 (mtt) cc_final: 0.9027 (mtp) REVERT: C 592 MET cc_start: 0.9078 (ptp) cc_final: 0.8831 (ptp) REVERT: C 694 PHE cc_start: 0.8646 (m-80) cc_final: 0.8429 (m-80) REVERT: C 698 MET cc_start: 0.8799 (mmm) cc_final: 0.8529 (mmm) REVERT: C 705 MET cc_start: 0.9257 (ttt) cc_final: 0.8929 (tpp) REVERT: C 721 PHE cc_start: 0.8157 (t80) cc_final: 0.7803 (t80) REVERT: C 754 ASN cc_start: 0.8348 (m110) cc_final: 0.8042 (m110) REVERT: C 786 TYR cc_start: 0.4588 (m-80) cc_final: 0.4309 (m-80) REVERT: C 881 MET cc_start: 0.8242 (mmm) cc_final: 0.7902 (mmt) REVERT: C 884 MET cc_start: 0.7934 (mtt) cc_final: 0.7606 (mmm) REVERT: D 71 ILE cc_start: 0.9177 (mm) cc_final: 0.8818 (mt) REVERT: D 98 ARG cc_start: 0.9023 (mmm-85) cc_final: 0.8673 (ttm170) REVERT: D 167 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7187 (pp20) REVERT: D 270 GLN cc_start: 0.8446 (mt0) cc_final: 0.8191 (mt0) REVERT: D 371 MET cc_start: 0.9099 (mtt) cc_final: 0.8354 (mtt) REVERT: D 407 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.8784 (pp) REVERT: D 413 ARG cc_start: 0.8193 (ttm170) cc_final: 0.7841 (ttt-90) REVERT: D 519 MET cc_start: 0.8933 (mmm) cc_final: 0.8536 (mmm) REVERT: D 537 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.7800 (t70) REVERT: D 562 GLN cc_start: 0.6858 (mp10) cc_final: 0.6629 (mp10) REVERT: D 620 MET cc_start: 0.9319 (mmt) cc_final: 0.9072 (mmt) REVERT: D 667 MET cc_start: 0.8984 (tpt) cc_final: 0.8672 (tpt) REVERT: D 693 ASP cc_start: 0.8435 (t0) cc_final: 0.7901 (t0) REVERT: D 698 MET cc_start: 0.9323 (mmm) cc_final: 0.9067 (mmm) REVERT: D 731 MET cc_start: 0.9375 (ttt) cc_final: 0.8766 (ttp) REVERT: D 759 ARG cc_start: 0.8033 (mtt180) cc_final: 0.7222 (tmt170) REVERT: E 120 GLU cc_start: 0.8463 (pm20) cc_final: 0.8073 (pm20) REVERT: E 218 ASN cc_start: 0.8391 (m110) cc_final: 0.8153 (m110) REVERT: E 276 GLN cc_start: 0.8634 (tp-100) cc_final: 0.8403 (mm-40) REVERT: E 502 ARG cc_start: 0.8864 (ptm-80) cc_final: 0.8466 (ttp-110) REVERT: E 667 MET cc_start: 0.7841 (tpp) cc_final: 0.7537 (tpt) REVERT: E 699 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8660 (pp) REVERT: E 709 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7903 (mmm) REVERT: E 754 ASN cc_start: 0.8980 (m-40) cc_final: 0.8577 (m-40) REVERT: E 848 MET cc_start: 0.7955 (mmm) cc_final: 0.7049 (mmm) REVERT: E 884 MET cc_start: 0.8444 (mtp) cc_final: 0.7906 (mmm) REVERT: F 98 ARG cc_start: 0.8533 (mtm-85) cc_final: 0.7972 (mtp-110) REVERT: F 121 ASP cc_start: 0.8444 (p0) cc_final: 0.8075 (p0) REVERT: F 156 MET cc_start: 0.7577 (ptt) cc_final: 0.7203 (ptt) REVERT: F 167 GLU cc_start: 0.8654 (tp30) cc_final: 0.8439 (tp30) REVERT: F 169 LYS cc_start: 0.8940 (mmmt) cc_final: 0.8589 (mttt) REVERT: F 185 ASN cc_start: 0.9120 (m-40) cc_final: 0.8912 (m110) REVERT: F 187 LEU cc_start: 0.9505 (tt) cc_final: 0.9263 (tt) REVERT: F 193 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7269 (tm-30) REVERT: F 233 ARG cc_start: 0.8151 (ttp-110) cc_final: 0.7844 (ttp-110) REVERT: F 471 TYR cc_start: 0.7701 (OUTLIER) cc_final: 0.6848 (m-80) REVERT: F 524 MET cc_start: 0.8961 (mmm) cc_final: 0.8111 (mmt) REVERT: F 638 LYS cc_start: 0.8785 (tptt) cc_final: 0.8491 (mmtt) REVERT: F 662 ASN cc_start: 0.8375 (p0) cc_final: 0.8034 (p0) REVERT: F 685 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7515 (tm-30) REVERT: F 694 PHE cc_start: 0.8954 (m-10) cc_final: 0.8580 (m-10) REVERT: F 698 MET cc_start: 0.9198 (mmm) cc_final: 0.8853 (mmm) REVERT: F 714 ARG cc_start: 0.7011 (ttp80) cc_final: 0.6537 (ptt-90) REVERT: F 726 PHE cc_start: 0.8352 (t80) cc_final: 0.8104 (t80) REVERT: F 733 GLU cc_start: 0.6280 (tm-30) cc_final: 0.5899 (tm-30) REVERT: F 771 TRP cc_start: 0.8968 (m-10) cc_final: 0.8479 (m-10) REVERT: G 10 GLU cc_start: 0.6161 (pp20) cc_final: 0.5779 (pp20) REVERT: G 250 TYR cc_start: 0.8221 (m-10) cc_final: 0.7956 (m-10) REVERT: G 492 MET cc_start: 0.7662 (ttm) cc_final: 0.7408 (ttm) REVERT: G 500 MET cc_start: 0.9374 (tpt) cc_final: 0.9160 (tpt) REVERT: G 614 MET cc_start: 0.8916 (mtt) cc_final: 0.8625 (mtt) REVERT: G 668 ARG cc_start: 0.8676 (ttp-170) cc_final: 0.8297 (ttm110) REVERT: G 709 MET cc_start: 0.8392 (mtm) cc_final: 0.8191 (mtm) REVERT: G 727 TYR cc_start: 0.8209 (p90) cc_final: 0.7606 (p90) REVERT: G 848 MET cc_start: 0.8284 (mmm) cc_final: 0.7863 (mmm) REVERT: H 40 MET cc_start: 0.6862 (ttt) cc_final: 0.6556 (ttt) REVERT: H 51 MET cc_start: 0.5629 (tmm) cc_final: 0.5350 (tmm) REVERT: H 98 ARG cc_start: 0.8508 (mtm-85) cc_final: 0.8044 (mtt-85) REVERT: H 231 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7684 (mm-30) REVERT: H 262 ASP cc_start: 0.8858 (p0) cc_final: 0.8311 (p0) REVERT: H 519 MET cc_start: 0.9192 (tpt) cc_final: 0.8627 (mmt) REVERT: H 532 GLN cc_start: 0.8566 (mt0) cc_final: 0.8252 (mt0) REVERT: H 535 ASN cc_start: 0.8879 (m-40) cc_final: 0.8425 (m-40) REVERT: H 632 ARG cc_start: 0.8371 (mpt180) cc_final: 0.8166 (mmt-90) REVERT: H 695 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8230 (mt-10) REVERT: H 698 MET cc_start: 0.9187 (mmm) cc_final: 0.8675 (mmm) REVERT: H 731 MET cc_start: 0.9190 (tpp) cc_final: 0.8929 (tpp) REVERT: H 739 ASP cc_start: 0.8214 (m-30) cc_final: 0.7937 (m-30) REVERT: H 740 ARG cc_start: 0.8167 (mtp85) cc_final: 0.7849 (ttm-80) REVERT: H 747 GLU cc_start: 0.8603 (mp0) cc_final: 0.8286 (mp0) REVERT: H 766 MET cc_start: 0.8217 (mmm) cc_final: 0.7474 (mtm) REVERT: H 786 TYR cc_start: 0.6170 (m-80) cc_final: 0.5686 (m-80) REVERT: H 848 MET cc_start: 0.9226 (mmp) cc_final: 0.8701 (mmp) REVERT: I 58 ASP cc_start: 0.8342 (t0) cc_final: 0.7974 (t0) REVERT: I 137 ILE cc_start: 0.9210 (mt) cc_final: 0.8986 (mp) REVERT: I 182 MET cc_start: 0.6562 (ttt) cc_final: 0.6256 (ttm) REVERT: I 503 MET cc_start: 0.9106 (tmm) cc_final: 0.8784 (ttt) REVERT: I 622 ARG cc_start: 0.8744 (mmm160) cc_final: 0.8378 (ttp-170) REVERT: I 694 PHE cc_start: 0.9255 (m-80) cc_final: 0.9025 (m-80) REVERT: I 856 ARG cc_start: 0.8797 (mmt180) cc_final: 0.8259 (ttm-80) REVERT: J 81 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8540 (ttpt) REVERT: J 95 MET cc_start: 0.8624 (mtm) cc_final: 0.8331 (mtm) REVERT: J 407 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8708 (pp) REVERT: J 449 TYR cc_start: 0.9125 (m-80) cc_final: 0.8845 (m-80) REVERT: J 532 GLN cc_start: 0.8665 (mt0) cc_final: 0.8373 (mt0) REVERT: J 592 MET cc_start: 0.7770 (mmt) cc_final: 0.7422 (mmt) REVERT: J 709 MET cc_start: 0.8633 (ptm) cc_final: 0.8399 (ptm) REVERT: J 720 ARG cc_start: 0.9176 (mmm-85) cc_final: 0.7997 (ptm160) REVERT: J 755 MET cc_start: 0.8890 (mtt) cc_final: 0.8593 (mtm) REVERT: K 172 LEU cc_start: 0.8515 (mt) cc_final: 0.8286 (mp) REVERT: K 182 MET cc_start: 0.6008 (mmm) cc_final: 0.5633 (ptm) REVERT: K 348 MET cc_start: 0.8537 (mtt) cc_final: 0.8336 (mtp) REVERT: K 449 TYR cc_start: 0.9174 (m-80) cc_final: 0.8919 (m-80) REVERT: K 480 ARG cc_start: 0.7880 (mtm-85) cc_final: 0.7485 (mtm-85) REVERT: K 610 MET cc_start: 0.8775 (mmm) cc_final: 0.8425 (mtt) REVERT: K 622 ARG cc_start: 0.9045 (mmm160) cc_final: 0.8381 (tpt90) REVERT: K 661 ILE cc_start: 0.8846 (mt) cc_final: 0.8613 (mm) REVERT: K 709 MET cc_start: 0.8503 (ttp) cc_final: 0.7399 (tpp) REVERT: K 764 ARG cc_start: 0.8785 (ttt-90) cc_final: 0.8575 (tpt-90) REVERT: K 769 ASP cc_start: 0.8077 (t0) cc_final: 0.7707 (t0) REVERT: K 774 PHE cc_start: 0.8629 (m-10) cc_final: 0.8250 (m-10) REVERT: K 800 PHE cc_start: 0.8867 (p90) cc_final: 0.8604 (p90) REVERT: K 878 LYS cc_start: 0.8391 (mmmt) cc_final: 0.8053 (mmmt) REVERT: K 881 MET cc_start: 0.9058 (mmt) cc_final: 0.8685 (mmt) outliers start: 222 outliers final: 144 residues processed: 1334 average time/residue: 0.7552 time to fit residues: 1713.3754 Evaluate side-chains 1270 residues out of total 8837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1114 time to evaluate : 7.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 829 MET Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 849 GLN Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 769 ASP Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 884 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 244 HIS Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 814 THR Chi-restraints excluded: chain D residue 840 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 388 THR Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 496 CYS Chi-restraints excluded: chain E residue 699 LEU Chi-restraints excluded: chain E residue 709 MET Chi-restraints excluded: chain E residue 793 ASP Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 194 ASN Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain F residue 471 TYR Chi-restraints excluded: chain F residue 492 MET Chi-restraints excluded: chain F residue 883 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 321 THR Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 179 HIS Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 227 VAL Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 391 THR Chi-restraints excluded: chain H residue 570 ASP Chi-restraints excluded: chain H residue 608 SER Chi-restraints excluded: chain H residue 851 VAL Chi-restraints excluded: chain H residue 861 VAL Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 271 LEU Chi-restraints excluded: chain I residue 391 THR Chi-restraints excluded: chain I residue 455 ILE Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 755 MET Chi-restraints excluded: chain I residue 772 VAL Chi-restraints excluded: chain I residue 792 ASP Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 191 ILE Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain J residue 271 LEU Chi-restraints excluded: chain J residue 407 LEU Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 595 VAL Chi-restraints excluded: chain J residue 739 ASP Chi-restraints excluded: chain J residue 777 VAL Chi-restraints excluded: chain J residue 857 ILE Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 244 HIS Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 354 ILE Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 478 ASP Chi-restraints excluded: chain K residue 510 ASP Chi-restraints excluded: chain K residue 570 ASP Chi-restraints excluded: chain K residue 595 VAL Chi-restraints excluded: chain K residue 619 LEU Chi-restraints excluded: chain K residue 652 MET Chi-restraints excluded: chain K residue 662 ASN Chi-restraints excluded: chain K residue 683 LEU Chi-restraints excluded: chain K residue 745 THR Chi-restraints excluded: chain K residue 794 VAL Chi-restraints excluded: chain K residue 839 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 996 random chunks: chunk 801 optimal weight: 30.0000 chunk 546 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 716 optimal weight: 6.9990 chunk 397 optimal weight: 20.0000 chunk 821 optimal weight: 20.0000 chunk 665 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 491 optimal weight: 6.9990 chunk 864 optimal weight: 6.9990 chunk 242 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 HIS ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1239 GLN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 581 ASN C 532 GLN D 417 ASN D 754 ASN E 244 HIS E 581 ASN ** E 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 261 GLN ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 HIS ** G 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 HIS ** H 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 288 ASN ** H 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 467 HIS ** H 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 196 ASN J 276 GLN J 288 ASN ** J 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 532 GLN ** K 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 82657 Z= 0.303 Angle : 0.562 10.784 112186 Z= 0.284 Chirality : 0.044 0.189 12540 Planarity : 0.004 0.046 14541 Dihedral : 4.637 56.281 11228 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.17 % Allowed : 16.70 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.08), residues: 9970 helix: -0.80 (0.08), residues: 4148 sheet: -1.22 (0.15), residues: 1164 loop : -1.63 (0.09), residues: 4658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 771 HIS 0.009 0.001 HIS E 244 PHE 0.022 0.001 PHE D 726 TYR 0.022 0.001 TYR C 494 ARG 0.007 0.000 ARG E 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19940 Ramachandran restraints generated. 9970 Oldfield, 0 Emsley, 9970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19940 Ramachandran restraints generated. 9970 Oldfield, 0 Emsley, 9970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1416 residues out of total 8837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 1136 time to evaluate : 7.196 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: A 35 TYR cc_start: 0.6645 (OUTLIER) cc_final: 0.5496 (p90) REVERT: A 119 ARG cc_start: 0.7813 (mmm160) cc_final: 0.7120 (mmm160) REVERT: A 124 MET cc_start: 0.6924 (pmm) cc_final: 0.6371 (pmm) REVERT: A 206 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7303 (tm-30) REVERT: A 207 MET cc_start: 0.8919 (ttp) cc_final: 0.8526 (ttp) REVERT: A 210 MET cc_start: 0.8247 (tpp) cc_final: 0.7897 (tpp) REVERT: A 230 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8201 (mm) REVERT: A 329 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8132 (tp30) REVERT: A 412 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8522 (mm) REVERT: A 431 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7758 (tp) REVERT: A 437 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8257 (tt) REVERT: A 441 MET cc_start: 0.9018 (ttm) cc_final: 0.7715 (mtp) REVERT: A 500 TYR cc_start: 0.8582 (m-80) cc_final: 0.8296 (m-80) REVERT: A 614 GLN cc_start: 0.8016 (mt0) cc_final: 0.7680 (mt0) REVERT: A 634 GLU cc_start: 0.7460 (mp0) cc_final: 0.7142 (mp0) REVERT: A 829 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7191 (mtm) REVERT: A 987 PHE cc_start: 0.6746 (OUTLIER) cc_final: 0.6497 (m-80) REVERT: A 990 MET cc_start: 0.1462 (ptp) cc_final: 0.1014 (ptp) REVERT: A 1087 ASP cc_start: 0.8740 (m-30) cc_final: 0.8021 (p0) REVERT: B 84 LYS cc_start: 0.8918 (mttp) cc_final: 0.8353 (mmtt) REVERT: B 524 MET cc_start: 0.9074 (mmt) cc_final: 0.8740 (mmt) REVERT: B 638 LYS cc_start: 0.8958 (tptt) cc_final: 0.8676 (tptm) REVERT: B 698 MET cc_start: 0.9058 (mmm) cc_final: 0.8768 (tpp) REVERT: B 714 ARG cc_start: 0.8428 (ttm170) cc_final: 0.8005 (ptt180) REVERT: B 769 ASP cc_start: 0.9139 (OUTLIER) cc_final: 0.8862 (t70) REVERT: B 816 LYS cc_start: 0.9305 (mttt) cc_final: 0.8985 (mtpp) REVERT: B 856 ARG cc_start: 0.8384 (ptt180) cc_final: 0.7678 (mmt-90) REVERT: C 187 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8287 (mt) REVERT: C 291 MET cc_start: 0.8648 (mmm) cc_final: 0.8202 (mmm) REVERT: C 394 MET cc_start: 0.9191 (tpt) cc_final: 0.8731 (tpt) REVERT: C 478 ASP cc_start: 0.7577 (t0) cc_final: 0.7216 (t0) REVERT: C 480 ARG cc_start: 0.8241 (ttp-110) cc_final: 0.7588 (ttp-110) REVERT: C 498 ASN cc_start: 0.8693 (t0) cc_final: 0.8491 (t0) REVERT: C 548 MET cc_start: 0.9263 (mtt) cc_final: 0.9037 (mtp) REVERT: C 592 MET cc_start: 0.9135 (ptp) cc_final: 0.8847 (ptp) REVERT: C 595 VAL cc_start: 0.8365 (OUTLIER) cc_final: 0.7994 (t) REVERT: C 694 PHE cc_start: 0.8631 (m-80) cc_final: 0.8404 (m-80) REVERT: C 698 MET cc_start: 0.8816 (mmm) cc_final: 0.8510 (mmm) REVERT: C 705 MET cc_start: 0.9295 (ttt) cc_final: 0.8955 (tpp) REVERT: C 721 PHE cc_start: 0.8161 (t80) cc_final: 0.7795 (t80) REVERT: C 862 ARG cc_start: 0.8014 (mtm180) cc_final: 0.7790 (mpp80) REVERT: C 881 MET cc_start: 0.8202 (mmm) cc_final: 0.7736 (mmt) REVERT: C 884 MET cc_start: 0.8000 (mtt) cc_final: 0.7591 (mmm) REVERT: D 71 ILE cc_start: 0.9254 (mm) cc_final: 0.8889 (mt) REVERT: D 98 ARG cc_start: 0.9068 (mmm-85) cc_final: 0.8808 (ttm170) REVERT: D 167 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7598 (pp20) REVERT: D 227 VAL cc_start: 0.9414 (OUTLIER) cc_final: 0.9164 (p) REVERT: D 270 GLN cc_start: 0.8567 (mt0) cc_final: 0.8247 (mt0) REVERT: D 371 MET cc_start: 0.9075 (mtt) cc_final: 0.8337 (mtt) REVERT: D 407 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.8718 (pp) REVERT: D 413 ARG cc_start: 0.8201 (ttm170) cc_final: 0.7850 (ttt-90) REVERT: D 519 MET cc_start: 0.8986 (mmm) cc_final: 0.8561 (mmm) REVERT: D 667 MET cc_start: 0.9137 (tpt) cc_final: 0.8824 (tpt) REVERT: D 693 ASP cc_start: 0.8371 (t0) cc_final: 0.8001 (t0) REVERT: D 731 MET cc_start: 0.9421 (ttt) cc_final: 0.8889 (ttp) REVERT: D 759 ARG cc_start: 0.8082 (mtt180) cc_final: 0.7233 (tmt170) REVERT: E 120 GLU cc_start: 0.8465 (pm20) cc_final: 0.8104 (pm20) REVERT: E 218 ASN cc_start: 0.8468 (m-40) cc_final: 0.8213 (m110) REVERT: E 667 MET cc_start: 0.7846 (tpp) cc_final: 0.7644 (tpt) REVERT: E 764 ARG cc_start: 0.8907 (mtp-110) cc_final: 0.8388 (tpt-90) REVERT: E 848 MET cc_start: 0.7953 (mmm) cc_final: 0.7529 (mmm) REVERT: E 884 MET cc_start: 0.8512 (mtp) cc_final: 0.7965 (mmm) REVERT: F 98 ARG cc_start: 0.8553 (mtm-85) cc_final: 0.8007 (mtp-110) REVERT: F 121 ASP cc_start: 0.8350 (p0) cc_final: 0.7967 (p0) REVERT: F 167 GLU cc_start: 0.8766 (tp30) cc_final: 0.8547 (tp30) REVERT: F 169 LYS cc_start: 0.8966 (mmmt) cc_final: 0.8712 (mmmt) REVERT: F 179 HIS cc_start: 0.8670 (OUTLIER) cc_final: 0.8420 (t70) REVERT: F 187 LEU cc_start: 0.9479 (tt) cc_final: 0.9224 (tt) REVERT: F 193 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7340 (tm-30) REVERT: F 524 MET cc_start: 0.8904 (mmm) cc_final: 0.8343 (mmt) REVERT: F 662 ASN cc_start: 0.8413 (p0) cc_final: 0.8093 (p0) REVERT: F 685 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7541 (tm-30) REVERT: F 694 PHE cc_start: 0.9031 (m-10) cc_final: 0.8585 (m-10) REVERT: F 698 MET cc_start: 0.9211 (mmm) cc_final: 0.8836 (mmm) REVERT: F 714 ARG cc_start: 0.7047 (ttp80) cc_final: 0.6569 (ptt-90) REVERT: F 726 PHE cc_start: 0.8282 (t80) cc_final: 0.7956 (t80) REVERT: F 733 GLU cc_start: 0.6421 (tm-30) cc_final: 0.6160 (tm-30) REVERT: F 771 TRP cc_start: 0.9046 (m-10) cc_final: 0.8602 (m-10) REVERT: G 10 GLU cc_start: 0.6225 (pp20) cc_final: 0.5805 (pp20) REVERT: G 250 TYR cc_start: 0.8256 (m-10) cc_final: 0.7945 (m-10) REVERT: G 500 MET cc_start: 0.9438 (tpt) cc_final: 0.9096 (tpt) REVERT: G 614 MET cc_start: 0.9087 (mtt) cc_final: 0.8793 (mtt) REVERT: G 668 ARG cc_start: 0.8739 (ttp-170) cc_final: 0.8247 (ttm110) REVERT: G 726 PHE cc_start: 0.8646 (t80) cc_final: 0.8259 (t80) REVERT: G 727 TYR cc_start: 0.8370 (p90) cc_final: 0.7814 (p90) REVERT: G 731 MET cc_start: 0.8674 (ttp) cc_final: 0.7964 (tmm) REVERT: G 848 MET cc_start: 0.8257 (mmm) cc_final: 0.7832 (mmm) REVERT: H 40 MET cc_start: 0.7039 (ttt) cc_final: 0.6656 (ttt) REVERT: H 51 MET cc_start: 0.5553 (tmm) cc_final: 0.5186 (tmm) REVERT: H 98 ARG cc_start: 0.8537 (mtm-85) cc_final: 0.8028 (mtt-85) REVERT: H 262 ASP cc_start: 0.8856 (p0) cc_final: 0.8298 (p0) REVERT: H 371 MET cc_start: 0.9351 (mtm) cc_final: 0.9142 (mtm) REVERT: H 532 GLN cc_start: 0.8631 (mt0) cc_final: 0.8233 (mt0) REVERT: H 535 ASN cc_start: 0.8919 (m-40) cc_final: 0.8469 (m-40) REVERT: H 624 PHE cc_start: 0.9058 (m-80) cc_final: 0.8578 (m-80) REVERT: H 632 ARG cc_start: 0.8458 (mpt180) cc_final: 0.8248 (mmt-90) REVERT: H 664 ARG cc_start: 0.8551 (mtp85) cc_final: 0.8150 (mtp85) REVERT: H 695 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8191 (mt-10) REVERT: H 698 MET cc_start: 0.9200 (mmm) cc_final: 0.8718 (mmm) REVERT: H 739 ASP cc_start: 0.8097 (m-30) cc_final: 0.7840 (m-30) REVERT: H 747 GLU cc_start: 0.8562 (mp0) cc_final: 0.8248 (mp0) REVERT: H 766 MET cc_start: 0.8315 (mmm) cc_final: 0.7532 (mtm) REVERT: H 786 TYR cc_start: 0.5980 (m-80) cc_final: 0.5697 (m-80) REVERT: H 848 MET cc_start: 0.9158 (mmp) cc_final: 0.8661 (mmp) REVERT: I 51 MET cc_start: 0.8539 (tmm) cc_final: 0.7927 (tmm) REVERT: I 58 ASP cc_start: 0.8435 (t0) cc_final: 0.8071 (t0) REVERT: I 137 ILE cc_start: 0.9204 (mt) cc_final: 0.8963 (mp) REVERT: I 182 MET cc_start: 0.6461 (ttt) cc_final: 0.6145 (ttm) REVERT: I 547 ASP cc_start: 0.8888 (p0) cc_final: 0.8669 (p0) REVERT: I 622 ARG cc_start: 0.8762 (mmm160) cc_final: 0.8403 (ttp-170) REVERT: I 694 PHE cc_start: 0.9263 (m-80) cc_final: 0.9032 (m-80) REVERT: I 819 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8263 (p) REVERT: J 81 LYS cc_start: 0.8801 (ttmt) cc_final: 0.8424 (ttpt) REVERT: J 407 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.8729 (pp) REVERT: J 532 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8377 (mt0) REVERT: J 592 MET cc_start: 0.7901 (mmt) cc_final: 0.7527 (mmt) REVERT: J 595 VAL cc_start: 0.8980 (OUTLIER) cc_final: 0.8714 (t) REVERT: J 709 MET cc_start: 0.8629 (ptm) cc_final: 0.8223 (ptm) REVERT: J 720 ARG cc_start: 0.9152 (mmm-85) cc_final: 0.8028 (ptm160) REVERT: J 755 MET cc_start: 0.8869 (mtt) cc_final: 0.8577 (mtm) REVERT: J 884 MET cc_start: 0.9161 (ptp) cc_final: 0.8867 (ptm) REVERT: K 166 VAL cc_start: 0.8689 (t) cc_final: 0.8434 (t) REVERT: K 182 MET cc_start: 0.6298 (mmm) cc_final: 0.5603 (ptm) REVERT: K 337 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9034 (tt) REVERT: K 396 ARG cc_start: 0.8220 (tpt170) cc_final: 0.7813 (tpp80) REVERT: K 622 ARG cc_start: 0.9069 (mmm160) cc_final: 0.8374 (tpt90) REVERT: K 661 ILE cc_start: 0.8921 (mt) cc_final: 0.8718 (mm) REVERT: K 709 MET cc_start: 0.8473 (ttp) cc_final: 0.7411 (tpp) REVERT: K 721 PHE cc_start: 0.7609 (t80) cc_final: 0.7206 (t80) REVERT: K 769 ASP cc_start: 0.8102 (t0) cc_final: 0.7752 (t0) REVERT: K 774 PHE cc_start: 0.8718 (m-10) cc_final: 0.8299 (m-10) REVERT: K 800 PHE cc_start: 0.8838 (p90) cc_final: 0.8628 (p90) REVERT: K 848 MET cc_start: 0.8442 (mpp) cc_final: 0.7834 (mpp) REVERT: K 878 LYS cc_start: 0.8481 (mmmt) cc_final: 0.8095 (mmmt) REVERT: K 881 MET cc_start: 0.9131 (mmt) cc_final: 0.8702 (mmt) outliers start: 280 outliers final: 197 residues processed: 1341 average time/residue: 0.7406 time to fit residues: 1696.7727 Evaluate side-chains 1304 residues out of total 8837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1089 time to evaluate : 7.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 736 MET Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 829 MET Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1260 ASP Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 662 ASN Chi-restraints excluded: chain B residue 769 ASP Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 884 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 792 ASP Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 244 HIS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 471 TYR Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 814 THR Chi-restraints excluded: chain D residue 840 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 244 HIS Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 388 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 496 CYS Chi-restraints excluded: chain E residue 524 MET Chi-restraints excluded: chain E residue 696 ASP Chi-restraints excluded: chain E residue 699 LEU Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain E residue 839 LEU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 179 HIS Chi-restraints excluded: chain F residue 194 ASN Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain F residue 492 MET Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 794 VAL Chi-restraints excluded: chain F residue 883 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 321 THR Chi-restraints excluded: chain G residue 378 HIS Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 496 CYS Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 666 MET Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 179 HIS Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 227 VAL Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 321 THR Chi-restraints excluded: chain H residue 391 THR Chi-restraints excluded: chain H residue 409 MET Chi-restraints excluded: chain H residue 414 VAL Chi-restraints excluded: chain H residue 570 ASP Chi-restraints excluded: chain H residue 575 SER Chi-restraints excluded: chain H residue 608 SER Chi-restraints excluded: chain H residue 741 VAL Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain H residue 819 THR Chi-restraints excluded: chain H residue 851 VAL Chi-restraints excluded: chain H residue 857 ILE Chi-restraints excluded: chain H residue 861 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 271 LEU Chi-restraints excluded: chain I residue 391 THR Chi-restraints excluded: chain I residue 433 GLN Chi-restraints excluded: chain I residue 455 ILE Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 755 MET Chi-restraints excluded: chain I residue 772 VAL Chi-restraints excluded: chain I residue 819 THR Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 191 ILE Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain J residue 271 LEU Chi-restraints excluded: chain J residue 295 THR Chi-restraints excluded: chain J residue 388 THR Chi-restraints excluded: chain J residue 407 LEU Chi-restraints excluded: chain J residue 445 THR Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 532 GLN Chi-restraints excluded: chain J residue 595 VAL Chi-restraints excluded: chain J residue 739 ASP Chi-restraints excluded: chain J residue 751 LEU Chi-restraints excluded: chain J residue 777 VAL Chi-restraints excluded: chain J residue 857 ILE Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 244 HIS Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 337 LEU Chi-restraints excluded: chain K residue 354 ILE Chi-restraints excluded: chain K residue 391 THR Chi-restraints excluded: chain K residue 445 THR Chi-restraints excluded: chain K residue 492 MET Chi-restraints excluded: chain K residue 510 ASP Chi-restraints excluded: chain K residue 525 VAL Chi-restraints excluded: chain K residue 547 ASP Chi-restraints excluded: chain K residue 567 VAL Chi-restraints excluded: chain K residue 595 VAL Chi-restraints excluded: chain K residue 619 LEU Chi-restraints excluded: chain K residue 652 MET Chi-restraints excluded: chain K residue 662 ASN Chi-restraints excluded: chain K residue 683 LEU Chi-restraints excluded: chain K residue 745 THR Chi-restraints excluded: chain K residue 794 VAL Chi-restraints excluded: chain K residue 830 VAL Chi-restraints excluded: chain K residue 839 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 996 random chunks: chunk 323 optimal weight: 5.9990 chunk 866 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 565 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 963 optimal weight: 9.9990 chunk 799 optimal weight: 0.0770 chunk 446 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 318 optimal weight: 0.1980 chunk 505 optimal weight: 0.0000 overall best weight: 0.8546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 GLN A1239 GLN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 829 ASN E 244 HIS F 185 ASN ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 HIS H 47 GLN H 179 HIS ** H 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 196 ASN J 288 ASN ** J 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 532 GLN K 706 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 82657 Z= 0.127 Angle : 0.500 11.979 112186 Z= 0.251 Chirality : 0.042 0.256 12540 Planarity : 0.003 0.047 14541 Dihedral : 4.313 56.448 11222 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.60 % Allowed : 17.72 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.08), residues: 9970 helix: -0.36 (0.08), residues: 4094 sheet: -1.09 (0.15), residues: 1141 loop : -1.48 (0.09), residues: 4735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 265 HIS 0.015 0.001 HIS E 244 PHE 0.028 0.001 PHE D 852 TYR 0.023 0.001 TYR C 786 ARG 0.013 0.000 ARG I 664 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19940 Ramachandran restraints generated. 9970 Oldfield, 0 Emsley, 9970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19940 Ramachandran restraints generated. 9970 Oldfield, 0 Emsley, 9970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1433 residues out of total 8837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1203 time to evaluate : 7.204 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: A 35 TYR cc_start: 0.6740 (OUTLIER) cc_final: 0.5656 (p90) REVERT: A 119 ARG cc_start: 0.7623 (mmm160) cc_final: 0.7280 (mmm160) REVERT: A 206 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7273 (tm-30) REVERT: A 207 MET cc_start: 0.8785 (ttp) cc_final: 0.8427 (ttp) REVERT: A 210 MET cc_start: 0.8205 (tpp) cc_final: 0.7758 (tpp) REVERT: A 329 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8131 (tp30) REVERT: A 412 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8449 (mm) REVERT: A 441 MET cc_start: 0.9016 (ttm) cc_final: 0.7722 (mtp) REVERT: A 500 TYR cc_start: 0.8566 (m-80) cc_final: 0.8280 (m-80) REVERT: A 614 GLN cc_start: 0.7989 (mt0) cc_final: 0.7658 (mt0) REVERT: A 634 GLU cc_start: 0.7581 (mp0) cc_final: 0.7347 (mp0) REVERT: A 635 GLN cc_start: 0.8269 (pt0) cc_final: 0.7950 (pt0) REVERT: A 829 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7469 (mtm) REVERT: A 990 MET cc_start: 0.1430 (ptp) cc_final: 0.1007 (ptp) REVERT: A 1087 ASP cc_start: 0.8682 (m-30) cc_final: 0.8008 (p0) REVERT: A 1192 LYS cc_start: 0.7166 (ptpp) cc_final: 0.6403 (ptpt) REVERT: A 1255 LYS cc_start: 0.8661 (ptpt) cc_final: 0.7431 (ptpp) REVERT: B 84 LYS cc_start: 0.8882 (mttp) cc_final: 0.8357 (mmtt) REVERT: B 118 ILE cc_start: 0.9180 (mm) cc_final: 0.8943 (tt) REVERT: B 512 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7488 (pm20) REVERT: B 524 MET cc_start: 0.9077 (mmt) cc_final: 0.8839 (mmt) REVERT: B 638 LYS cc_start: 0.8878 (tptt) cc_final: 0.8614 (tptm) REVERT: B 714 ARG cc_start: 0.8414 (ttm170) cc_final: 0.7991 (ptt180) REVERT: B 755 MET cc_start: 0.9277 (ptp) cc_final: 0.8875 (ptp) REVERT: B 816 LYS cc_start: 0.9301 (mttt) cc_final: 0.8987 (mtpp) REVERT: B 856 ARG cc_start: 0.8356 (ptt180) cc_final: 0.7642 (mmt-90) REVERT: C 187 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8313 (mt) REVERT: C 291 MET cc_start: 0.8604 (mmm) cc_final: 0.8157 (mmm) REVERT: C 478 ASP cc_start: 0.7667 (t0) cc_final: 0.7324 (t0) REVERT: C 480 ARG cc_start: 0.8219 (ttp-110) cc_final: 0.7898 (ttp-110) REVERT: C 548 MET cc_start: 0.9260 (mtt) cc_final: 0.9022 (mtp) REVERT: C 595 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.7975 (t) REVERT: C 666 MET cc_start: 0.8766 (ptp) cc_final: 0.8217 (ptm) REVERT: C 686 GLU cc_start: 0.8555 (tp30) cc_final: 0.8291 (tp30) REVERT: C 698 MET cc_start: 0.8811 (mmm) cc_final: 0.8496 (mmm) REVERT: C 705 MET cc_start: 0.9303 (ttt) cc_final: 0.8764 (tpp) REVERT: C 721 PHE cc_start: 0.8103 (t80) cc_final: 0.7788 (t80) REVERT: C 754 ASN cc_start: 0.8313 (m110) cc_final: 0.8015 (m110) REVERT: C 786 TYR cc_start: 0.4284 (m-80) cc_final: 0.4006 (m-80) REVERT: C 881 MET cc_start: 0.8116 (mmm) cc_final: 0.7663 (mmt) REVERT: C 884 MET cc_start: 0.7957 (mtt) cc_final: 0.7602 (mmm) REVERT: D 71 ILE cc_start: 0.9182 (mm) cc_final: 0.8833 (mt) REVERT: D 98 ARG cc_start: 0.9027 (mmm-85) cc_final: 0.8771 (ttm170) REVERT: D 167 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7093 (pp20) REVERT: D 270 GLN cc_start: 0.8362 (mt0) cc_final: 0.8047 (mt0) REVERT: D 371 MET cc_start: 0.9051 (mtt) cc_final: 0.8309 (mtt) REVERT: D 407 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8750 (pp) REVERT: D 413 ARG cc_start: 0.8160 (ttm170) cc_final: 0.7826 (ttt-90) REVERT: D 519 MET cc_start: 0.8868 (mmm) cc_final: 0.8365 (mmm) REVERT: D 536 GLU cc_start: 0.7865 (pt0) cc_final: 0.7565 (mt-10) REVERT: D 537 ASP cc_start: 0.8801 (OUTLIER) cc_final: 0.7790 (t70) REVERT: D 693 ASP cc_start: 0.8455 (t0) cc_final: 0.8017 (t0) REVERT: D 698 MET cc_start: 0.9343 (mmm) cc_final: 0.9131 (mmm) REVERT: D 731 MET cc_start: 0.9377 (ttt) cc_final: 0.8811 (ttp) REVERT: D 759 ARG cc_start: 0.7989 (mtt180) cc_final: 0.7187 (tmt170) REVERT: E 120 GLU cc_start: 0.8408 (pm20) cc_final: 0.8024 (pm20) REVERT: E 218 ASN cc_start: 0.8448 (m-40) cc_final: 0.8183 (m110) REVERT: E 592 MET cc_start: 0.8348 (ptp) cc_final: 0.8087 (ptp) REVERT: E 754 ASN cc_start: 0.8985 (m-40) cc_final: 0.8583 (m-40) REVERT: E 764 ARG cc_start: 0.8893 (mtp-110) cc_final: 0.8409 (tpt-90) REVERT: E 848 MET cc_start: 0.7960 (mmm) cc_final: 0.7505 (mmm) REVERT: E 856 ARG cc_start: 0.8300 (mmm160) cc_final: 0.7959 (mmm-85) REVERT: E 881 MET cc_start: 0.8408 (mmp) cc_final: 0.7546 (mmp) REVERT: E 884 MET cc_start: 0.8508 (mtp) cc_final: 0.7996 (mmm) REVERT: F 98 ARG cc_start: 0.8562 (mtm-85) cc_final: 0.7980 (mtp-110) REVERT: F 121 ASP cc_start: 0.8392 (p0) cc_final: 0.8066 (p0) REVERT: F 167 GLU cc_start: 0.8736 (tp30) cc_final: 0.8502 (tp30) REVERT: F 169 LYS cc_start: 0.9130 (mmmt) cc_final: 0.8799 (mmmt) REVERT: F 179 HIS cc_start: 0.8162 (OUTLIER) cc_final: 0.7855 (t70) REVERT: F 187 LEU cc_start: 0.9440 (tt) cc_final: 0.9197 (tt) REVERT: F 193 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7448 (tm-30) REVERT: F 229 LEU cc_start: 0.9209 (mt) cc_final: 0.8506 (tt) REVERT: F 233 ARG cc_start: 0.8220 (ttp-110) cc_final: 0.7871 (ptp90) REVERT: F 524 MET cc_start: 0.8953 (mmm) cc_final: 0.8092 (mmt) REVERT: F 662 ASN cc_start: 0.8301 (p0) cc_final: 0.8027 (p0) REVERT: F 685 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7492 (tm-30) REVERT: F 694 PHE cc_start: 0.8835 (m-10) cc_final: 0.8472 (m-10) REVERT: F 698 MET cc_start: 0.9174 (mmm) cc_final: 0.8945 (mmm) REVERT: F 714 ARG cc_start: 0.7009 (ttp80) cc_final: 0.6535 (ptt-90) REVERT: F 726 PHE cc_start: 0.8275 (t80) cc_final: 0.7793 (t80) REVERT: F 733 GLU cc_start: 0.6286 (tm-30) cc_final: 0.6027 (tm-30) REVERT: F 771 TRP cc_start: 0.8928 (m-10) cc_final: 0.8549 (m-10) REVERT: G 10 GLU cc_start: 0.6178 (pp20) cc_final: 0.5764 (pp20) REVERT: G 250 TYR cc_start: 0.8225 (m-10) cc_final: 0.7924 (m-10) REVERT: G 585 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7341 (tt0) REVERT: G 614 MET cc_start: 0.9005 (mtt) cc_final: 0.8722 (mtt) REVERT: G 668 ARG cc_start: 0.8655 (ttp-170) cc_final: 0.8097 (ttm110) REVERT: G 726 PHE cc_start: 0.8585 (t80) cc_final: 0.8281 (t80) REVERT: G 727 TYR cc_start: 0.8262 (p90) cc_final: 0.7738 (p90) REVERT: G 731 MET cc_start: 0.8683 (ttp) cc_final: 0.8006 (tmm) REVERT: G 848 MET cc_start: 0.8236 (mmm) cc_final: 0.7808 (mmm) REVERT: H 40 MET cc_start: 0.7237 (ttt) cc_final: 0.6752 (ttt) REVERT: H 51 MET cc_start: 0.5491 (tmm) cc_final: 0.5213 (tmm) REVERT: H 98 ARG cc_start: 0.8450 (mtm-85) cc_final: 0.8007 (mtt-85) REVERT: H 229 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9091 (tt) REVERT: H 231 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7683 (mm-30) REVERT: H 262 ASP cc_start: 0.8801 (p0) cc_final: 0.8207 (p0) REVERT: H 512 GLU cc_start: 0.7978 (mp0) cc_final: 0.7735 (mp0) REVERT: H 532 GLN cc_start: 0.8533 (mt0) cc_final: 0.8183 (mt0) REVERT: H 535 ASN cc_start: 0.8909 (m-40) cc_final: 0.8408 (m-40) REVERT: H 632 ARG cc_start: 0.8432 (mpt180) cc_final: 0.8115 (mmt-90) REVERT: H 664 ARG cc_start: 0.8418 (mtp85) cc_final: 0.8143 (mtp85) REVERT: H 695 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8301 (mt-10) REVERT: H 698 MET cc_start: 0.9189 (mmm) cc_final: 0.8652 (mmm) REVERT: H 739 ASP cc_start: 0.8082 (m-30) cc_final: 0.7768 (m-30) REVERT: H 740 ARG cc_start: 0.8102 (mtp85) cc_final: 0.7639 (ttm-80) REVERT: H 747 GLU cc_start: 0.8566 (mp0) cc_final: 0.8262 (mp0) REVERT: H 766 MET cc_start: 0.8254 (mmm) cc_final: 0.7488 (mtm) REVERT: H 786 TYR cc_start: 0.5880 (m-80) cc_final: 0.5661 (m-80) REVERT: I 51 MET cc_start: 0.8409 (tmm) cc_final: 0.7862 (tmm) REVERT: I 137 ILE cc_start: 0.9152 (mt) cc_final: 0.8902 (mp) REVERT: I 182 MET cc_start: 0.6377 (ttt) cc_final: 0.6074 (ttm) REVERT: I 196 ASN cc_start: 0.6786 (t0) cc_final: 0.6211 (p0) REVERT: I 379 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8980 (pp) REVERT: I 622 ARG cc_start: 0.8748 (mmm160) cc_final: 0.8401 (ttp-170) REVERT: I 685 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8325 (mm-30) REVERT: I 856 ARG cc_start: 0.8786 (mmt180) cc_final: 0.8248 (ttm-80) REVERT: J 81 LYS cc_start: 0.8758 (ttmt) cc_final: 0.8446 (ttpt) REVERT: J 111 MET cc_start: 0.9483 (tpt) cc_final: 0.9207 (tpp) REVERT: J 407 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8731 (pp) REVERT: J 592 MET cc_start: 0.7843 (mmt) cc_final: 0.7459 (mmt) REVERT: J 709 MET cc_start: 0.8630 (ptm) cc_final: 0.8235 (ptm) REVERT: J 720 ARG cc_start: 0.9157 (mmm-85) cc_final: 0.8046 (ptm160) REVERT: J 755 MET cc_start: 0.8846 (mtt) cc_final: 0.8575 (mtm) REVERT: J 884 MET cc_start: 0.9005 (ptp) cc_final: 0.8714 (ptm) REVERT: K 10 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7149 (mt-10) REVERT: K 182 MET cc_start: 0.6411 (mmm) cc_final: 0.5499 (ptp) REVERT: K 291 MET cc_start: 0.9255 (mmm) cc_final: 0.9031 (mmm) REVERT: K 359 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8165 (mm) REVERT: K 449 TYR cc_start: 0.9187 (m-80) cc_final: 0.8869 (m-80) REVERT: K 646 GLU cc_start: 0.8019 (tp30) cc_final: 0.7778 (tp30) REVERT: K 705 MET cc_start: 0.8850 (tmm) cc_final: 0.8463 (tmm) REVERT: K 709 MET cc_start: 0.8450 (ttp) cc_final: 0.7434 (tpp) REVERT: K 769 ASP cc_start: 0.8203 (t0) cc_final: 0.7916 (t0) REVERT: K 774 PHE cc_start: 0.8686 (m-10) cc_final: 0.8371 (m-10) REVERT: K 848 MET cc_start: 0.8678 (mpp) cc_final: 0.8042 (mmp) REVERT: K 878 LYS cc_start: 0.8422 (mmmt) cc_final: 0.8026 (mmmt) REVERT: K 881 MET cc_start: 0.9117 (mmt) cc_final: 0.8681 (mmt) outliers start: 230 outliers final: 152 residues processed: 1367 average time/residue: 0.7528 time to fit residues: 1760.4355 Evaluate side-chains 1284 residues out of total 8837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1119 time to evaluate : 7.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 736 MET Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 829 MET Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 662 ASN Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 884 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 244 HIS Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 814 THR Chi-restraints excluded: chain D residue 840 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 388 THR Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 496 CYS Chi-restraints excluded: chain E residue 709 MET Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain E residue 839 LEU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 179 HIS Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain F residue 477 ILE Chi-restraints excluded: chain F residue 492 MET Chi-restraints excluded: chain F residue 794 VAL Chi-restraints excluded: chain F residue 883 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 378 HIS Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 493 THR Chi-restraints excluded: chain G residue 496 CYS Chi-restraints excluded: chain G residue 570 ASP Chi-restraints excluded: chain G residue 666 MET Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 179 HIS Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 227 VAL Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 391 THR Chi-restraints excluded: chain H residue 414 VAL Chi-restraints excluded: chain H residue 608 SER Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain H residue 819 THR Chi-restraints excluded: chain H residue 861 VAL Chi-restraints excluded: chain H residue 863 VAL Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 271 LEU Chi-restraints excluded: chain I residue 327 LEU Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 391 THR Chi-restraints excluded: chain I residue 455 ILE Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 755 MET Chi-restraints excluded: chain I residue 772 VAL Chi-restraints excluded: chain I residue 793 ASP Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 271 LEU Chi-restraints excluded: chain J residue 407 LEU Chi-restraints excluded: chain J residue 445 THR Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 595 VAL Chi-restraints excluded: chain J residue 739 ASP Chi-restraints excluded: chain J residue 777 VAL Chi-restraints excluded: chain J residue 857 ILE Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 244 HIS Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 354 ILE Chi-restraints excluded: chain K residue 359 ILE Chi-restraints excluded: chain K residue 391 THR Chi-restraints excluded: chain K residue 510 ASP Chi-restraints excluded: chain K residue 547 ASP Chi-restraints excluded: chain K residue 595 VAL Chi-restraints excluded: chain K residue 683 LEU Chi-restraints excluded: chain K residue 745 THR Chi-restraints excluded: chain K residue 839 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 996 random chunks: chunk 929 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 549 optimal weight: 20.0000 chunk 703 optimal weight: 8.9990 chunk 545 optimal weight: 9.9990 chunk 811 optimal weight: 30.0000 chunk 538 optimal weight: 9.9990 chunk 959 optimal weight: 6.9990 chunk 600 optimal weight: 0.7980 chunk 585 optimal weight: 20.0000 chunk 443 optimal weight: 10.0000 overall best weight: 7.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1239 GLN A1290 ASN B 221 GLN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 GLN ** E 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 ASN ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 HIS ** G 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 HIS ** H 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 484 ASN J 196 ASN J 288 ASN J 352 GLN ** J 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 550 ASN ** K 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 82657 Z= 0.370 Angle : 0.593 11.071 112186 Z= 0.299 Chirality : 0.046 0.197 12540 Planarity : 0.004 0.043 14541 Dihedral : 4.551 59.120 11220 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.11 % Allowed : 17.74 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.08), residues: 9970 helix: -0.35 (0.08), residues: 4151 sheet: -1.10 (0.15), residues: 1154 loop : -1.48 (0.09), residues: 4665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 577 HIS 0.010 0.001 HIS D 244 PHE 0.023 0.002 PHE E 726 TYR 0.024 0.001 TYR B 50 ARG 0.007 0.000 ARG G 740 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19940 Ramachandran restraints generated. 9970 Oldfield, 0 Emsley, 9970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19940 Ramachandran restraints generated. 9970 Oldfield, 0 Emsley, 9970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1385 residues out of total 8837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 1110 time to evaluate : 7.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TYR cc_start: 0.7089 (OUTLIER) cc_final: 0.5893 (p90) REVERT: A 119 ARG cc_start: 0.7851 (mmm160) cc_final: 0.7259 (mmm160) REVERT: A 134 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7678 (tpp80) REVERT: A 206 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7347 (tm-30) REVERT: A 207 MET cc_start: 0.8905 (ttp) cc_final: 0.8557 (ttp) REVERT: A 210 MET cc_start: 0.8250 (tpp) cc_final: 0.7886 (tpp) REVERT: A 230 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8246 (mm) REVERT: A 329 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8179 (tp30) REVERT: A 412 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8518 (mm) REVERT: A 437 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8247 (tt) REVERT: A 441 MET cc_start: 0.9056 (ttm) cc_final: 0.7739 (mtp) REVERT: A 443 ARG cc_start: 0.6476 (mpt180) cc_final: 0.6204 (mmt180) REVERT: A 500 TYR cc_start: 0.8612 (m-80) cc_final: 0.8324 (m-80) REVERT: A 614 GLN cc_start: 0.8002 (mt0) cc_final: 0.7694 (mt0) REVERT: A 829 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7193 (mtm) REVERT: A 990 MET cc_start: 0.1403 (ptp) cc_final: 0.0746 (ptp) REVERT: A 1087 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.7895 (p0) REVERT: B 84 LYS cc_start: 0.8895 (mttp) cc_final: 0.8337 (mmtt) REVERT: B 118 ILE cc_start: 0.9238 (mm) cc_final: 0.9013 (tt) REVERT: B 221 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8134 (tm130) REVERT: B 524 MET cc_start: 0.9088 (mmt) cc_final: 0.8803 (mmt) REVERT: B 638 LYS cc_start: 0.8830 (tptt) cc_final: 0.8594 (tptm) REVERT: B 714 ARG cc_start: 0.8428 (ttm170) cc_final: 0.8037 (ptt180) REVERT: B 755 MET cc_start: 0.9252 (ptp) cc_final: 0.8846 (ptp) REVERT: B 807 ARG cc_start: 0.8368 (mtm-85) cc_final: 0.7957 (mtm-85) REVERT: B 816 LYS cc_start: 0.9319 (mttt) cc_final: 0.8980 (mtpp) REVERT: B 856 ARG cc_start: 0.8342 (ptt180) cc_final: 0.7625 (mmt-90) REVERT: C 187 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8289 (mt) REVERT: C 253 GLU cc_start: 0.7696 (tt0) cc_final: 0.7073 (tt0) REVERT: C 291 MET cc_start: 0.8647 (mmm) cc_final: 0.8203 (mmm) REVERT: C 394 MET cc_start: 0.9196 (tpt) cc_final: 0.8758 (tpt) REVERT: C 480 ARG cc_start: 0.8264 (ttp-110) cc_final: 0.7969 (ttp-110) REVERT: C 548 MET cc_start: 0.9256 (mtt) cc_final: 0.9037 (mtp) REVERT: C 595 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.8016 (t) REVERT: C 698 MET cc_start: 0.8844 (mmm) cc_final: 0.8501 (mmm) REVERT: C 705 MET cc_start: 0.9242 (ttt) cc_final: 0.8759 (tpp) REVERT: C 881 MET cc_start: 0.8190 (mmm) cc_final: 0.7713 (mmt) REVERT: C 884 MET cc_start: 0.7994 (mtt) cc_final: 0.7644 (mmm) REVERT: D 71 ILE cc_start: 0.9272 (mm) cc_final: 0.8906 (mt) REVERT: D 98 ARG cc_start: 0.9044 (mmm-85) cc_final: 0.8771 (ttm170) REVERT: D 167 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7604 (pp20) REVERT: D 227 VAL cc_start: 0.9388 (t) cc_final: 0.9145 (p) REVERT: D 270 GLN cc_start: 0.8573 (mt0) cc_final: 0.8287 (mt0) REVERT: D 371 MET cc_start: 0.9048 (mtt) cc_final: 0.8323 (mtt) REVERT: D 407 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.8727 (pp) REVERT: D 413 ARG cc_start: 0.8201 (ttm170) cc_final: 0.7852 (ttt-90) REVERT: D 519 MET cc_start: 0.8997 (mmm) cc_final: 0.8550 (mmm) REVERT: D 693 ASP cc_start: 0.8372 (t0) cc_final: 0.7996 (t0) REVERT: D 731 MET cc_start: 0.9436 (ttt) cc_final: 0.8915 (ttp) REVERT: D 759 ARG cc_start: 0.8079 (mtt180) cc_final: 0.7236 (tmt170) REVERT: E 120 GLU cc_start: 0.8444 (pm20) cc_final: 0.8064 (pm20) REVERT: E 218 ASN cc_start: 0.8520 (m-40) cc_final: 0.8257 (m110) REVERT: E 848 MET cc_start: 0.7939 (mmm) cc_final: 0.7513 (mmm) REVERT: E 856 ARG cc_start: 0.8280 (mmm160) cc_final: 0.7926 (mmm-85) REVERT: E 881 MET cc_start: 0.8434 (mmp) cc_final: 0.7797 (mmp) REVERT: E 884 MET cc_start: 0.8593 (mtp) cc_final: 0.8032 (mmm) REVERT: F 98 ARG cc_start: 0.8608 (mtm-85) cc_final: 0.8052 (mtp-110) REVERT: F 121 ASP cc_start: 0.8345 (p0) cc_final: 0.7927 (p0) REVERT: F 156 MET cc_start: 0.7598 (ptt) cc_final: 0.7335 (ptt) REVERT: F 167 GLU cc_start: 0.8780 (tp30) cc_final: 0.8539 (tp30) REVERT: F 169 LYS cc_start: 0.9014 (mmmt) cc_final: 0.8702 (mmmt) REVERT: F 179 HIS cc_start: 0.8373 (OUTLIER) cc_final: 0.8078 (t70) REVERT: F 187 LEU cc_start: 0.9418 (tt) cc_final: 0.9163 (tt) REVERT: F 193 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7332 (tm-30) REVERT: F 229 LEU cc_start: 0.9225 (mt) cc_final: 0.8933 (tt) REVERT: F 524 MET cc_start: 0.8929 (mmm) cc_final: 0.8400 (mmt) REVERT: F 662 ASN cc_start: 0.8427 (p0) cc_final: 0.8129 (p0) REVERT: F 685 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7537 (tm-30) REVERT: F 694 PHE cc_start: 0.8949 (m-10) cc_final: 0.8546 (m-10) REVERT: F 714 ARG cc_start: 0.7052 (ttp80) cc_final: 0.6575 (ptt-90) REVERT: F 733 GLU cc_start: 0.6262 (tm-30) cc_final: 0.5989 (tm-30) REVERT: F 771 TRP cc_start: 0.9066 (m-10) cc_final: 0.8716 (m-10) REVERT: G 10 GLU cc_start: 0.6266 (pp20) cc_final: 0.5810 (pp20) REVERT: G 250 TYR cc_start: 0.8268 (m-10) cc_final: 0.7943 (m-10) REVERT: G 363 GLU cc_start: 0.8722 (tp30) cc_final: 0.8376 (tp30) REVERT: G 614 MET cc_start: 0.9119 (mtt) cc_final: 0.8814 (mtt) REVERT: G 668 ARG cc_start: 0.8733 (ttp-170) cc_final: 0.8218 (ttm110) REVERT: G 726 PHE cc_start: 0.8675 (t80) cc_final: 0.8255 (t80) REVERT: G 727 TYR cc_start: 0.8411 (p90) cc_final: 0.7867 (p90) REVERT: G 731 MET cc_start: 0.8694 (ttp) cc_final: 0.8377 (ttp) REVERT: G 848 MET cc_start: 0.8252 (mmm) cc_final: 0.7844 (mmm) REVERT: H 40 MET cc_start: 0.7200 (ttt) cc_final: 0.6884 (ttt) REVERT: H 51 MET cc_start: 0.5410 (tmm) cc_final: 0.5040 (tmm) REVERT: H 98 ARG cc_start: 0.8524 (mtm-85) cc_final: 0.8010 (mtt-85) REVERT: H 262 ASP cc_start: 0.8811 (p0) cc_final: 0.8222 (p0) REVERT: H 512 GLU cc_start: 0.7999 (mp0) cc_final: 0.7755 (mp0) REVERT: H 532 GLN cc_start: 0.8668 (mt0) cc_final: 0.8242 (mt0) REVERT: H 535 ASN cc_start: 0.8934 (m-40) cc_final: 0.8495 (m-40) REVERT: H 664 ARG cc_start: 0.8541 (mtp85) cc_final: 0.8333 (mtp85) REVERT: H 695 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8289 (mt-10) REVERT: H 698 MET cc_start: 0.9224 (mmm) cc_final: 0.8731 (mmm) REVERT: H 739 ASP cc_start: 0.7969 (m-30) cc_final: 0.7570 (m-30) REVERT: H 747 GLU cc_start: 0.8625 (mp0) cc_final: 0.8247 (mp0) REVERT: H 766 MET cc_start: 0.8325 (mmm) cc_final: 0.7553 (mtm) REVERT: H 786 TYR cc_start: 0.6015 (m-80) cc_final: 0.5715 (m-80) REVERT: I 51 MET cc_start: 0.8460 (tmm) cc_final: 0.7878 (tmm) REVERT: I 111 MET cc_start: 0.9050 (tpp) cc_final: 0.8428 (tpp) REVERT: I 137 ILE cc_start: 0.9174 (mt) cc_final: 0.8924 (mp) REVERT: I 182 MET cc_start: 0.6561 (ttt) cc_final: 0.6229 (ttm) REVERT: I 622 ARG cc_start: 0.8773 (mmm160) cc_final: 0.8425 (ttp-170) REVERT: I 643 ASP cc_start: 0.7898 (t70) cc_final: 0.7626 (t70) REVERT: J 81 LYS cc_start: 0.8785 (ttmt) cc_final: 0.8416 (ttpt) REVERT: J 179 HIS cc_start: 0.7601 (OUTLIER) cc_final: 0.6932 (t70) REVERT: J 196 ASN cc_start: 0.8465 (t0) cc_final: 0.8065 (t0) REVERT: J 407 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.8760 (pp) REVERT: J 592 MET cc_start: 0.7942 (mmt) cc_final: 0.7563 (mmt) REVERT: J 595 VAL cc_start: 0.9029 (OUTLIER) cc_final: 0.8764 (t) REVERT: J 709 MET cc_start: 0.8534 (ptm) cc_final: 0.8214 (ptm) REVERT: J 720 ARG cc_start: 0.9149 (mmm-85) cc_final: 0.8019 (ptm160) REVERT: J 755 MET cc_start: 0.8863 (mtt) cc_final: 0.8580 (mtm) REVERT: J 884 MET cc_start: 0.9160 (ptp) cc_final: 0.8854 (ptm) REVERT: K 182 MET cc_start: 0.6538 (mmm) cc_final: 0.5442 (ptp) REVERT: K 337 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9068 (tt) REVERT: K 396 ARG cc_start: 0.8274 (tpt170) cc_final: 0.7864 (tpp80) REVERT: K 622 ARG cc_start: 0.9056 (mmm160) cc_final: 0.8367 (tpt170) REVERT: K 646 GLU cc_start: 0.8179 (tp30) cc_final: 0.7941 (tp30) REVERT: K 669 TRP cc_start: 0.9245 (t60) cc_final: 0.9020 (t60) REVERT: K 709 MET cc_start: 0.8455 (ttp) cc_final: 0.7397 (tpp) REVERT: K 769 ASP cc_start: 0.8382 (t0) cc_final: 0.8070 (t0) REVERT: K 774 PHE cc_start: 0.8694 (m-10) cc_final: 0.8288 (m-10) REVERT: K 800 PHE cc_start: 0.8881 (p90) cc_final: 0.8654 (p90) REVERT: K 848 MET cc_start: 0.8492 (mpp) cc_final: 0.8030 (mpp) REVERT: K 878 LYS cc_start: 0.8565 (mmmt) cc_final: 0.8124 (mmmt) REVERT: K 881 MET cc_start: 0.9169 (mmt) cc_final: 0.8692 (mmt) outliers start: 275 outliers final: 203 residues processed: 1311 average time/residue: 0.7552 time to fit residues: 1695.3813 Evaluate side-chains 1309 residues out of total 8837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1090 time to evaluate : 7.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 736 MET Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 829 MET Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1087 ASP Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1260 ASP Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 662 ASN Chi-restraints excluded: chain B residue 820 GLU Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 884 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 563 ASN Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 244 HIS Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 471 TYR Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 814 THR Chi-restraints excluded: chain D residue 840 VAL Chi-restraints excluded: chain D residue 901 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 388 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 496 CYS Chi-restraints excluded: chain E residue 696 ASP Chi-restraints excluded: chain E residue 698 MET Chi-restraints excluded: chain E residue 709 MET Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain E residue 839 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 179 HIS Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 240 GLU Chi-restraints excluded: chain F residue 257 ASP Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain F residue 492 MET Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain F residue 794 VAL Chi-restraints excluded: chain F residue 883 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 321 THR Chi-restraints excluded: chain G residue 354 ILE Chi-restraints excluded: chain G residue 378 HIS Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 388 THR Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 391 THR Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 493 THR Chi-restraints excluded: chain G residue 496 CYS Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 666 MET Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 179 HIS Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 227 VAL Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 321 THR Chi-restraints excluded: chain H residue 391 THR Chi-restraints excluded: chain H residue 414 VAL Chi-restraints excluded: chain H residue 570 ASP Chi-restraints excluded: chain H residue 575 SER Chi-restraints excluded: chain H residue 608 SER Chi-restraints excluded: chain H residue 741 VAL Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain H residue 780 THR Chi-restraints excluded: chain H residue 819 THR Chi-restraints excluded: chain H residue 857 ILE Chi-restraints excluded: chain H residue 861 VAL Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 271 LEU Chi-restraints excluded: chain I residue 327 LEU Chi-restraints excluded: chain I residue 391 THR Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 755 MET Chi-restraints excluded: chain I residue 772 VAL Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 179 HIS Chi-restraints excluded: chain J residue 191 ILE Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 271 LEU Chi-restraints excluded: chain J residue 388 THR Chi-restraints excluded: chain J residue 407 LEU Chi-restraints excluded: chain J residue 445 THR Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 595 VAL Chi-restraints excluded: chain J residue 667 MET Chi-restraints excluded: chain J residue 739 ASP Chi-restraints excluded: chain J residue 751 LEU Chi-restraints excluded: chain J residue 777 VAL Chi-restraints excluded: chain J residue 857 ILE Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 244 HIS Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 337 LEU Chi-restraints excluded: chain K residue 354 ILE Chi-restraints excluded: chain K residue 378 HIS Chi-restraints excluded: chain K residue 391 THR Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 421 THR Chi-restraints excluded: chain K residue 445 THR Chi-restraints excluded: chain K residue 478 ASP Chi-restraints excluded: chain K residue 510 ASP Chi-restraints excluded: chain K residue 547 ASP Chi-restraints excluded: chain K residue 595 VAL Chi-restraints excluded: chain K residue 619 LEU Chi-restraints excluded: chain K residue 652 MET Chi-restraints excluded: chain K residue 662 ASN Chi-restraints excluded: chain K residue 683 LEU Chi-restraints excluded: chain K residue 745 THR Chi-restraints excluded: chain K residue 830 VAL Chi-restraints excluded: chain K residue 839 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 996 random chunks: chunk 593 optimal weight: 5.9990 chunk 383 optimal weight: 9.9990 chunk 573 optimal weight: 40.0000 chunk 289 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 610 optimal weight: 2.9990 chunk 654 optimal weight: 5.9990 chunk 474 optimal weight: 20.0000 chunk 89 optimal weight: 8.9990 chunk 754 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1053 ASN B 221 GLN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 GLN ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 HIS F 658 HIS ** G 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 HIS ** H 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 630 GLN ** H 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 288 ASN ** J 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 550 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 82657 Z= 0.232 Angle : 0.546 14.086 112186 Z= 0.273 Chirality : 0.044 0.279 12540 Planarity : 0.004 0.053 14541 Dihedral : 4.496 59.254 11220 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.82 % Allowed : 18.40 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.08), residues: 9970 helix: -0.16 (0.08), residues: 4143 sheet: -1.01 (0.15), residues: 1162 loop : -1.40 (0.09), residues: 4665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 669 HIS 0.006 0.001 HIS B 656 PHE 0.030 0.001 PHE A1273 TYR 0.020 0.001 TYR A 142 ARG 0.013 0.000 ARG I 664 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19940 Ramachandran restraints generated. 9970 Oldfield, 0 Emsley, 9970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19940 Ramachandran restraints generated. 9970 Oldfield, 0 Emsley, 9970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1371 residues out of total 8837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 1122 time to evaluate : 7.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TYR cc_start: 0.7154 (OUTLIER) cc_final: 0.5954 (p90) REVERT: A 119 ARG cc_start: 0.7689 (mmm160) cc_final: 0.7180 (mmm160) REVERT: A 206 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7353 (tm-30) REVERT: A 207 MET cc_start: 0.8867 (ttp) cc_final: 0.8502 (ttp) REVERT: A 210 MET cc_start: 0.8222 (tpp) cc_final: 0.7868 (tpp) REVERT: A 230 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8282 (mm) REVERT: A 329 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8184 (tp30) REVERT: A 412 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8524 (mm) REVERT: A 437 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8209 (tt) REVERT: A 441 MET cc_start: 0.9050 (ttm) cc_final: 0.7714 (mtp) REVERT: A 500 TYR cc_start: 0.8610 (m-80) cc_final: 0.8335 (m-80) REVERT: A 614 GLN cc_start: 0.8067 (mt0) cc_final: 0.7846 (mt0) REVERT: A 829 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7166 (mtm) REVERT: A 990 MET cc_start: 0.1353 (ptp) cc_final: 0.0702 (ptp) REVERT: A 1087 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.7944 (p0) REVERT: A 1298 GLU cc_start: 0.8645 (tp30) cc_final: 0.8427 (tp30) REVERT: B 84 LYS cc_start: 0.8877 (mttp) cc_final: 0.8357 (mmtt) REVERT: B 118 ILE cc_start: 0.9235 (mm) cc_final: 0.9013 (tt) REVERT: B 221 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8258 (tm130) REVERT: B 524 MET cc_start: 0.9098 (mmt) cc_final: 0.8857 (mmt) REVERT: B 638 LYS cc_start: 0.8770 (tptt) cc_final: 0.8514 (tptm) REVERT: B 714 ARG cc_start: 0.8427 (ttm170) cc_final: 0.8036 (ptt180) REVERT: B 755 MET cc_start: 0.9265 (ptp) cc_final: 0.8867 (ptp) REVERT: B 816 LYS cc_start: 0.9329 (mttt) cc_final: 0.8984 (mtpp) REVERT: B 856 ARG cc_start: 0.8337 (ptt180) cc_final: 0.7619 (mmt-90) REVERT: C 187 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8277 (mt) REVERT: C 291 MET cc_start: 0.8704 (mmm) cc_final: 0.8257 (mmm) REVERT: C 480 ARG cc_start: 0.8157 (ttp-110) cc_final: 0.7862 (ttp-110) REVERT: C 548 MET cc_start: 0.9250 (mtt) cc_final: 0.9042 (mtp) REVERT: C 595 VAL cc_start: 0.8440 (OUTLIER) cc_final: 0.8135 (t) REVERT: C 686 GLU cc_start: 0.8675 (tp30) cc_final: 0.8425 (tp30) REVERT: C 698 MET cc_start: 0.8828 (mmm) cc_final: 0.8468 (mmm) REVERT: C 705 MET cc_start: 0.9216 (ttt) cc_final: 0.8743 (tpp) REVERT: C 754 ASN cc_start: 0.8319 (m110) cc_final: 0.8047 (m110) REVERT: C 800 PHE cc_start: 0.8564 (p90) cc_final: 0.8337 (p90) REVERT: C 881 MET cc_start: 0.8168 (mmm) cc_final: 0.7676 (mmt) REVERT: C 884 MET cc_start: 0.7989 (mtt) cc_final: 0.7639 (mmm) REVERT: D 71 ILE cc_start: 0.9241 (mm) cc_final: 0.8880 (mt) REVERT: D 98 ARG cc_start: 0.9048 (mmm-85) cc_final: 0.8766 (ttm170) REVERT: D 105 ASP cc_start: 0.8835 (OUTLIER) cc_final: 0.8601 (t0) REVERT: D 167 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7387 (pp20) REVERT: D 227 VAL cc_start: 0.9362 (t) cc_final: 0.9141 (p) REVERT: D 270 GLN cc_start: 0.8500 (mt0) cc_final: 0.8204 (mt0) REVERT: D 371 MET cc_start: 0.9025 (mtt) cc_final: 0.8282 (mtt) REVERT: D 407 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.8831 (pp) REVERT: D 413 ARG cc_start: 0.8178 (ttm170) cc_final: 0.7840 (ttt-90) REVERT: D 519 MET cc_start: 0.8932 (mmm) cc_final: 0.8515 (mmm) REVERT: D 686 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7067 (pt0) REVERT: D 693 ASP cc_start: 0.8426 (t0) cc_final: 0.8016 (t0) REVERT: D 731 MET cc_start: 0.9421 (ttt) cc_final: 0.8898 (ttp) REVERT: D 759 ARG cc_start: 0.8044 (mtt180) cc_final: 0.7222 (tmt170) REVERT: E 120 GLU cc_start: 0.8415 (pm20) cc_final: 0.8039 (pm20) REVERT: E 218 ASN cc_start: 0.8524 (m-40) cc_final: 0.8249 (m110) REVERT: E 592 MET cc_start: 0.8443 (ptp) cc_final: 0.8228 (ptp) REVERT: E 699 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8798 (pp) REVERT: E 764 ARG cc_start: 0.8906 (mtp-110) cc_final: 0.8485 (ttt180) REVERT: E 848 MET cc_start: 0.7937 (mmm) cc_final: 0.7649 (mmm) REVERT: E 856 ARG cc_start: 0.8277 (mmm160) cc_final: 0.7925 (mmm-85) REVERT: E 881 MET cc_start: 0.8482 (mmp) cc_final: 0.7831 (mmp) REVERT: E 884 MET cc_start: 0.8585 (mtp) cc_final: 0.8037 (mmm) REVERT: F 98 ARG cc_start: 0.8578 (mtm-85) cc_final: 0.8039 (mtp-110) REVERT: F 121 ASP cc_start: 0.8506 (p0) cc_final: 0.8173 (p0) REVERT: F 167 GLU cc_start: 0.8767 (tp30) cc_final: 0.8565 (tp30) REVERT: F 169 LYS cc_start: 0.9024 (mmmt) cc_final: 0.8691 (mmmt) REVERT: F 187 LEU cc_start: 0.9404 (tt) cc_final: 0.9156 (tt) REVERT: F 193 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7434 (tm-30) REVERT: F 229 LEU cc_start: 0.9232 (mt) cc_final: 0.8947 (tt) REVERT: F 524 MET cc_start: 0.8839 (mmm) cc_final: 0.8226 (mmt) REVERT: F 662 ASN cc_start: 0.8400 (p0) cc_final: 0.8097 (p0) REVERT: F 685 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7568 (tm-30) REVERT: F 694 PHE cc_start: 0.8895 (m-10) cc_final: 0.8464 (m-10) REVERT: F 714 ARG cc_start: 0.7050 (ttp80) cc_final: 0.6574 (ptt-90) REVERT: F 726 PHE cc_start: 0.7860 (t80) cc_final: 0.7451 (t80) REVERT: F 733 GLU cc_start: 0.6232 (tm-30) cc_final: 0.5943 (tm-30) REVERT: F 771 TRP cc_start: 0.9012 (m-10) cc_final: 0.8695 (m-10) REVERT: G 10 GLU cc_start: 0.6268 (pp20) cc_final: 0.5805 (pp20) REVERT: G 250 TYR cc_start: 0.8257 (m-10) cc_final: 0.7938 (m-10) REVERT: G 363 GLU cc_start: 0.8737 (tp30) cc_final: 0.8501 (tp30) REVERT: G 614 MET cc_start: 0.9098 (mtt) cc_final: 0.8789 (mtt) REVERT: G 668 ARG cc_start: 0.8612 (ttp-170) cc_final: 0.8118 (ttm110) REVERT: G 726 PHE cc_start: 0.8658 (t80) cc_final: 0.8248 (t80) REVERT: G 727 TYR cc_start: 0.8367 (p90) cc_final: 0.7830 (p90) REVERT: G 731 MET cc_start: 0.8683 (ttp) cc_final: 0.8372 (ttp) REVERT: G 848 MET cc_start: 0.8297 (mmm) cc_final: 0.7873 (mmm) REVERT: G 856 ARG cc_start: 0.8290 (mpp-170) cc_final: 0.8074 (mpp-170) REVERT: H 40 MET cc_start: 0.7178 (ttt) cc_final: 0.6859 (ttt) REVERT: H 51 MET cc_start: 0.5435 (tmm) cc_final: 0.5064 (tmm) REVERT: H 98 ARG cc_start: 0.8487 (mtm-85) cc_final: 0.7983 (mtt-85) REVERT: H 262 ASP cc_start: 0.8797 (p0) cc_final: 0.8201 (p0) REVERT: H 512 GLU cc_start: 0.7991 (mp0) cc_final: 0.7736 (mp0) REVERT: H 532 GLN cc_start: 0.8623 (mt0) cc_final: 0.8237 (mt0) REVERT: H 535 ASN cc_start: 0.8951 (m-40) cc_final: 0.8497 (m-40) REVERT: H 663 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8341 (tp) REVERT: H 695 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8323 (mt-10) REVERT: H 698 MET cc_start: 0.9211 (mmm) cc_final: 0.8716 (mmm) REVERT: H 739 ASP cc_start: 0.7908 (m-30) cc_final: 0.7479 (m-30) REVERT: H 747 GLU cc_start: 0.8640 (mp0) cc_final: 0.8248 (mp0) REVERT: H 766 MET cc_start: 0.8304 (mmm) cc_final: 0.7631 (mtm) REVERT: H 786 TYR cc_start: 0.6003 (m-80) cc_final: 0.5698 (m-80) REVERT: I 51 MET cc_start: 0.8430 (tmm) cc_final: 0.7896 (tmm) REVERT: I 58 ASP cc_start: 0.8555 (t0) cc_final: 0.8138 (t0) REVERT: I 111 MET cc_start: 0.9029 (tpp) cc_final: 0.8429 (tpp) REVERT: I 137 ILE cc_start: 0.9162 (mt) cc_final: 0.8896 (mp) REVERT: I 182 MET cc_start: 0.6647 (ttt) cc_final: 0.6336 (ttm) REVERT: I 622 ARG cc_start: 0.8751 (mmm160) cc_final: 0.8419 (ttp-170) REVERT: I 643 ASP cc_start: 0.7888 (t70) cc_final: 0.7602 (t70) REVERT: I 819 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8234 (p) REVERT: J 81 LYS cc_start: 0.8761 (ttmt) cc_final: 0.8398 (ttpt) REVERT: J 179 HIS cc_start: 0.7605 (OUTLIER) cc_final: 0.6860 (t70) REVERT: J 196 ASN cc_start: 0.8431 (t0) cc_final: 0.8094 (t0) REVERT: J 407 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.8757 (pp) REVERT: J 592 MET cc_start: 0.7932 (mmt) cc_final: 0.7546 (mmt) REVERT: J 595 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8752 (t) REVERT: J 709 MET cc_start: 0.8529 (ptm) cc_final: 0.8203 (ptm) REVERT: J 720 ARG cc_start: 0.9144 (mmm-85) cc_final: 0.8009 (ptm160) REVERT: J 755 MET cc_start: 0.8851 (mtt) cc_final: 0.8578 (mtm) REVERT: J 884 MET cc_start: 0.9062 (ptp) cc_final: 0.8746 (ptm) REVERT: K 182 MET cc_start: 0.6511 (mmm) cc_final: 0.5408 (ptp) REVERT: K 291 MET cc_start: 0.9296 (mmm) cc_final: 0.9069 (mmm) REVERT: K 337 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9018 (tt) REVERT: K 480 ARG cc_start: 0.7866 (mtm-85) cc_final: 0.7319 (mtm-85) REVERT: K 646 GLU cc_start: 0.8140 (tp30) cc_final: 0.7887 (tp30) REVERT: K 705 MET cc_start: 0.8803 (tmm) cc_final: 0.8375 (tpp) REVERT: K 709 MET cc_start: 0.8404 (ttp) cc_final: 0.7364 (tpp) REVERT: K 769 ASP cc_start: 0.8381 (t0) cc_final: 0.8113 (t0) REVERT: K 774 PHE cc_start: 0.8655 (m-10) cc_final: 0.8236 (m-10) REVERT: K 800 PHE cc_start: 0.8911 (p90) cc_final: 0.8670 (p90) REVERT: K 848 MET cc_start: 0.8602 (mpp) cc_final: 0.7577 (mmp) REVERT: K 878 LYS cc_start: 0.8535 (mmmt) cc_final: 0.8082 (mmmt) outliers start: 249 outliers final: 200 residues processed: 1312 average time/residue: 0.7423 time to fit residues: 1672.6837 Evaluate side-chains 1308 residues out of total 8837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1089 time to evaluate : 7.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 736 MET Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 829 MET Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1087 ASP Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 662 ASN Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 884 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 563 ASN Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 792 ASP Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 244 HIS Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 686 GLU Chi-restraints excluded: chain D residue 814 THR Chi-restraints excluded: chain D residue 840 VAL Chi-restraints excluded: chain D residue 901 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 388 THR Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 496 CYS Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 698 MET Chi-restraints excluded: chain E residue 699 LEU Chi-restraints excluded: chain E residue 709 MET Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain E residue 839 LEU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 240 GLU Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain F residue 492 MET Chi-restraints excluded: chain F residue 794 VAL Chi-restraints excluded: chain F residue 883 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 378 HIS Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 391 THR Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 493 THR Chi-restraints excluded: chain G residue 496 CYS Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 666 MET Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 179 HIS Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 227 VAL Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 321 THR Chi-restraints excluded: chain H residue 391 THR Chi-restraints excluded: chain H residue 414 VAL Chi-restraints excluded: chain H residue 575 SER Chi-restraints excluded: chain H residue 595 VAL Chi-restraints excluded: chain H residue 608 SER Chi-restraints excluded: chain H residue 663 ILE Chi-restraints excluded: chain H residue 741 VAL Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain H residue 780 THR Chi-restraints excluded: chain H residue 819 THR Chi-restraints excluded: chain H residue 857 ILE Chi-restraints excluded: chain H residue 861 VAL Chi-restraints excluded: chain H residue 863 VAL Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 271 LEU Chi-restraints excluded: chain I residue 327 LEU Chi-restraints excluded: chain I residue 391 THR Chi-restraints excluded: chain I residue 433 GLN Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 755 MET Chi-restraints excluded: chain I residue 772 VAL Chi-restraints excluded: chain I residue 819 THR Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 179 HIS Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 271 LEU Chi-restraints excluded: chain J residue 309 ILE Chi-restraints excluded: chain J residue 388 THR Chi-restraints excluded: chain J residue 407 LEU Chi-restraints excluded: chain J residue 445 THR Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 595 VAL Chi-restraints excluded: chain J residue 667 MET Chi-restraints excluded: chain J residue 739 ASP Chi-restraints excluded: chain J residue 751 LEU Chi-restraints excluded: chain J residue 777 VAL Chi-restraints excluded: chain J residue 857 ILE Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 244 HIS Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 337 LEU Chi-restraints excluded: chain K residue 354 ILE Chi-restraints excluded: chain K residue 378 HIS Chi-restraints excluded: chain K residue 391 THR Chi-restraints excluded: chain K residue 478 ASP Chi-restraints excluded: chain K residue 510 ASP Chi-restraints excluded: chain K residue 547 ASP Chi-restraints excluded: chain K residue 567 VAL Chi-restraints excluded: chain K residue 595 VAL Chi-restraints excluded: chain K residue 619 LEU Chi-restraints excluded: chain K residue 662 ASN Chi-restraints excluded: chain K residue 683 LEU Chi-restraints excluded: chain K residue 745 THR Chi-restraints excluded: chain K residue 830 VAL Chi-restraints excluded: chain K residue 839 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 996 random chunks: chunk 873 optimal weight: 10.0000 chunk 919 optimal weight: 5.9990 chunk 839 optimal weight: 0.0470 chunk 894 optimal weight: 8.9990 chunk 538 optimal weight: 9.9990 chunk 389 optimal weight: 0.3980 chunk 702 optimal weight: 10.0000 chunk 274 optimal weight: 10.0000 chunk 808 optimal weight: 30.0000 chunk 846 optimal weight: 1.9990 chunk 891 optimal weight: 0.9990 overall best weight: 1.8884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 ASN ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 HIS ** H 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 653 ASN ** H 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 288 ASN ** J 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 550 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 82657 Z= 0.149 Angle : 0.520 14.799 112186 Z= 0.258 Chirality : 0.042 0.218 12540 Planarity : 0.003 0.046 14541 Dihedral : 4.324 57.585 11220 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.38 % Allowed : 18.84 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.09), residues: 9970 helix: 0.10 (0.09), residues: 4094 sheet: -0.97 (0.15), residues: 1203 loop : -1.33 (0.09), residues: 4673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 386 HIS 0.009 0.001 HIS H 179 PHE 0.024 0.001 PHE E 726 TYR 0.025 0.001 TYR B 50 ARG 0.010 0.000 ARG G 740 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19940 Ramachandran restraints generated. 9970 Oldfield, 0 Emsley, 9970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19940 Ramachandran restraints generated. 9970 Oldfield, 0 Emsley, 9970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1373 residues out of total 8837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1163 time to evaluate : 7.440 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: A 35 TYR cc_start: 0.7148 (OUTLIER) cc_final: 0.5960 (p90) REVERT: A 119 ARG cc_start: 0.7632 (mmm160) cc_final: 0.7121 (mmm160) REVERT: A 206 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7293 (tm-30) REVERT: A 207 MET cc_start: 0.8733 (ttp) cc_final: 0.8360 (ttp) REVERT: A 210 MET cc_start: 0.8198 (tpp) cc_final: 0.7842 (tpp) REVERT: A 230 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8190 (mm) REVERT: A 329 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8186 (tp30) REVERT: A 412 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8491 (mm) REVERT: A 441 MET cc_start: 0.9073 (ttm) cc_final: 0.7808 (mtp) REVERT: A 500 TYR cc_start: 0.8610 (m-80) cc_final: 0.8354 (m-80) REVERT: A 614 GLN cc_start: 0.8062 (mt0) cc_final: 0.7826 (mt0) REVERT: A 635 GLN cc_start: 0.8345 (pt0) cc_final: 0.8079 (pt0) REVERT: A 829 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7152 (mtm) REVERT: A 940 MET cc_start: 0.9044 (mmm) cc_final: 0.8822 (mmm) REVERT: A 963 ASP cc_start: 0.7727 (t0) cc_final: 0.7449 (t0) REVERT: A 990 MET cc_start: 0.1324 (ptp) cc_final: 0.0712 (ptp) REVERT: A 1087 ASP cc_start: 0.8677 (m-30) cc_final: 0.7954 (p0) REVERT: A 1192 LYS cc_start: 0.7148 (ptpp) cc_final: 0.6332 (ptpt) REVERT: A 1255 LYS cc_start: 0.8600 (ptpt) cc_final: 0.7927 (ptpt) REVERT: B 84 LYS cc_start: 0.8861 (mttp) cc_final: 0.8374 (mmtt) REVERT: B 118 ILE cc_start: 0.9215 (mm) cc_final: 0.9011 (tt) REVERT: B 221 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8328 (tm130) REVERT: B 524 MET cc_start: 0.9101 (mmt) cc_final: 0.8895 (mmt) REVERT: B 638 LYS cc_start: 0.8728 (tptt) cc_final: 0.8470 (tptm) REVERT: B 714 ARG cc_start: 0.8417 (ttm170) cc_final: 0.8023 (ptt180) REVERT: B 816 LYS cc_start: 0.9359 (mttt) cc_final: 0.9015 (mtpp) REVERT: B 848 MET cc_start: 0.9063 (mmm) cc_final: 0.8585 (mmm) REVERT: B 856 ARG cc_start: 0.8317 (ptt180) cc_final: 0.7626 (mmt-90) REVERT: C 187 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8307 (mt) REVERT: C 253 GLU cc_start: 0.7763 (tt0) cc_final: 0.7406 (tt0) REVERT: C 291 MET cc_start: 0.8703 (mmm) cc_final: 0.8243 (mmm) REVERT: C 449 TYR cc_start: 0.9030 (m-80) cc_final: 0.8776 (m-80) REVERT: C 480 ARG cc_start: 0.8164 (ttp-110) cc_final: 0.7899 (ttp-110) REVERT: C 519 MET cc_start: 0.8892 (tpp) cc_final: 0.8515 (tpp) REVERT: C 548 MET cc_start: 0.9262 (mtt) cc_final: 0.9050 (mtp) REVERT: C 595 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8101 (t) REVERT: C 666 MET cc_start: 0.8762 (ptp) cc_final: 0.8478 (ptm) REVERT: C 698 MET cc_start: 0.8799 (mmm) cc_final: 0.8431 (mmm) REVERT: C 705 MET cc_start: 0.9176 (ttt) cc_final: 0.8930 (tpp) REVERT: C 754 ASN cc_start: 0.8267 (m110) cc_final: 0.7977 (m110) REVERT: C 800 PHE cc_start: 0.8564 (p90) cc_final: 0.8336 (p90) REVERT: C 881 MET cc_start: 0.8074 (mmm) cc_final: 0.7559 (mmt) REVERT: C 884 MET cc_start: 0.7938 (mtt) cc_final: 0.7614 (mmm) REVERT: D 71 ILE cc_start: 0.9213 (mm) cc_final: 0.8860 (mt) REVERT: D 98 ARG cc_start: 0.9074 (mmm-85) cc_final: 0.8779 (ttm170) REVERT: D 125 LYS cc_start: 0.8836 (mmmm) cc_final: 0.8489 (mmmm) REVERT: D 167 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7300 (pp20) REVERT: D 270 GLN cc_start: 0.8474 (mt0) cc_final: 0.8141 (mt0) REVERT: D 371 MET cc_start: 0.9014 (mtt) cc_final: 0.8262 (mtt) REVERT: D 407 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.8790 (pp) REVERT: D 413 ARG cc_start: 0.8169 (ttm170) cc_final: 0.7833 (ttt-90) REVERT: D 519 MET cc_start: 0.8869 (mmm) cc_final: 0.8364 (mmm) REVERT: D 693 ASP cc_start: 0.8377 (t0) cc_final: 0.7962 (t0) REVERT: D 731 MET cc_start: 0.9419 (ttt) cc_final: 0.8872 (ttp) REVERT: D 759 ARG cc_start: 0.7991 (mtt180) cc_final: 0.7194 (tmt170) REVERT: D 807 ARG cc_start: 0.7774 (ptp90) cc_final: 0.7331 (ptp-170) REVERT: E 120 GLU cc_start: 0.8384 (pm20) cc_final: 0.7983 (pm20) REVERT: E 218 ASN cc_start: 0.8506 (m-40) cc_final: 0.8225 (m110) REVERT: E 592 MET cc_start: 0.8271 (ptp) cc_final: 0.8017 (ptp) REVERT: E 699 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8797 (pp) REVERT: E 754 ASN cc_start: 0.8986 (m-40) cc_final: 0.8573 (m-40) REVERT: E 764 ARG cc_start: 0.8896 (mtp-110) cc_final: 0.8559 (ttt180) REVERT: E 771 TRP cc_start: 0.8739 (m100) cc_final: 0.8429 (m100) REVERT: E 848 MET cc_start: 0.8039 (mmm) cc_final: 0.7179 (mmm) REVERT: E 856 ARG cc_start: 0.8281 (mmm160) cc_final: 0.7932 (mmm-85) REVERT: E 881 MET cc_start: 0.8416 (mmp) cc_final: 0.7608 (mmp) REVERT: E 884 MET cc_start: 0.8534 (mtp) cc_final: 0.8021 (mmm) REVERT: F 98 ARG cc_start: 0.8515 (mtm-85) cc_final: 0.7982 (mtp-110) REVERT: F 121 ASP cc_start: 0.8559 (p0) cc_final: 0.8268 (p0) REVERT: F 167 GLU cc_start: 0.8762 (tp30) cc_final: 0.8559 (tp30) REVERT: F 169 LYS cc_start: 0.9028 (mmmt) cc_final: 0.8697 (mmmt) REVERT: F 182 MET cc_start: 0.8773 (ptm) cc_final: 0.7836 (ptp) REVERT: F 187 LEU cc_start: 0.9408 (tt) cc_final: 0.9189 (tt) REVERT: F 193 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7434 (tm-30) REVERT: F 229 LEU cc_start: 0.9192 (mt) cc_final: 0.8961 (tt) REVERT: F 524 MET cc_start: 0.8928 (mmm) cc_final: 0.8122 (mmt) REVERT: F 662 ASN cc_start: 0.8280 (p0) cc_final: 0.8020 (p0) REVERT: F 685 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7538 (tm-30) REVERT: F 694 PHE cc_start: 0.8798 (m-10) cc_final: 0.8431 (m-10) REVERT: F 705 MET cc_start: 0.8915 (ttp) cc_final: 0.8538 (tmm) REVERT: F 714 ARG cc_start: 0.7036 (ttp80) cc_final: 0.6558 (ptt-90) REVERT: F 726 PHE cc_start: 0.7615 (t80) cc_final: 0.7178 (t80) REVERT: F 733 GLU cc_start: 0.6264 (tm-30) cc_final: 0.5991 (tm-30) REVERT: F 771 TRP cc_start: 0.9067 (m-10) cc_final: 0.8669 (m-10) REVERT: G 10 GLU cc_start: 0.6205 (pp20) cc_final: 0.5742 (pp20) REVERT: G 250 TYR cc_start: 0.8262 (m-10) cc_final: 0.7951 (m-10) REVERT: G 365 MET cc_start: 0.8294 (mtp) cc_final: 0.7937 (mtm) REVERT: G 585 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7381 (tt0) REVERT: G 614 MET cc_start: 0.9050 (mtt) cc_final: 0.8753 (mtt) REVERT: G 668 ARG cc_start: 0.8599 (ttp-170) cc_final: 0.8101 (ttm110) REVERT: G 726 PHE cc_start: 0.8630 (t80) cc_final: 0.8267 (t80) REVERT: G 727 TYR cc_start: 0.8303 (p90) cc_final: 0.7780 (p90) REVERT: G 731 MET cc_start: 0.8671 (ttp) cc_final: 0.8022 (tmm) REVERT: G 848 MET cc_start: 0.8298 (mmm) cc_final: 0.7881 (mmm) REVERT: G 856 ARG cc_start: 0.8334 (mpp-170) cc_final: 0.8093 (mpp-170) REVERT: H 40 MET cc_start: 0.7040 (ttt) cc_final: 0.6795 (ttt) REVERT: H 51 MET cc_start: 0.5421 (tmm) cc_final: 0.5066 (tmm) REVERT: H 98 ARG cc_start: 0.8435 (mtm-85) cc_final: 0.7907 (mtt-85) REVERT: H 262 ASP cc_start: 0.8780 (p0) cc_final: 0.8185 (p0) REVERT: H 265 TRP cc_start: 0.9216 (OUTLIER) cc_final: 0.8705 (m100) REVERT: H 337 LEU cc_start: 0.9071 (mm) cc_final: 0.8832 (mm) REVERT: H 512 GLU cc_start: 0.8064 (mp0) cc_final: 0.7855 (mp0) REVERT: H 532 GLN cc_start: 0.8559 (mt0) cc_final: 0.8171 (mt0) REVERT: H 535 ASN cc_start: 0.8919 (m-40) cc_final: 0.8460 (m-40) REVERT: H 695 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8207 (mt-10) REVERT: H 698 MET cc_start: 0.9186 (mmm) cc_final: 0.8681 (mmm) REVERT: H 739 ASP cc_start: 0.7900 (m-30) cc_final: 0.7466 (m-30) REVERT: H 747 GLU cc_start: 0.8646 (mp0) cc_final: 0.8253 (mp0) REVERT: H 766 MET cc_start: 0.8326 (mmm) cc_final: 0.7642 (mtm) REVERT: H 786 TYR cc_start: 0.6001 (m-80) cc_final: 0.5742 (m-80) REVERT: H 848 MET cc_start: 0.9036 (mmp) cc_final: 0.8560 (mmp) REVERT: I 51 MET cc_start: 0.8415 (tmm) cc_final: 0.7913 (tmm) REVERT: I 137 ILE cc_start: 0.9175 (mt) cc_final: 0.8930 (mp) REVERT: I 182 MET cc_start: 0.6464 (ttt) cc_final: 0.6169 (ttm) REVERT: I 547 ASP cc_start: 0.8741 (p0) cc_final: 0.8468 (p0) REVERT: I 819 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8162 (p) REVERT: I 856 ARG cc_start: 0.8791 (mmt180) cc_final: 0.8247 (ttm-80) REVERT: J 81 LYS cc_start: 0.8739 (ttmt) cc_final: 0.8372 (ttpt) REVERT: J 179 HIS cc_start: 0.7568 (OUTLIER) cc_final: 0.6890 (t70) REVERT: J 407 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8739 (pp) REVERT: J 592 MET cc_start: 0.7905 (mmt) cc_final: 0.7426 (mmt) REVERT: J 595 VAL cc_start: 0.8947 (OUTLIER) cc_final: 0.8672 (t) REVERT: J 709 MET cc_start: 0.8599 (ptm) cc_final: 0.8191 (ptm) REVERT: J 720 ARG cc_start: 0.9166 (mmm-85) cc_final: 0.8000 (ptm160) REVERT: J 755 MET cc_start: 0.8822 (mtt) cc_final: 0.8562 (mtm) REVERT: J 884 MET cc_start: 0.8990 (ptp) cc_final: 0.8697 (ptm) REVERT: K 182 MET cc_start: 0.6343 (mmm) cc_final: 0.5483 (ptp) REVERT: K 291 MET cc_start: 0.9277 (mmm) cc_final: 0.9062 (mmm) REVERT: K 337 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9016 (tt) REVERT: K 396 ARG cc_start: 0.8140 (tpt170) cc_final: 0.7794 (tpp80) REVERT: K 480 ARG cc_start: 0.7725 (mtm-85) cc_final: 0.7196 (mtm-85) REVERT: K 610 MET cc_start: 0.8801 (mmm) cc_final: 0.8444 (mtt) REVERT: K 698 MET cc_start: 0.8874 (mmm) cc_final: 0.8649 (mmm) REVERT: K 705 MET cc_start: 0.9006 (tmm) cc_final: 0.8212 (tpt) REVERT: K 709 MET cc_start: 0.8469 (ttp) cc_final: 0.7508 (tpp) REVERT: K 769 ASP cc_start: 0.8403 (t0) cc_final: 0.8151 (t0) REVERT: K 774 PHE cc_start: 0.8598 (m-10) cc_final: 0.8220 (m-10) REVERT: K 848 MET cc_start: 0.8336 (mpp) cc_final: 0.7073 (mmp) REVERT: K 878 LYS cc_start: 0.8457 (mmmt) cc_final: 0.8055 (mmmt) REVERT: K 881 MET cc_start: 0.9118 (mmt) cc_final: 0.8734 (mmt) outliers start: 210 outliers final: 175 residues processed: 1319 average time/residue: 0.7634 time to fit residues: 1727.0591 Evaluate side-chains 1309 residues out of total 8837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1119 time to evaluate : 7.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 736 MET Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 829 MET Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 662 ASN Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 884 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 563 ASN Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 244 HIS Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 814 THR Chi-restraints excluded: chain D residue 840 VAL Chi-restraints excluded: chain D residue 901 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 388 THR Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 496 CYS Chi-restraints excluded: chain E residue 699 LEU Chi-restraints excluded: chain E residue 709 MET Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain E residue 839 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain F residue 492 MET Chi-restraints excluded: chain F residue 794 VAL Chi-restraints excluded: chain F residue 883 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 321 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain G residue 493 THR Chi-restraints excluded: chain G residue 496 CYS Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 666 MET Chi-restraints excluded: chain G residue 792 ASP Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 179 HIS Chi-restraints excluded: chain H residue 227 VAL Chi-restraints excluded: chain H residue 265 TRP Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 391 THR Chi-restraints excluded: chain H residue 414 VAL Chi-restraints excluded: chain H residue 575 SER Chi-restraints excluded: chain H residue 608 SER Chi-restraints excluded: chain H residue 741 VAL Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain H residue 780 THR Chi-restraints excluded: chain H residue 819 THR Chi-restraints excluded: chain H residue 861 VAL Chi-restraints excluded: chain H residue 863 VAL Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 271 LEU Chi-restraints excluded: chain I residue 327 LEU Chi-restraints excluded: chain I residue 391 THR Chi-restraints excluded: chain I residue 455 ILE Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 772 VAL Chi-restraints excluded: chain I residue 819 THR Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 179 HIS Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 271 LEU Chi-restraints excluded: chain J residue 407 LEU Chi-restraints excluded: chain J residue 445 THR Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 595 VAL Chi-restraints excluded: chain J residue 739 ASP Chi-restraints excluded: chain J residue 751 LEU Chi-restraints excluded: chain J residue 777 VAL Chi-restraints excluded: chain J residue 857 ILE Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 244 HIS Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 337 LEU Chi-restraints excluded: chain K residue 354 ILE Chi-restraints excluded: chain K residue 391 THR Chi-restraints excluded: chain K residue 478 ASP Chi-restraints excluded: chain K residue 510 ASP Chi-restraints excluded: chain K residue 547 ASP Chi-restraints excluded: chain K residue 595 VAL Chi-restraints excluded: chain K residue 619 LEU Chi-restraints excluded: chain K residue 662 ASN Chi-restraints excluded: chain K residue 683 LEU Chi-restraints excluded: chain K residue 745 THR Chi-restraints excluded: chain K residue 830 VAL Chi-restraints excluded: chain K residue 839 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 996 random chunks: chunk 587 optimal weight: 6.9990 chunk 945 optimal weight: 4.9990 chunk 577 optimal weight: 40.0000 chunk 448 optimal weight: 8.9990 chunk 657 optimal weight: 9.9990 chunk 992 optimal weight: 3.9990 chunk 913 optimal weight: 7.9990 chunk 790 optimal weight: 0.0170 chunk 82 optimal weight: 10.0000 chunk 610 optimal weight: 7.9990 chunk 484 optimal weight: 5.9990 overall best weight: 4.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 ASN ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 HIS ** G 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 HIS ** H 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 467 HIS J 196 ASN J 288 ASN ** J 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 550 ASN ** K 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 82657 Z= 0.244 Angle : 0.553 14.296 112186 Z= 0.275 Chirality : 0.044 0.306 12540 Planarity : 0.004 0.066 14541 Dihedral : 4.386 58.002 11220 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.51 % Allowed : 18.98 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.09), residues: 9970 helix: 0.12 (0.09), residues: 4116 sheet: -0.94 (0.15), residues: 1180 loop : -1.30 (0.09), residues: 4674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 386 HIS 0.006 0.001 HIS H 656 PHE 0.024 0.001 PHE E 726 TYR 0.020 0.001 TYR K 217 ARG 0.012 0.000 ARG I 664 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19940 Ramachandran restraints generated. 9970 Oldfield, 0 Emsley, 9970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19940 Ramachandran restraints generated. 9970 Oldfield, 0 Emsley, 9970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1339 residues out of total 8837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1117 time to evaluate : 7.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TYR cc_start: 0.7200 (OUTLIER) cc_final: 0.5983 (p90) REVERT: A 119 ARG cc_start: 0.7714 (mmm160) cc_final: 0.7121 (mmm160) REVERT: A 206 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7351 (tm-30) REVERT: A 207 MET cc_start: 0.8772 (ttp) cc_final: 0.8408 (ttp) REVERT: A 210 MET cc_start: 0.8207 (tpp) cc_final: 0.7865 (tpp) REVERT: A 329 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8190 (tp30) REVERT: A 412 LEU cc_start: 0.8729 (mm) cc_final: 0.8483 (mm) REVERT: A 437 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8211 (tt) REVERT: A 441 MET cc_start: 0.9083 (ttm) cc_final: 0.7796 (mtp) REVERT: A 443 ARG cc_start: 0.6137 (mmt180) cc_final: 0.5909 (mmt180) REVERT: A 500 TYR cc_start: 0.8637 (m-80) cc_final: 0.8374 (m-80) REVERT: A 614 GLN cc_start: 0.8041 (mt0) cc_final: 0.7832 (mt0) REVERT: A 828 MET cc_start: 0.7023 (pmm) cc_final: 0.6604 (pmm) REVERT: A 829 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7116 (mtm) REVERT: A 963 ASP cc_start: 0.7714 (t0) cc_final: 0.7415 (t0) REVERT: A 990 MET cc_start: 0.1376 (ptp) cc_final: 0.0737 (ptp) REVERT: A 1087 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.7868 (p0) REVERT: A 1192 LYS cc_start: 0.7226 (ptpp) cc_final: 0.6375 (ptpt) REVERT: B 84 LYS cc_start: 0.8899 (mttp) cc_final: 0.8397 (mmtt) REVERT: B 98 ARG cc_start: 0.8605 (mtt90) cc_final: 0.8322 (mmt90) REVERT: B 118 ILE cc_start: 0.9228 (mm) cc_final: 0.9027 (tt) REVERT: B 524 MET cc_start: 0.9117 (mmt) cc_final: 0.8889 (mmt) REVERT: B 638 LYS cc_start: 0.8753 (tptt) cc_final: 0.8504 (tptm) REVERT: B 714 ARG cc_start: 0.8401 (ttm170) cc_final: 0.8081 (ptt180) REVERT: B 816 LYS cc_start: 0.9367 (mttt) cc_final: 0.9018 (mtpp) REVERT: B 848 MET cc_start: 0.9084 (mmm) cc_final: 0.8614 (mmm) REVERT: B 856 ARG cc_start: 0.8335 (ptt180) cc_final: 0.7627 (mmt-90) REVERT: C 187 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8312 (mt) REVERT: C 291 MET cc_start: 0.8731 (mmm) cc_final: 0.8257 (mmm) REVERT: C 394 MET cc_start: 0.9172 (tpt) cc_final: 0.8879 (tpt) REVERT: C 480 ARG cc_start: 0.8129 (ttp-110) cc_final: 0.7869 (ttp-110) REVERT: C 548 MET cc_start: 0.9260 (mtt) cc_final: 0.9052 (mtp) REVERT: C 595 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.8234 (t) REVERT: C 686 GLU cc_start: 0.8680 (tp30) cc_final: 0.8428 (tp30) REVERT: C 698 MET cc_start: 0.8812 (mmm) cc_final: 0.8443 (mmm) REVERT: C 705 MET cc_start: 0.9235 (ttt) cc_final: 0.8716 (tpp) REVERT: C 754 ASN cc_start: 0.8258 (m110) cc_final: 0.7963 (m110) REVERT: C 766 MET cc_start: 0.8529 (mmm) cc_final: 0.8213 (mmm) REVERT: C 800 PHE cc_start: 0.8594 (p90) cc_final: 0.8365 (p90) REVERT: C 848 MET cc_start: 0.7740 (mmm) cc_final: 0.7096 (mmp) REVERT: C 881 MET cc_start: 0.8105 (mmm) cc_final: 0.7592 (mmt) REVERT: C 884 MET cc_start: 0.7997 (mtt) cc_final: 0.7637 (mmm) REVERT: D 71 ILE cc_start: 0.9246 (mm) cc_final: 0.8883 (mt) REVERT: D 98 ARG cc_start: 0.9074 (mmm-85) cc_final: 0.8775 (ttm170) REVERT: D 125 LYS cc_start: 0.8875 (mmmm) cc_final: 0.8547 (mmmm) REVERT: D 167 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7289 (pp20) REVERT: D 227 VAL cc_start: 0.9366 (t) cc_final: 0.9154 (p) REVERT: D 270 GLN cc_start: 0.8530 (mt0) cc_final: 0.8193 (mt0) REVERT: D 371 MET cc_start: 0.9028 (mtt) cc_final: 0.8289 (mtt) REVERT: D 407 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.8828 (pp) REVERT: D 413 ARG cc_start: 0.8183 (ttm170) cc_final: 0.7845 (ttt-90) REVERT: D 519 MET cc_start: 0.8934 (mmm) cc_final: 0.8455 (mmm) REVERT: D 693 ASP cc_start: 0.8374 (t0) cc_final: 0.7958 (t0) REVERT: D 731 MET cc_start: 0.9440 (ttt) cc_final: 0.8960 (ttp) REVERT: D 759 ARG cc_start: 0.8022 (mtt180) cc_final: 0.7212 (tmt170) REVERT: D 807 ARG cc_start: 0.7890 (ptp90) cc_final: 0.7546 (ptp-170) REVERT: E 120 GLU cc_start: 0.8350 (pm20) cc_final: 0.7933 (pm20) REVERT: E 218 ASN cc_start: 0.8530 (m-40) cc_final: 0.8235 (m110) REVERT: E 592 MET cc_start: 0.8296 (ptp) cc_final: 0.8039 (ptp) REVERT: E 754 ASN cc_start: 0.8998 (m-40) cc_final: 0.8588 (m-40) REVERT: E 764 ARG cc_start: 0.8903 (mtp-110) cc_final: 0.8567 (ttt180) REVERT: E 771 TRP cc_start: 0.8757 (m100) cc_final: 0.8448 (m100) REVERT: E 848 MET cc_start: 0.7915 (mmm) cc_final: 0.7172 (mmm) REVERT: E 856 ARG cc_start: 0.8280 (mmm160) cc_final: 0.7932 (mmm-85) REVERT: E 881 MET cc_start: 0.8433 (mmp) cc_final: 0.7634 (mmp) REVERT: E 884 MET cc_start: 0.8608 (mtp) cc_final: 0.8077 (mmm) REVERT: F 98 ARG cc_start: 0.8551 (mtm-85) cc_final: 0.7997 (mtp-110) REVERT: F 121 ASP cc_start: 0.8345 (p0) cc_final: 0.7940 (p0) REVERT: F 156 MET cc_start: 0.7545 (ptt) cc_final: 0.7321 (ptt) REVERT: F 167 GLU cc_start: 0.8786 (tp30) cc_final: 0.8581 (tp30) REVERT: F 169 LYS cc_start: 0.9031 (mmmt) cc_final: 0.8704 (mmmt) REVERT: F 179 HIS cc_start: 0.8169 (OUTLIER) cc_final: 0.7852 (t70) REVERT: F 187 LEU cc_start: 0.9397 (tt) cc_final: 0.9173 (tt) REVERT: F 193 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7477 (tm-30) REVERT: F 524 MET cc_start: 0.8909 (mmm) cc_final: 0.8219 (mmt) REVERT: F 662 ASN cc_start: 0.8334 (p0) cc_final: 0.8052 (p0) REVERT: F 685 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7526 (tm-30) REVERT: F 694 PHE cc_start: 0.8841 (m-10) cc_final: 0.8432 (m-10) REVERT: F 714 ARG cc_start: 0.7044 (ttp80) cc_final: 0.6573 (ptt-90) REVERT: F 726 PHE cc_start: 0.7153 (t80) cc_final: 0.6860 (t80) REVERT: F 733 GLU cc_start: 0.6213 (tm-30) cc_final: 0.5920 (tm-30) REVERT: F 771 TRP cc_start: 0.9168 (m-10) cc_final: 0.8741 (m-10) REVERT: G 10 GLU cc_start: 0.6255 (pp20) cc_final: 0.5785 (pp20) REVERT: G 95 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.6858 (ttm) REVERT: G 250 TYR cc_start: 0.8272 (m-10) cc_final: 0.7953 (m-10) REVERT: G 614 MET cc_start: 0.9072 (mtt) cc_final: 0.8766 (mtt) REVERT: G 668 ARG cc_start: 0.8630 (ttp-170) cc_final: 0.8172 (ttm110) REVERT: G 726 PHE cc_start: 0.8608 (t80) cc_final: 0.8234 (t80) REVERT: G 727 TYR cc_start: 0.8378 (p90) cc_final: 0.7859 (p90) REVERT: G 731 MET cc_start: 0.8668 (ttp) cc_final: 0.8401 (ttp) REVERT: G 848 MET cc_start: 0.8291 (mmm) cc_final: 0.7803 (mmm) REVERT: G 856 ARG cc_start: 0.8318 (mpp-170) cc_final: 0.8079 (mpp-170) REVERT: H 40 MET cc_start: 0.7048 (ttt) cc_final: 0.6785 (ttt) REVERT: H 51 MET cc_start: 0.5570 (tmm) cc_final: 0.5275 (tmm) REVERT: H 98 ARG cc_start: 0.8458 (mtm-85) cc_final: 0.7948 (mtt-85) REVERT: H 262 ASP cc_start: 0.8798 (p0) cc_final: 0.8202 (p0) REVERT: H 265 TRP cc_start: 0.9246 (OUTLIER) cc_final: 0.8696 (m100) REVERT: H 337 LEU cc_start: 0.9117 (mm) cc_final: 0.8889 (mm) REVERT: H 512 GLU cc_start: 0.8078 (mp0) cc_final: 0.7867 (mp0) REVERT: H 532 GLN cc_start: 0.8611 (mt0) cc_final: 0.8212 (mt0) REVERT: H 535 ASN cc_start: 0.8913 (m-40) cc_final: 0.8470 (m-40) REVERT: H 592 MET cc_start: 0.8447 (mtp) cc_final: 0.8196 (mtp) REVERT: H 663 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8289 (tp) REVERT: H 695 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8193 (mt-10) REVERT: H 698 MET cc_start: 0.9196 (mmm) cc_final: 0.8707 (mmm) REVERT: H 739 ASP cc_start: 0.7896 (m-30) cc_final: 0.7474 (m-30) REVERT: H 747 GLU cc_start: 0.8645 (mp0) cc_final: 0.8268 (mp0) REVERT: H 766 MET cc_start: 0.8354 (mmm) cc_final: 0.7658 (mtm) REVERT: H 786 TYR cc_start: 0.6023 (m-80) cc_final: 0.5749 (m-80) REVERT: H 848 MET cc_start: 0.9035 (mmp) cc_final: 0.8509 (mmp) REVERT: I 51 MET cc_start: 0.8440 (tmm) cc_final: 0.7916 (tmm) REVERT: I 58 ASP cc_start: 0.8583 (t0) cc_final: 0.8186 (t0) REVERT: I 137 ILE cc_start: 0.9186 (mt) cc_final: 0.8942 (mp) REVERT: I 182 MET cc_start: 0.6468 (ttt) cc_final: 0.6038 (ttm) REVERT: I 547 ASP cc_start: 0.8841 (p0) cc_final: 0.8554 (p0) REVERT: I 819 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8172 (p) REVERT: J 81 LYS cc_start: 0.8708 (ttmt) cc_final: 0.8369 (ttpt) REVERT: J 179 HIS cc_start: 0.7557 (OUTLIER) cc_final: 0.6896 (t70) REVERT: J 196 ASN cc_start: 0.8499 (t0) cc_final: 0.8154 (t0) REVERT: J 407 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.8752 (pp) REVERT: J 592 MET cc_start: 0.7963 (mmt) cc_final: 0.7488 (mmt) REVERT: J 595 VAL cc_start: 0.8990 (OUTLIER) cc_final: 0.8709 (t) REVERT: J 709 MET cc_start: 0.8607 (ptm) cc_final: 0.8204 (ptm) REVERT: J 720 ARG cc_start: 0.9170 (mmm-85) cc_final: 0.8004 (ptm160) REVERT: J 755 MET cc_start: 0.8811 (mtt) cc_final: 0.8551 (mtm) REVERT: J 884 MET cc_start: 0.9043 (ptp) cc_final: 0.8720 (ptm) REVERT: K 182 MET cc_start: 0.6440 (mmm) cc_final: 0.5399 (ptp) REVERT: K 291 MET cc_start: 0.9308 (mmm) cc_final: 0.9085 (mmm) REVERT: K 337 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9021 (tt) REVERT: K 610 MET cc_start: 0.8707 (mmm) cc_final: 0.8412 (mtt) REVERT: K 646 GLU cc_start: 0.8154 (tp30) cc_final: 0.7901 (tp30) REVERT: K 698 MET cc_start: 0.8829 (mmm) cc_final: 0.8623 (mmm) REVERT: K 705 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8336 (tmm) REVERT: K 709 MET cc_start: 0.8416 (ttp) cc_final: 0.7426 (tpp) REVERT: K 769 ASP cc_start: 0.8466 (t0) cc_final: 0.8246 (t0) REVERT: K 774 PHE cc_start: 0.8615 (m-10) cc_final: 0.8246 (m-10) REVERT: K 848 MET cc_start: 0.8370 (mpp) cc_final: 0.7641 (mmp) REVERT: K 878 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8234 (mmmt) REVERT: K 881 MET cc_start: 0.9123 (mmt) cc_final: 0.8701 (mmt) outliers start: 222 outliers final: 193 residues processed: 1293 average time/residue: 0.7502 time to fit residues: 1663.9208 Evaluate side-chains 1312 residues out of total 8837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1102 time to evaluate : 7.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 736 MET Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 829 MET Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1087 ASP Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 662 ASN Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 884 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 563 ASN Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 244 HIS Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 814 THR Chi-restraints excluded: chain D residue 840 VAL Chi-restraints excluded: chain D residue 901 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 388 THR Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 496 CYS Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 696 ASP Chi-restraints excluded: chain E residue 709 MET Chi-restraints excluded: chain E residue 794 VAL Chi-restraints excluded: chain E residue 839 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 179 HIS Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 240 GLU Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain F residue 492 MET Chi-restraints excluded: chain F residue 794 VAL Chi-restraints excluded: chain F residue 883 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 321 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 391 THR Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 493 THR Chi-restraints excluded: chain G residue 496 CYS Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 666 MET Chi-restraints excluded: chain G residue 792 ASP Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 179 HIS Chi-restraints excluded: chain H residue 227 VAL Chi-restraints excluded: chain H residue 265 TRP Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 388 THR Chi-restraints excluded: chain H residue 391 THR Chi-restraints excluded: chain H residue 414 VAL Chi-restraints excluded: chain H residue 575 SER Chi-restraints excluded: chain H residue 595 VAL Chi-restraints excluded: chain H residue 608 SER Chi-restraints excluded: chain H residue 663 ILE Chi-restraints excluded: chain H residue 741 VAL Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain H residue 780 THR Chi-restraints excluded: chain H residue 819 THR Chi-restraints excluded: chain H residue 861 VAL Chi-restraints excluded: chain H residue 863 VAL Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 271 LEU Chi-restraints excluded: chain I residue 327 LEU Chi-restraints excluded: chain I residue 391 THR Chi-restraints excluded: chain I residue 455 ILE Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 772 VAL Chi-restraints excluded: chain I residue 819 THR Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 179 HIS Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 271 LEU Chi-restraints excluded: chain J residue 407 LEU Chi-restraints excluded: chain J residue 445 THR Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 595 VAL Chi-restraints excluded: chain J residue 739 ASP Chi-restraints excluded: chain J residue 751 LEU Chi-restraints excluded: chain J residue 777 VAL Chi-restraints excluded: chain J residue 857 ILE Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 244 HIS Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 337 LEU Chi-restraints excluded: chain K residue 354 ILE Chi-restraints excluded: chain K residue 391 THR Chi-restraints excluded: chain K residue 478 ASP Chi-restraints excluded: chain K residue 510 ASP Chi-restraints excluded: chain K residue 547 ASP Chi-restraints excluded: chain K residue 567 VAL Chi-restraints excluded: chain K residue 595 VAL Chi-restraints excluded: chain K residue 619 LEU Chi-restraints excluded: chain K residue 662 ASN Chi-restraints excluded: chain K residue 683 LEU Chi-restraints excluded: chain K residue 705 MET Chi-restraints excluded: chain K residue 745 THR Chi-restraints excluded: chain K residue 830 VAL Chi-restraints excluded: chain K residue 839 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 996 random chunks: chunk 627 optimal weight: 20.0000 chunk 841 optimal weight: 6.9990 chunk 242 optimal weight: 9.9990 chunk 728 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 219 optimal weight: 7.9990 chunk 791 optimal weight: 2.9990 chunk 331 optimal weight: 6.9990 chunk 812 optimal weight: 30.0000 chunk 100 optimal weight: 20.0000 chunk 145 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS E 113 GLN ** E 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 HIS ** H 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 288 ASN J 531 ASN J 550 ASN ** K 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 888 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.126233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.078432 restraints weight = 137255.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.080747 restraints weight = 71132.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.082189 restraints weight = 47734.414| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 82657 Z= 0.358 Angle : 0.605 13.087 112186 Z= 0.303 Chirality : 0.046 0.201 12540 Planarity : 0.004 0.084 14541 Dihedral : 4.588 56.842 11220 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.80 % Allowed : 18.84 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.09), residues: 9970 helix: -0.00 (0.08), residues: 4198 sheet: -1.06 (0.15), residues: 1213 loop : -1.42 (0.09), residues: 4559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 81 HIS 0.015 0.001 HIS H 179 PHE 0.024 0.001 PHE E 726 TYR 0.026 0.001 TYR B 50 ARG 0.011 0.000 ARG G 740 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23952.61 seconds wall clock time: 418 minutes 37.77 seconds (25117.77 seconds total)