Starting phenix.real_space_refine on Tue Feb 13 03:07:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xy3_6784/02_2024/5xy3_6784_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xy3_6784/02_2024/5xy3_6784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xy3_6784/02_2024/5xy3_6784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xy3_6784/02_2024/5xy3_6784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xy3_6784/02_2024/5xy3_6784_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xy3_6784/02_2024/5xy3_6784_neut.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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: 5 Type Number sf(0) Gaussians P 2815 5.49 5 S 193 5.16 5 C 56650 2.51 5 N 19769 2.21 5 O 27718 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 6": "NH1" <-> "NH2" Residue "A ARG 10": "NH1" <-> "NH2" Residue "A ARG 23": "NH1" <-> "NH2" Residue "A ARG 125": "NH1" <-> "NH2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 240": "NH1" <-> "NH2" Residue "B ARG 4": "NH1" <-> "NH2" Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B ARG 250": "NH1" <-> "NH2" Residue "B TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 262": "NH1" <-> "NH2" Residue "B TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 160": "NH1" <-> "NH2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 266": "NH1" <-> "NH2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "D ARG 32": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E ARG 145": "NH1" <-> "NH2" Residue "E PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 15": "NH1" <-> "NH2" Residue "F GLU 59": "OE1" <-> "OE2" Residue "F PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 95": "OD1" <-> "OD2" Residue "F PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 142": "NH1" <-> "NH2" Residue "F TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 54": "NH1" <-> "NH2" Residue "G PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 146": "OD1" <-> "OD2" Residue "G TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 139": "NH1" <-> "NH2" Residue "H TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 7": "NH1" <-> "NH2" Residue "I ARG 21": "NH1" <-> "NH2" Residue "I ARG 24": "NH1" <-> "NH2" Residue "I TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 69": "NH1" <-> "NH2" Residue "I PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 202": "NH1" <-> "NH2" Residue "J TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 114": "NH1" <-> "NH2" Residue "L PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 101": "NH1" <-> "NH2" Residue "L ARG 115": "NH1" <-> "NH2" Residue "L ARG 153": "NH1" <-> "NH2" Residue "M ARG 96": "NH1" <-> "NH2" Residue "M ARG 117": "NH1" <-> "NH2" Residue "N ARG 67": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N ARG 73": "NH1" <-> "NH2" Residue "N ARG 85": "NH1" <-> "NH2" Residue "N TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 182": "NH1" <-> "NH2" Residue "N ARG 188": "NH1" <-> "NH2" Residue "N TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 201": "NH1" <-> "NH2" Residue "N ARG 202": "NH1" <-> "NH2" Residue "O TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 131": "NH1" <-> "NH2" Residue "P TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 24": "NH1" <-> "NH2" Residue "P PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 83": "NH1" <-> "NH2" Residue "P ARG 128": "NH1" <-> "NH2" Residue "P ARG 130": "NH1" <-> "NH2" Residue "Q ARG 8": "NH1" <-> "NH2" Residue "Q TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 36": "NH1" <-> "NH2" Residue "Q ARG 54": "NH1" <-> "NH2" Residue "Q TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 89": "NH1" <-> "NH2" Residue "Q ARG 143": "NH1" <-> "NH2" Residue "Q ASP 156": "OD1" <-> "OD2" Residue "Q ASP 157": "OD1" <-> "OD2" Residue "Q ARG 178": "NH1" <-> "NH2" Residue "Q ARG 179": "NH1" <-> "NH2" Residue "Q TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 20": "NH1" <-> "NH2" Residue "R ARG 62": "NH1" <-> "NH2" Residue "R ARG 66": "NH1" <-> "NH2" Residue "R ARG 85": "NH1" <-> "NH2" Residue "R ARG 97": "NH1" <-> "NH2" Residue "R ARG 110": "NH1" <-> "NH2" Residue "R ARG 121": "NH1" <-> "NH2" Residue "R ARG 151": "NH1" <-> "NH2" Residue "S ARG 11": "NH1" <-> "NH2" Residue "S ARG 25": "NH1" <-> "NH2" Residue "S PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 49": "NH1" <-> "NH2" Residue "S TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 12": "NH1" <-> "NH2" Residue "T ARG 20": "NH1" <-> "NH2" Residue "T ARG 55": "NH1" <-> "NH2" Residue "T ARG 79": "NH1" <-> "NH2" Residue "T TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 131": "NH1" <-> "NH2" Residue "U PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 67": "NH1" <-> "NH2" Residue "U ARG 74": "NH1" <-> "NH2" Residue "U ARG 83": "NH1" <-> "NH2" Residue "U TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 21": "NH1" <-> "NH2" Residue "W ARG 40": "NH1" <-> "NH2" Residue "W ARG 49": "NH1" <-> "NH2" Residue "W ARG 58": "NH1" <-> "NH2" Residue "X ARG 39": "NH1" <-> "NH2" Residue "X PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 13": "NH1" <-> "NH2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Y PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 123": "NH1" <-> "NH2" Residue "Y ARG 126": "NH1" <-> "NH2" Residue "Z PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 35": "NH1" <-> "NH2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 122": "NH1" <-> "NH2" Residue "a ARG 67": "NH1" <-> "NH2" Residue "a PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 56": "NH1" <-> "NH2" Residue "d ARG 25": "NH1" <-> "NH2" Residue "d ASP 47": "OD1" <-> "OD2" Residue "e ARG 17": "NH1" <-> "NH2" Residue "e PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 28": "NH1" <-> "NH2" Residue "e ARG 34": "NH1" <-> "NH2" Residue "e ARG 37": "NH1" <-> "NH2" Residue "e ARG 42": "NH1" <-> "NH2" Residue "e PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 65": "NH1" <-> "NH2" Residue "e ARG 125": "NH1" <-> "NH2" Residue "f ARG 17": "NH1" <-> "NH2" Residue "f PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 5": "NH1" <-> "NH2" Residue "g TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 10": "NH1" <-> "NH2" Residue "g ARG 18": "NH1" <-> "NH2" Residue "g ARG 20": "NH1" <-> "NH2" Residue "g TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 39": "NH1" <-> "NH2" Residue "g ARG 51": "NH1" <-> "NH2" Residue "g ARG 64": "NH1" <-> "NH2" Residue "h ARG 14": "NH1" <-> "NH2" Residue "h PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 23": "NH1" <-> "NH2" Residue "i ARG 28": "NH1" <-> "NH2" Residue "i TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 52": "NH1" <-> "NH2" Residue "i ARG 53": "NH1" <-> "NH2" Residue "i ARG 54": "NH1" <-> "NH2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j ARG 55": "NH1" <-> "NH2" Residue "j ARG 65": "NH1" <-> "NH2" Residue "k ARG 17": "NH1" <-> "NH2" Residue "l ARG 8": "NH1" <-> "NH2" Residue "l ARG 11": "NH1" <-> "NH2" Residue "l ARG 21": "NH1" <-> "NH2" Residue "l PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 34": "NH1" <-> "NH2" Residue "l ARG 37": "NH1" <-> "NH2" Residue "m ARG 105": "NH1" <-> "NH2" Residue "m ARG 125": "NH1" <-> "NH2" Residue "o ARG 39": "NH1" <-> "NH2" Residue "o ARG 43": "NH1" <-> "NH2" Residue "o ARG 69": "NH1" <-> "NH2" Residue "o ARG 85": "NH1" <-> "NH2" Residue "p ARG 3": "NH1" <-> "NH2" Residue "p ASP 45": "OD1" <-> "OD2" Residue "p ARG 85": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 107145 Number of models: 1 Model: "" Number of chains: 43 Chain: "1" Number of atoms: 54325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2544, 54325 Classifications: {'RNA': 2544} Modifications used: {'rna2p_pur': 254, 'rna2p_pyr': 181, 'rna3p_pur': 1135, 'rna3p_pyr': 974} Link IDs: {'rna2p': 434, 'rna3p': 2109} Chain breaks: 12 Chain: "3" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2493 Classifications: {'RNA': 117} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 52, 'rna3p_pyr': 50} Link IDs: {'rna2p': 14, 'rna3p': 102} Chain: "4" Number of atoms: 3289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 3289 Classifications: {'RNA': 154} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 13, 'rna3p_pur': 69, 'rna3p_pyr': 55} Link IDs: {'rna2p': 30, 'rna3p': 123} Chain breaks: 1 Chain: "A" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1785 Classifications: {'peptide': 237} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 222} Chain breaks: 2 Chain: "B" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3175 Classifications: {'peptide': 400} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 384} Chain breaks: 2 Chain: "C" Number of atoms: 2772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2772 Classifications: {'peptide': 362} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 339} Chain breaks: 2 Chain: "D" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2167 Classifications: {'peptide': 272} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 260} Chain breaks: 2 Chain: "E" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1014 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain breaks: 3 Chain: "F" Number of atoms: 1832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1832 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain: "G" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1384 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 9, 'TRANS': 164} Chain breaks: 2 Chain: "H" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1556 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 188} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1569 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain breaks: 1 Chain: "J" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1320 Classifications: {'peptide': 164} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "L" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1498 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 174} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1004 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "N" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1696 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 192} Chain breaks: 1 Chain: "O" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1559 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "P" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1230 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain breaks: 1 Chain: "Q" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1465 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 176} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1299 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 1, 'TRANS': 160} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "S" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1384 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 163} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "T" Number of atoms: 1255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1255 Classifications: {'peptide': 158} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 145} Chain: "U" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 794 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain breaks: 1 Chain: "V" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 986 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain: "W" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 513 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "X" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 803 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "Y" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1068 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "Z" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1042 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain breaks: 2 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "a" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1179 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 7, 'TRANS': 141} Chain: "b" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 415 Classifications: {'peptide': 50} Link IDs: {'TRANS': 49} Chain breaks: 1 Chain: "c" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 727 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain breaks: 1 Chain: "d" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 783 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 2 Chain: "e" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 8, 'TRANS': 114} Chain: "f" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 781 Classifications: {'peptide': 97} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 89} Chain breaks: 1 Chain: "g" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 921 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "h" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 984 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "i" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 616 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "j" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 73} Chain breaks: 1 Chain: "k" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 547 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "l" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 428 Classifications: {'peptide': 50} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 45} Chain: "m" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 417 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "o" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 773 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "p" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 678 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Time building chain proxies: 41.11, per 1000 atoms: 0.38 Number of scatterers: 107145 At special positions: 0 Unit cell: (211.2, 229.68, 241.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 193 16.00 P 2815 15.00 O 27718 8.00 N 19769 7.00 C 56650 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS O 36 " - pdb=" SG CYS O 102 " distance=2.05 Simple disulfide: pdb=" SG CYS j 19 " - pdb=" SG CYS j 22 " distance=2.15 Simple disulfide: pdb=" SG CYS j 19 " - pdb=" SG CYS j 34 " distance=2.94 Simple disulfide: pdb=" SG CYS j 22 " - pdb=" SG CYS j 34 " distance=1.97 Simple disulfide: pdb=" SG CYS j 22 " - pdb=" SG CYS j 37 " distance=2.36 Simple disulfide: pdb=" SG CYS m 99 " - pdb=" SG CYS m 113 " distance=2.78 Simple disulfide: pdb=" SG CYS o 12 " - pdb=" SG CYS o 75 " distance=2.04 Simple disulfide: pdb=" SG CYS o 15 " - pdb=" SG CYS o 75 " distance=2.03 Simple disulfide: pdb=" SG CYS p 42 " - pdb=" SG CYS p 60 " distance=2.03 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: 38.49 Conformation dependent library (CDL) restraints added in 6.5 seconds 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11078 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 71 sheets defined 36.9% alpha, 14.1% beta 774 base pairs and 1579 stacking pairs defined. Time for finding SS restraints: 33.69 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 removed outlier: 3.559A pdb=" N ARG A 10 " --> pdb=" O ARG A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 190 removed outlier: 3.633A pdb=" N VAL A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 116 removed outlier: 3.698A pdb=" N LYS B 115 " --> pdb=" O ASN B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 135 through 153 removed outlier: 3.529A pdb=" N ALA B 139 " --> pdb=" O SER B 135 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU B 141 " --> pdb=" O GLY B 137 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 removed outlier: 3.698A pdb=" N LYS B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 226 removed outlier: 3.769A pdb=" N ASP B 225 " --> pdb=" O LYS B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 252 Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.617A pdb=" N ARG B 398 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 27 Processing helix chain 'C' and resid 30 through 45 removed outlier: 3.632A pdb=" N ASN C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS C 43 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN C 44 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 128 removed outlier: 3.568A pdb=" N ALA C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 138 removed outlier: 4.035A pdb=" N VAL C 134 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN C 135 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY C 138 " --> pdb=" O VAL C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 160 through 171 removed outlier: 3.524A pdb=" N ALA C 164 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS C 169 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 182 removed outlier: 3.711A pdb=" N VAL C 177 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 180 " --> pdb=" O ASP C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 196 removed outlier: 4.392A pdb=" N ARG C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA C 196 " --> pdb=" O LYS C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 219 Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'C' and resid 239 through 242 Processing helix chain 'C' and resid 251 through 255 Processing helix chain 'C' and resid 256 through 263 removed outlier: 3.560A pdb=" N SER C 263 " --> pdb=" O GLY C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 285 removed outlier: 3.538A pdb=" N ILE C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C 285 " --> pdb=" O ALA C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 290 Processing helix chain 'C' and resid 315 through 337 removed outlier: 3.634A pdb=" N GLN C 319 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS C 323 " --> pdb=" O GLN C 319 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 353 removed outlier: 3.724A pdb=" N LYS C 343 " --> pdb=" O PRO C 339 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN C 353 " --> pdb=" O ALA C 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 15 removed outlier: 3.526A pdb=" N ARG D 14 " --> pdb=" O GLY D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 37 removed outlier: 3.824A pdb=" N GLN D 34 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN D 37 " --> pdb=" O THR D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 82 No H-bonds generated for 'chain 'D' and resid 80 through 82' Processing helix chain 'D' and resid 93 through 112 Processing helix chain 'D' and resid 151 through 164 Processing helix chain 'D' and resid 209 through 220 removed outlier: 3.553A pdb=" N TYR D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG D 215 " --> pdb=" O ALA D 211 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D 217 " --> pdb=" O TYR D 213 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 229 removed outlier: 3.588A pdb=" N ASN D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 236 removed outlier: 4.044A pdb=" N GLY D 236 " --> pdb=" O TYR D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 256 removed outlier: 4.379A pdb=" N LYS D 244 " --> pdb=" O ASP D 240 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS D 247 " --> pdb=" O GLU D 243 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 276 removed outlier: 3.542A pdb=" N HIS D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 303 removed outlier: 3.542A pdb=" N ARG D 292 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA D 301 " --> pdb=" O GLU D 297 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA D 302 " --> pdb=" O HIS D 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 125 removed outlier: 3.762A pdb=" N VAL E 120 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU E 121 " --> pdb=" O GLU E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 136 removed outlier: 3.515A pdb=" N LYS E 135 " --> pdb=" O VAL E 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 70 removed outlier: 4.078A pdb=" N GLU F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA F 18 " --> pdb=" O ALA F 14 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS F 26 " --> pdb=" O ALA F 22 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN F 42 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU F 43 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG F 44 " --> pdb=" O LYS F 40 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP F 61 " --> pdb=" O LYS F 57 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA F 66 " --> pdb=" O ALA F 62 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 103 removed outlier: 4.083A pdb=" N LEU F 100 " --> pdb=" O VAL F 96 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE F 103 " --> pdb=" O ILE F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 127 removed outlier: 3.581A pdb=" N GLU F 122 " --> pdb=" O LYS F 118 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG F 126 " --> pdb=" O GLU F 122 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL F 127 " --> pdb=" O MET F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 148 removed outlier: 3.567A pdb=" N ILE F 145 " --> pdb=" O VAL F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 171 removed outlier: 4.304A pdb=" N ILE F 166 " --> pdb=" O ASP F 162 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL F 168 " --> pdb=" O GLN F 164 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA F 169 " --> pdb=" O ILE F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 187 Processing helix chain 'F' and resid 191 through 199 Processing helix chain 'F' and resid 217 through 221 Processing helix chain 'F' and resid 230 through 239 removed outlier: 4.299A pdb=" N ARG F 237 " --> pdb=" O GLU F 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 60 removed outlier: 3.626A pdb=" N LYS G 58 " --> pdb=" O ARG G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 69 removed outlier: 4.012A pdb=" N PHE G 69 " --> pdb=" O PRO G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 88 removed outlier: 3.862A pdb=" N VAL G 79 " --> pdb=" O LYS G 75 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA G 80 " --> pdb=" O ASP G 76 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS G 83 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE G 84 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 135 Processing helix chain 'G' and resid 155 through 163 Processing helix chain 'G' and resid 173 through 181 removed outlier: 3.552A pdb=" N VAL G 180 " --> pdb=" O LEU G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 212 removed outlier: 3.665A pdb=" N LYS G 203 " --> pdb=" O ALA G 199 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE G 204 " --> pdb=" O ALA G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 219 removed outlier: 4.171A pdb=" N LYS G 217 " --> pdb=" O LEU G 213 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU G 218 " --> pdb=" O ALA G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 222 No H-bonds generated for 'chain 'G' and resid 220 through 222' Processing helix chain 'G' and resid 230 through 237 removed outlier: 3.510A pdb=" N LYS G 235 " --> pdb=" O LYS G 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 92 removed outlier: 3.715A pdb=" N ALA H 74 " --> pdb=" O ARG H 70 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG H 75 " --> pdb=" O LYS H 71 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE H 76 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN H 85 " --> pdb=" O GLY H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 126 removed outlier: 3.658A pdb=" N GLY H 125 " --> pdb=" O GLY H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 172 removed outlier: 3.575A pdb=" N VAL H 164 " --> pdb=" O ASP H 160 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU H 171 " --> pdb=" O GLN H 167 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR H 172 " --> pdb=" O ILE H 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 80 removed outlier: 3.629A pdb=" N TYR I 75 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 143 No H-bonds generated for 'chain 'I' and resid 141 through 143' Processing helix chain 'I' and resid 144 through 157 removed outlier: 3.534A pdb=" N GLU I 150 " --> pdb=" O LYS I 146 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG I 154 " --> pdb=" O GLU I 150 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 188 removed outlier: 3.689A pdb=" N LYS I 182 " --> pdb=" O PHE I 178 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU I 183 " --> pdb=" O GLU I 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 38 removed outlier: 4.294A pdb=" N THR J 27 " --> pdb=" O GLY J 23 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG J 31 " --> pdb=" O THR J 27 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU J 36 " --> pdb=" O VAL J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 80 removed outlier: 3.664A pdb=" N LEU J 73 " --> pdb=" O GLY J 69 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN J 77 " --> pdb=" O LEU J 73 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG J 78 " --> pdb=" O GLU J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.725A pdb=" N PHE J 92 " --> pdb=" O GLY J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 137 removed outlier: 3.998A pdb=" N ARG J 136 " --> pdb=" O ASN J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 164 removed outlier: 3.510A pdb=" N PHE J 163 " --> pdb=" O PHE J 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 19 removed outlier: 3.542A pdb=" N HIS L 19 " --> pdb=" O TYR L 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 16 through 19' Processing helix chain 'L' and resid 26 through 46 removed outlier: 4.021A pdb=" N LYS L 44 " --> pdb=" O LEU L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 66 removed outlier: 3.658A pdb=" N ASN L 66 " --> pdb=" O VAL L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 84 removed outlier: 3.530A pdb=" N VAL L 81 " --> pdb=" O PRO L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 92 removed outlier: 3.643A pdb=" N ARG L 91 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 122 removed outlier: 3.517A pdb=" N VAL L 109 " --> pdb=" O LYS L 105 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS L 110 " --> pdb=" O ASP L 106 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN L 111 " --> pdb=" O ALA L 107 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG L 122 " --> pdb=" O ALA L 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 142 removed outlier: 3.906A pdb=" N PHE L 141 " --> pdb=" O ASP L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 163 through 186 removed outlier: 3.546A pdb=" N GLU L 167 " --> pdb=" O ASP L 163 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS L 171 " --> pdb=" O GLU L 167 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU L 177 " --> pdb=" O LYS L 173 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS L 179 " --> pdb=" O PHE L 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 77 removed outlier: 3.775A pdb=" N ALA M 76 " --> pdb=" O ALA M 72 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA M 77 " --> pdb=" O ALA M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 87 removed outlier: 3.919A pdb=" N LYS M 82 " --> pdb=" O LYS M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 101 removed outlier: 3.786A pdb=" N GLN M 92 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL M 93 " --> pdb=" O TRP M 89 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE M 94 " --> pdb=" O GLY M 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 125 removed outlier: 3.525A pdb=" N PHE M 108 " --> pdb=" O ASP M 104 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU M 124 " --> pdb=" O LEU M 120 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU M 125 " --> pdb=" O VAL M 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 12 removed outlier: 3.590A pdb=" N LEU N 7 " --> pdb=" O ALA N 3 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG N 8 " --> pdb=" O PHE N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 33 removed outlier: 3.517A pdb=" N PHE N 21 " --> pdb=" O GLU N 17 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN N 32 " --> pdb=" O TRP N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 75 through 79 removed outlier: 4.026A pdb=" N ASN N 78 " --> pdb=" O ALA N 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 87 removed outlier: 3.618A pdb=" N HIS N 87 " --> pdb=" O PRO N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 148 through 157 removed outlier: 5.164A pdb=" N SER N 154 " --> pdb=" O ILE N 151 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL N 155 " --> pdb=" O CYS N 152 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR N 157 " --> pdb=" O SER N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 163 removed outlier: 3.994A pdb=" N ARG N 162 " --> pdb=" O ARG N 158 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 172 removed outlier: 3.500A pdb=" N LYS N 170 " --> pdb=" O ALA N 166 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS N 171 " --> pdb=" O ALA N 167 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG N 172 " --> pdb=" O GLY N 168 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 197 Processing helix chain 'O' and resid 13 through 27 removed outlier: 3.547A pdb=" N LEU O 26 " --> pdb=" O ALA O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 38 No H-bonds generated for 'chain 'O' and resid 36 through 38' Processing helix chain 'O' and resid 44 through 58 removed outlier: 3.522A pdb=" N ASN O 57 " --> pdb=" O GLU O 53 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS O 58 " --> pdb=" O ARG O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 67 removed outlier: 3.628A pdb=" N ASP O 66 " --> pdb=" O ASN O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 84 removed outlier: 3.760A pdb=" N ALA O 79 " --> pdb=" O HIS O 75 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG O 80 " --> pdb=" O GLU O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 99 removed outlier: 3.651A pdb=" N ASN O 99 " --> pdb=" O ASP O 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 118 through 121 Processing helix chain 'O' and resid 122 through 127 Processing helix chain 'O' and resid 136 through 143 Processing helix chain 'O' and resid 147 through 188 removed outlier: 3.628A pdb=" N ALA O 152 " --> pdb=" O GLY O 148 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN O 153 " --> pdb=" O ASN O 149 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE O 166 " --> pdb=" O SER O 162 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA O 168 " --> pdb=" O LYS O 164 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA O 171 " --> pdb=" O GLU O 167 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS O 175 " --> pdb=" O ALA O 171 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS O 182 " --> pdb=" O ALA O 178 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN O 184 " --> pdb=" O ILE O 180 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS O 185 " --> pdb=" O GLU O 181 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN O 186 " --> pdb=" O LYS O 182 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 197 removed outlier: 3.735A pdb=" N VAL O 192 " --> pdb=" O GLY O 188 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS O 193 " --> pdb=" O ALA O 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 38 removed outlier: 3.679A pdb=" N MET P 30 " --> pdb=" O HIS P 26 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL P 36 " --> pdb=" O GLU P 32 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS P 38 " --> pdb=" O GLY P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 54 removed outlier: 3.681A pdb=" N ALA P 47 " --> pdb=" O GLN P 43 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA P 51 " --> pdb=" O ALA P 47 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 100 removed outlier: 3.636A pdb=" N LEU P 91 " --> pdb=" O LYS P 87 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR P 98 " --> pdb=" O LYS P 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 38 removed outlier: 3.548A pdb=" N TYR Q 31 " --> pdb=" O LEU Q 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 52 removed outlier: 3.576A pdb=" N CYS Q 51 " --> pdb=" O ALA Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 70 Processing helix chain 'Q' and resid 104 through 114 removed outlier: 3.539A pdb=" N ALA Q 109 " --> pdb=" O GLU Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 128 removed outlier: 3.913A pdb=" N GLN Q 126 " --> pdb=" O ASP Q 122 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU Q 127 " --> pdb=" O GLN Q 123 " (cutoff:3.500A) Processing helix chain 'Q' and resid 140 through 144 removed outlier: 3.798A pdb=" N ARG Q 143 " --> pdb=" O ASP Q 140 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG Q 144 " --> pdb=" O ARG Q 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 140 through 144' Processing helix chain 'Q' and resid 145 through 149 Processing helix chain 'R' and resid 4 through 16 removed outlier: 3.597A pdb=" N LYS R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG R 9 " --> pdb=" O LYS R 5 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER R 13 " --> pdb=" O ARG R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 34 removed outlier: 3.696A pdb=" N ILE R 32 " --> pdb=" O GLU R 28 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET R 34 " --> pdb=" O SER R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 47 removed outlier: 3.821A pdb=" N LYS R 43 " --> pdb=" O GLN R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 73 removed outlier: 4.005A pdb=" N LEU R 72 " --> pdb=" O LEU R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 81 removed outlier: 4.001A pdb=" N ARG R 81 " --> pdb=" O TYR R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 89 Processing helix chain 'R' and resid 90 through 112 removed outlier: 3.589A pdb=" N ARG R 100 " --> pdb=" O ILE R 96 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL R 101 " --> pdb=" O ARG R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 129 removed outlier: 3.739A pdb=" N TYR R 120 " --> pdb=" O ASP R 116 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG R 121 " --> pdb=" O CYS R 117 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS R 122 " --> pdb=" O HIS R 118 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY R 129 " --> pdb=" O LEU R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 148 Processing helix chain 'R' and resid 148 through 163 removed outlier: 3.946A pdb=" N GLU R 152 " --> pdb=" O GLU R 148 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER R 157 " --> pdb=" O LYS R 153 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE R 159 " --> pdb=" O LEU R 155 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG R 162 " --> pdb=" O GLN R 158 " (cutoff:3.500A) Processing helix chain 'S' and resid 32 through 47 removed outlier: 3.688A pdb=" N SER S 38 " --> pdb=" O VAL S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 97 through 113 removed outlier: 3.586A pdb=" N ALA S 107 " --> pdb=" O THR S 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 135 through 140 Processing helix chain 'S' and resid 141 through 143 No H-bonds generated for 'chain 'S' and resid 141 through 143' Processing helix chain 'T' and resid 102 through 123 removed outlier: 3.722A pdb=" N LYS T 120 " --> pdb=" O HIS T 116 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA T 122 " --> pdb=" O GLU T 118 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 17 removed outlier: 3.658A pdb=" N ALA U 15 " --> pdb=" O SER U 11 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP U 16 " --> pdb=" O ALA U 12 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS U 17 " --> pdb=" O PRO U 13 " (cutoff:3.500A) Processing helix chain 'U' and resid 20 through 30 removed outlier: 3.524A pdb=" N SER U 30 " --> pdb=" O GLU U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 80 removed outlier: 4.048A pdb=" N VAL U 69 " --> pdb=" O SER U 65 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA U 78 " --> pdb=" O ARG U 74 " (cutoff:3.500A) Processing helix chain 'V' and resid 123 through 129 Processing helix chain 'V' and resid 129 through 135 removed outlier: 3.591A pdb=" N VAL V 135 " --> pdb=" O LYS V 131 " (cutoff:3.500A) Processing helix chain 'W' and resid 35 through 44 Processing helix chain 'W' and resid 54 through 61 removed outlier: 3.877A pdb=" N ARG W 58 " --> pdb=" O THR W 54 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP W 60 " --> pdb=" O HIS W 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 60 Processing helix chain 'X' and resid 67 through 76 removed outlier: 3.550A pdb=" N GLU X 75 " --> pdb=" O THR X 71 " (cutoff:3.500A) Processing helix chain 'X' and resid 89 through 102 Processing helix chain 'X' and resid 129 through 138 removed outlier: 3.726A pdb=" N GLU X 136 " --> pdb=" O ASN X 132 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE X 137 " --> pdb=" O ILE X 133 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 21 Processing helix chain 'Y' and resid 23 through 31 removed outlier: 3.648A pdb=" N VAL Y 29 " --> pdb=" O ASP Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 44 removed outlier: 3.622A pdb=" N GLU Y 41 " --> pdb=" O LYS Y 37 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA Y 42 " --> pdb=" O GLU Y 38 " (cutoff:3.500A) Processing helix chain 'Y' and resid 100 through 102 No H-bonds generated for 'chain 'Y' and resid 100 through 102' Processing helix chain 'Y' and resid 112 through 134 removed outlier: 3.735A pdb=" N LEU Y 121 " --> pdb=" O ASN Y 117 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU Y 124 " --> pdb=" O GLU Y 120 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA Y 131 " --> pdb=" O ASP Y 127 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 66 removed outlier: 3.868A pdb=" N LYS Z 63 " --> pdb=" O GLU Z 59 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS Z 64 " --> pdb=" O VAL Z 60 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN Z 66 " --> pdb=" O VAL Z 62 " (cutoff:3.500A) Processing helix chain 'Z' and resid 90 through 96 removed outlier: 3.701A pdb=" N ILE Z 95 " --> pdb=" O PHE Z 91 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER Z 96 " --> pdb=" O PHE Z 92 " (cutoff:3.500A) Processing helix chain 'Z' and resid 99 through 105 Processing helix chain 'Z' and resid 106 through 127 removed outlier: 3.738A pdb=" N LEU Z 113 " --> pdb=" O ALA Z 109 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA Z 119 " --> pdb=" O THR Z 115 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN Z 123 " --> pdb=" O ALA Z 119 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS Z 124 " --> pdb=" O VAL Z 120 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR Z 125 " --> pdb=" O LEU Z 121 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN Z 127 " --> pdb=" O GLN Z 123 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 135 removed outlier: 3.559A pdb=" N PHE Z 134 " --> pdb=" O MET Z 130 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS Z 135 " --> pdb=" O ALA Z 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 130 through 135' Processing helix chain 'a' and resid 6 through 11 removed outlier: 4.111A pdb=" N LYS a 10 " --> pdb=" O HIS a 6 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 49 Processing helix chain 'a' and resid 85 through 94 removed outlier: 4.210A pdb=" N ARG a 89 " --> pdb=" O PRO a 85 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL a 90 " --> pdb=" O GLU a 86 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS a 91 " --> pdb=" O GLU a 87 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA a 94 " --> pdb=" O VAL a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 106 through 110 Processing helix chain 'a' and resid 133 through 144 Processing helix chain 'b' and resid 11 through 17 removed outlier: 3.800A pdb=" N GLN b 15 " --> pdb=" O ASN b 11 " (cutoff:3.500A) Processing helix chain 'b' and resid 36 through 52 removed outlier: 3.636A pdb=" N ASN b 42 " --> pdb=" O LYS b 38 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR b 45 " --> pdb=" O ARG b 41 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS b 47 " --> pdb=" O ALA b 43 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN b 50 " --> pdb=" O ALA b 46 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN b 51 " --> pdb=" O LYS b 47 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS b 52 " --> pdb=" O ALA b 48 " (cutoff:3.500A) Processing helix chain 'c' and resid 13 through 24 removed outlier: 3.857A pdb=" N LEU c 19 " --> pdb=" O ASN c 15 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR c 21 " --> pdb=" O LEU c 17 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS c 22 " --> pdb=" O SER c 18 " (cutoff:3.500A) Processing helix chain 'c' and resid 29 through 39 removed outlier: 3.569A pdb=" N GLN c 35 " --> pdb=" O ASP c 31 " (cutoff:3.500A) Processing helix chain 'c' and resid 54 through 67 removed outlier: 3.720A pdb=" N GLU c 60 " --> pdb=" O ARG c 56 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR c 61 " --> pdb=" O SER c 57 " (cutoff:3.500A) Processing helix chain 'c' and resid 76 through 85 removed outlier: 3.818A pdb=" N CYS c 84 " --> pdb=" O LEU c 80 " (cutoff:3.500A) Processing helix chain 'c' and resid 103 through 108 removed outlier: 3.656A pdb=" N ILE c 107 " --> pdb=" O ILE c 103 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 24 through 26 No H-bonds generated for 'chain 'd' and resid 24 through 26' Processing helix chain 'd' and resid 27 through 45 removed outlier: 3.674A pdb=" N LYS d 34 " --> pdb=" O GLU d 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 60 Processing helix chain 'e' and resid 41 through 46 removed outlier: 3.582A pdb=" N ARG e 45 " --> pdb=" O SER e 41 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 59 Processing helix chain 'e' and resid 81 through 87 removed outlier: 3.548A pdb=" N ASP e 84 " --> pdb=" O LYS e 81 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU e 86 " --> pdb=" O LEU e 83 " (cutoff:3.500A) Processing helix chain 'e' and resid 102 through 117 removed outlier: 3.659A pdb=" N GLN e 107 " --> pdb=" O ALA e 103 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU e 115 " --> pdb=" O LYS e 111 " (cutoff:3.500A) Processing helix chain 'f' and resid 85 through 89 Processing helix chain 'g' and resid 59 through 66 removed outlier: 3.935A pdb=" N ARG g 65 " --> pdb=" O CYS g 61 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET g 66 " --> pdb=" O GLU g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 83 through 112 removed outlier: 3.748A pdb=" N GLU g 97 " --> pdb=" O ALA g 93 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN g 111 " --> pdb=" O MET g 107 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'h' and resid 13 through 38 removed outlier: 3.649A pdb=" N LYS h 27 " --> pdb=" O GLY h 23 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU h 28 " --> pdb=" O LEU h 24 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU h 31 " --> pdb=" O LYS h 27 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ALA h 36 " --> pdb=" O LYS h 32 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA h 37 " --> pdb=" O GLY h 33 " (cutoff:3.500A) Processing helix chain 'h' and resid 42 through 74 removed outlier: 3.762A pdb=" N LYS h 48 " --> pdb=" O LEU h 44 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA h 55 " --> pdb=" O ARG h 51 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA h 68 " --> pdb=" O SER h 64 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU h 71 " --> pdb=" O LYS h 67 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS h 72 " --> pdb=" O ALA h 68 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR h 73 " --> pdb=" O LEU h 69 " (cutoff:3.500A) Processing helix chain 'h' and resid 88 through 94 Processing helix chain 'h' and resid 96 through 102 removed outlier: 3.648A pdb=" N ALA h 100 " --> pdb=" O ALA h 96 " (cutoff:3.500A) Processing helix chain 'h' and resid 104 through 112 removed outlier: 3.620A pdb=" N ARG h 109 " --> pdb=" O ALA h 105 " (cutoff:3.500A) Processing helix chain 'i' and resid 22 through 36 removed outlier: 3.527A pdb=" N ILE i 30 " --> pdb=" O PHE i 26 " (cutoff:3.500A) Processing helix chain 'i' and resid 38 through 50 Processing helix chain 'i' and resid 52 through 65 removed outlier: 3.553A pdb=" N GLN i 58 " --> pdb=" O ARG i 54 " (cutoff:3.500A) Processing helix chain 'i' and resid 66 through 88 removed outlier: 3.516A pdb=" N ALA i 70 " --> pdb=" O THR i 66 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS i 72 " --> pdb=" O ARG i 68 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU i 79 " --> pdb=" O ASN i 75 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU i 84 " --> pdb=" O VAL i 80 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU i 86 " --> pdb=" O GLN i 82 " (cutoff:3.500A) Processing helix chain 'j' and resid 5 through 9 Processing helix chain 'j' and resid 47 through 49 No H-bonds generated for 'chain 'j' and resid 47 through 49' Processing helix chain 'j' and resid 50 through 58 removed outlier: 3.761A pdb=" N ARG j 55 " --> pdb=" O LYS j 51 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS j 56 " --> pdb=" O LYS j 52 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) Processing helix chain 'j' and resid 64 through 78 removed outlier: 4.430A pdb=" N VAL j 69 " --> pdb=" O ARG j 65 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR j 70 " --> pdb=" O HIS j 66 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU j 74 " --> pdb=" O THR j 70 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG j 76 " --> pdb=" O ALA j 72 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR j 78 " --> pdb=" O LEU j 74 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 16 removed outlier: 3.657A pdb=" N LEU k 12 " --> pdb=" O PRO k 8 " (cutoff:3.500A) Processing helix chain 'k' and resid 29 through 31 No H-bonds generated for 'chain 'k' and resid 29 through 31' Processing helix chain 'k' and resid 52 through 60 removed outlier: 3.656A pdb=" N VAL k 56 " --> pdb=" O PHE k 52 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN k 57 " --> pdb=" O VAL k 53 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN k 58 " --> pdb=" O GLU k 54 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 19 removed outlier: 3.572A pdb=" N ILE l 12 " --> pdb=" O ARG l 8 " (cutoff:3.500A) Processing helix chain 'l' and resid 25 through 32 removed outlier: 3.523A pdb=" N GLN l 29 " --> pdb=" O GLN l 25 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 93 removed outlier: 3.832A pdb=" N ALA m 89 " --> pdb=" O LEU m 85 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR m 92 " --> pdb=" O LEU m 88 " (cutoff:3.500A) Processing helix chain 'o' and resid 35 through 46 Processing helix chain 'p' and resid 8 through 15 removed outlier: 4.274A pdb=" N CYS p 11 " --> pdb=" O VAL p 8 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS p 13 " --> pdb=" O ILE p 10 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 35 removed outlier: 3.665A pdb=" N ARG p 23 " --> pdb=" O GLY p 19 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS p 28 " --> pdb=" O LYS p 24 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE p 29 " --> pdb=" O THR p 25 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE p 31 " --> pdb=" O LYS p 27 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG p 34 " --> pdb=" O GLU p 30 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS p 35 " --> pdb=" O ILE p 31 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 89 removed outlier: 3.509A pdb=" N ARG p 80 " --> pdb=" O ALA p 76 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA p 81 " --> pdb=" O LEU p 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 77 removed outlier: 3.675A pdb=" N GLU A 47 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE A 62 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL A 45 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 103 removed outlier: 7.154A pdb=" N ARG A 145 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N HIS A 139 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR A 143 " --> pdb=" O HIS A 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 222 through 223 Processing sheet with id=AA4, first strand: chain 'B' and resid 378 through 381 removed outlier: 6.051A pdb=" N LEU B 378 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ASP B 59 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP B 380 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ALA B 357 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N VAL B 238 " --> pdb=" O ALA B 357 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR B 235 " --> pdb=" O MET B 296 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N MET B 296 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLY B 237 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N THR B 294 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ARG B 299 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N MET B 345 " --> pdb=" O TYR B 301 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE B 303 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE B 343 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP B 342 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B 70 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY B 52 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLU B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LYS B 50 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.516A pdb=" N VAL B 156 " --> pdb=" O TYR B 92 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR B 104 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLY B 91 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA7, first strand: chain 'B' and resid 167 through 169 Processing sheet with id=AA8, first strand: chain 'B' and resid 243 through 245 removed outlier: 3.558A pdb=" N GLY B 243 " --> pdb=" O ARG B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 15 through 20 removed outlier: 3.658A pdb=" N SER C 17 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL C 150 " --> pdb=" O ASN C 7 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE C 149 " --> pdb=" O TRP C 249 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 185 through 186 removed outlier: 4.088A pdb=" N VAL C 185 " --> pdb=" O LYS C 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 296 through 298 Processing sheet with id=AB3, first strand: chain 'D' and resid 72 through 78 removed outlier: 5.415A pdb=" N THR D 73 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL D 65 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N CYS D 75 " --> pdb=" O ILE D 63 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 96 through 98 removed outlier: 7.658A pdb=" N ILE E 84 " --> pdb=" O ASP E 79 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASP E 79 " --> pdb=" O ILE E 84 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LYS E 86 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL E 77 " --> pdb=" O LYS E 86 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS E 72 " --> pdb=" O ILE E 64 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 72 through 73 Processing sheet with id=AB6, first strand: chain 'F' and resid 202 through 203 removed outlier: 3.981A pdb=" N ASN F 110 " --> pdb=" O ARG F 85 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE F 112 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL F 131 " --> pdb=" O GLY F 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 150 through 151 Processing sheet with id=AB8, first strand: chain 'G' and resid 140 through 142 removed outlier: 4.068A pdb=" N LEU G 140 " --> pdb=" O LEU G 190 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 6 through 12 removed outlier: 4.047A pdb=" N HIS H 7 " --> pdb=" O CYS H 65 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 18 through 21 removed outlier: 3.523A pdb=" N LYS H 43 " --> pdb=" O VAL H 26 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 138 through 141 removed outlier: 3.502A pdb=" N MET H 98 " --> pdb=" O ILE H 151 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LYS H 97 " --> pdb=" O GLN H 189 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR H 187 " --> pdb=" O HIS H 99 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 110 through 112 removed outlier: 3.885A pdb=" N SER H 112 " --> pdb=" O ASP H 119 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 35 through 37 removed outlier: 5.993A pdb=" N GLN I 134 " --> pdb=" O LEU I 54 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU I 54 " --> pdb=" O GLN I 134 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET I 136 " --> pdb=" O LEU I 52 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 59 through 61 removed outlier: 6.043A pdb=" N ILE I 99 " --> pdb=" O PRO I 122 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY I 124 " --> pdb=" O LEU I 97 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 190 through 192 Processing sheet with id=AC7, first strand: chain 'J' and resid 42 through 45 removed outlier: 3.744A pdb=" N ALA J 62 " --> pdb=" O ALA J 44 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL J 126 " --> pdb=" O ALA J 11 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU J 13 " --> pdb=" O TYR J 124 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N TYR J 124 " --> pdb=" O LEU J 13 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE J 15 " --> pdb=" O ASP J 122 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASP J 122 " --> pdb=" O ILE J 15 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU J 123 " --> pdb=" O PHE J 100 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 21 through 23 Processing sheet with id=AC9, first strand: chain 'L' and resid 57 through 59 Processing sheet with id=AD1, first strand: chain 'L' and resid 123 through 124 Processing sheet with id=AD2, first strand: chain 'M' and resid 48 through 51 removed outlier: 8.586A pdb=" N ARG M 35 " --> pdb=" O ILE M 30 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE M 30 " --> pdb=" O ARG M 35 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU M 37 " --> pdb=" O VAL M 28 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL M 28 " --> pdb=" O LEU M 37 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS M 23 " --> pdb=" O ILE M 15 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE M 15 " --> pdb=" O LYS M 23 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ARG M 11 " --> pdb=" O ILE M 27 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N TYR M 60 " --> pdb=" O VAL M 12 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU M 14 " --> pdb=" O THR M 58 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N THR M 58 " --> pdb=" O LEU M 14 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 37 through 39 removed outlier: 4.718A pdb=" N VAL N 61 " --> pdb=" O LEU N 39 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 37 through 39 removed outlier: 4.718A pdb=" N VAL N 61 " --> pdb=" O LEU N 39 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN N 122 " --> pdb=" O TYR N 129 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLU N 131 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TRP N 120 " --> pdb=" O GLU N 131 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 6 through 7 removed outlier: 6.511A pdb=" N VAL O 6 " --> pdb=" O LEU O 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'O' and resid 31 through 34 Processing sheet with id=AD7, first strand: chain 'O' and resid 40 through 42 Processing sheet with id=AD8, first strand: chain 'P' and resid 16 through 19 removed outlier: 6.720A pdb=" N GLN P 150 " --> pdb=" O VAL P 119 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL P 119 " --> pdb=" O GLN P 150 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL P 152 " --> pdb=" O ALA P 117 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 59 through 60 Processing sheet with id=AE1, first strand: chain 'P' and resid 122 through 123 Processing sheet with id=AE2, first strand: chain 'P' and resid 131 through 134 Processing sheet with id=AE3, first strand: chain 'Q' and resid 60 through 61 removed outlier: 3.815A pdb=" N THR Q 85 " --> pdb=" O TYR Q 60 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ALA Q 78 " --> pdb=" O CYS Q 99 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N LEU Q 101 " --> pdb=" O ALA Q 78 " (cutoff:3.500A) removed outlier: 9.828A pdb=" N LEU Q 80 " --> pdb=" O LEU Q 101 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N PHE Q 103 " --> pdb=" O LEU Q 80 " (cutoff:3.500A) removed outlier: 10.688A pdb=" N ALA Q 82 " --> pdb=" O PHE Q 103 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL Q 98 " --> pdb=" O ILE Q 119 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 60 through 61 removed outlier: 3.815A pdb=" N THR Q 85 " --> pdb=" O TYR Q 60 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE Q 77 " --> pdb=" O LEU Q 135 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'S' and resid 56 through 62 removed outlier: 5.082A pdb=" N VAL S 57 " --> pdb=" O ARG S 11 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG S 11 " --> pdb=" O VAL S 57 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA S 59 " --> pdb=" O ILE S 9 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA S 30 " --> pdb=" O LYS S 4 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 85 through 95 removed outlier: 7.280A pdb=" N ASN S 73 " --> pdb=" O GLU S 127 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU S 127 " --> pdb=" O ASN S 73 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N GLY S 75 " --> pdb=" O ILE S 125 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE S 125 " --> pdb=" O GLY S 75 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TRP S 77 " --> pdb=" O ILE S 123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'T' and resid 84 through 92 removed outlier: 7.076A pdb=" N ALA T 71 " --> pdb=" O VAL T 67 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N VAL T 67 " --> pdb=" O ALA T 71 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY T 73 " --> pdb=" O TRP T 65 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LYS T 77 " --> pdb=" O THR T 61 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N THR T 61 " --> pdb=" O LYS T 77 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'U' and resid 4 through 6 Processing sheet with id=AE9, first strand: chain 'U' and resid 8 through 9 removed outlier: 3.542A pdb=" N ARG U 99 " --> pdb=" O HIS U 87 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'V' and resid 20 through 21 Processing sheet with id=AF2, first strand: chain 'V' and resid 25 through 28 removed outlier: 5.250A pdb=" N ILE V 39 " --> pdb=" O THR V 64 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR V 64 " --> pdb=" O ILE V 39 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER V 41 " --> pdb=" O VAL V 62 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET V 78 " --> pdb=" O ILE V 106 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA V 102 " --> pdb=" O VAL V 82 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N GLY V 103 " --> pdb=" O VAL V 25 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASN V 27 " --> pdb=" O GLY V 103 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ILE V 105 " --> pdb=" O ASN V 27 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'V' and resid 88 through 89 removed outlier: 6.390A pdb=" N VAL V 95 " --> pdb=" O VAL W 22 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE W 24 " --> pdb=" O VAL V 95 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLY V 97 " --> pdb=" O ILE W 24 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG W 21 " --> pdb=" O PHE W 33 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET W 31 " --> pdb=" O HIS W 23 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'V' and resid 121 through 122 removed outlier: 6.515A pdb=" N VAL V 121 " --> pdb=" O PHE V 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'W' and resid 6 through 7 Processing sheet with id=AF6, first strand: chain 'X' and resid 61 through 64 removed outlier: 3.696A pdb=" N GLY X 63 " --> pdb=" O TRP X 83 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS X 118 " --> pdb=" O VAL X 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS X 107 " --> pdb=" O ARG X 123 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Y' and resid 32 through 34 Processing sheet with id=AF8, first strand: chain 'Y' and resid 67 through 69 removed outlier: 7.141A pdb=" N GLU Y 55 " --> pdb=" O THR Y 107 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Y' and resid 72 through 74 removed outlier: 3.807A pdb=" N ALA Y 72 " --> pdb=" O TYR Y 81 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Y' and resid 86 through 88 removed outlier: 3.731A pdb=" N THR Y 87 " --> pdb=" O VAL Y 95 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Z' and resid 69 through 75 removed outlier: 7.467A pdb=" N TYR Z 39 " --> pdb=" O ALA Z 27 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ALA Z 27 " --> pdb=" O TYR Z 39 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE Z 41 " --> pdb=" O LEU Z 25 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE Z 45 " --> pdb=" O LYS Z 21 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LYS Z 21 " --> pdb=" O ILE Z 45 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'a' and resid 74 through 76 removed outlier: 6.505A pdb=" N ILE a 75 " --> pdb=" O LEU a 115 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'a' and resid 103 through 105 removed outlier: 6.519A pdb=" N VAL a 127 " --> pdb=" O GLU a 148 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'c' and resid 69 through 72 removed outlier: 6.669A pdb=" N VAL c 45 " --> pdb=" O LEU c 71 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU c 44 " --> pdb=" O ILE c 95 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'd' and resid 49 through 51 removed outlier: 6.106A pdb=" N LYS d 50 " --> pdb=" O ALA d 91 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL d 71 " --> pdb=" O ILE d 14 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'e' and resid 73 through 77 Processing sheet with id=AG8, first strand: chain 'f' and resid 60 through 62 removed outlier: 5.742A pdb=" N VAL f 52 " --> pdb=" O GLN f 92 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLN f 92 " --> pdb=" O VAL f 52 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N PHE f 13 " --> pdb=" O GLU f 31 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLU f 31 " --> pdb=" O PHE f 13 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER f 15 " --> pdb=" O LEU f 29 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL f 75 " --> pdb=" O HIS f 70 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'g' and resid 21 through 25 Processing sheet with id=AH1, first strand: chain 'j' and resid 16 through 17 Processing sheet with id=AH2, first strand: chain 'k' and resid 43 through 44 Processing sheet with id=AH3, first strand: chain 'k' and resid 43 through 44 removed outlier: 4.678A pdb=" N TRP k 22 " --> pdb=" O ARG k 38 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL k 23 " --> pdb=" O ILE k 67 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'm' and resid 105 through 106 Processing sheet with id=AH5, first strand: chain 'o' and resid 3 through 4 Processing sheet with id=AH6, first strand: chain 'o' and resid 7 through 12 removed outlier: 3.688A pdb=" N LYS o 8 " --> pdb=" O CYS o 21 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE o 10 " --> pdb=" O THR o 19 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LYS o 64 " --> pdb=" O ARG o 85 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ARG o 85 " --> pdb=" O LYS o 64 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE o 66 " --> pdb=" O LEU o 83 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE o 70 " --> pdb=" O THR o 79 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'p' and resid 37 through 38 Processing sheet with id=AH8, first strand: chain 'p' and resid 54 through 56 1551 hydrogen bonds defined for protein. 4374 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1865 hydrogen bonds 3100 hydrogen bond angles 0 basepair planarities 774 basepair parallelities 1579 stacking parallelities Total time for adding SS restraints: 123.71 Time building geometry restraints manager: 42.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 19990 1.33 - 1.46: 41936 1.46 - 1.58: 47336 1.58 - 1.70: 5614 1.70 - 1.82: 296 Bond restraints: 115172 Sorted by residual: bond pdb=" C LYS A 175 " pdb=" N PRO A 176 " ideal model delta sigma weight residual 1.329 1.389 -0.060 1.20e-02 6.94e+03 2.50e+01 bond pdb=" CA ALA Q 175 " pdb=" C ALA Q 175 " ideal model delta sigma weight residual 1.520 1.543 -0.024 4.80e-03 4.34e+04 2.45e+01 bond pdb=" C GLY O 67 " pdb=" N PRO O 68 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.20e-02 6.94e+03 2.42e+01 bond pdb=" C PRO G 63 " pdb=" N PRO G 64 " ideal model delta sigma weight residual 1.329 1.386 -0.057 1.18e-02 7.18e+03 2.34e+01 bond pdb=" C VAL G 62 " pdb=" N PRO G 63 " ideal model delta sigma weight residual 1.335 1.390 -0.056 1.15e-02 7.56e+03 2.33e+01 ... (remaining 115167 not shown) Histogram of bond angle deviations from ideal: 98.17 - 106.31: 16787 106.31 - 114.44: 71284 114.44 - 122.58: 56644 122.58 - 130.71: 23313 130.71 - 138.85: 1084 Bond angle restraints: 169112 Sorted by residual: angle pdb=" N LEU J 108 " pdb=" CA LEU J 108 " pdb=" C LEU J 108 " ideal model delta sigma weight residual 111.07 122.08 -11.01 1.07e+00 8.73e-01 1.06e+02 angle pdb=" N LEU B 338 " pdb=" CA LEU B 338 " pdb=" C LEU B 338 " ideal model delta sigma weight residual 111.28 121.24 -9.96 1.09e+00 8.42e-01 8.35e+01 angle pdb=" N TRP E 20 " pdb=" CA TRP E 20 " pdb=" C TRP E 20 " ideal model delta sigma weight residual 111.36 121.26 -9.90 1.09e+00 8.42e-01 8.26e+01 angle pdb=" C4' U 11348 " pdb=" C3' U 11348 " pdb=" O3' U 11348 " ideal model delta sigma weight residual 109.40 122.95 -13.55 1.50e+00 4.44e-01 8.16e+01 angle pdb=" N ILE F 158 " pdb=" CA ILE F 158 " pdb=" C ILE F 158 " ideal model delta sigma weight residual 109.02 116.98 -7.96 9.30e-01 1.16e+00 7.33e+01 ... (remaining 169107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 65819 35.99 - 71.99: 6176 71.99 - 107.98: 746 107.98 - 143.97: 23 143.97 - 179.96: 56 Dihedral angle restraints: 72820 sinusoidal: 55728 harmonic: 17092 Sorted by residual: dihedral pdb=" O4' U 3 113 " pdb=" C1' U 3 113 " pdb=" N1 U 3 113 " pdb=" C2 U 3 113 " ideal model delta sinusoidal sigma weight residual 200.00 20.04 179.96 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 11416 " pdb=" C1' U 11416 " pdb=" N1 U 11416 " pdb=" C2 U 11416 " ideal model delta sinusoidal sigma weight residual 200.00 22.68 177.32 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 12292 " pdb=" C1' U 12292 " pdb=" N1 U 12292 " pdb=" C2 U 12292 " ideal model delta sinusoidal sigma weight residual 200.00 25.00 175.00 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 72817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 17731 0.141 - 0.282: 3329 0.282 - 0.423: 38 0.423 - 0.564: 26 0.564 - 0.705: 4 Chirality restraints: 21128 Sorted by residual: chirality pdb=" C3' U 11348 " pdb=" C4' U 11348 " pdb=" O3' U 11348 " pdb=" C2' U 11348 " both_signs ideal model delta sigma weight residual False -2.74 -2.04 -0.70 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" C3' G 12743 " pdb=" C4' G 12743 " pdb=" O3' G 12743 " pdb=" C2' G 12743 " both_signs ideal model delta sigma weight residual False -2.74 -2.14 -0.60 2.00e-01 2.50e+01 9.00e+00 chirality pdb=" C3' U 12678 " pdb=" C4' U 12678 " pdb=" O3' U 12678 " pdb=" C2' U 12678 " both_signs ideal model delta sigma weight residual False -2.74 -2.15 -0.59 2.00e-01 2.50e+01 8.81e+00 ... (remaining 21125 not shown) Planarity restraints: 11007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 23 " -0.064 5.00e-02 4.00e+02 9.80e-02 1.54e+01 pdb=" N PRO E 24 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO E 24 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO E 24 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 17 " 0.053 5.00e-02 4.00e+02 8.08e-02 1.04e+01 pdb=" N PRO E 18 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO E 18 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 18 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET G 156 " 0.053 5.00e-02 4.00e+02 8.00e-02 1.03e+01 pdb=" N PRO G 157 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO G 157 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO G 157 " 0.043 5.00e-02 4.00e+02 ... (remaining 11004 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.88: 21 1.88 - 2.63: 1505 2.63 - 3.39: 123733 3.39 - 4.14: 319133 4.14 - 4.90: 476436 Nonbonded interactions: 920828 Sorted by model distance: nonbonded pdb=" OD1 ASN B 328 " pdb=" O LEU B 338 " model vdw 1.123 3.040 nonbonded pdb=" CD2 HIS G 71 " pdb=" OE2 GLU G 219 " model vdw 1.129 3.260 nonbonded pdb=" OD1 ASN P 110 " pdb=" OE1 GLU P 155 " model vdw 1.243 3.040 nonbonded pdb=" OP1 G 3 48 " pdb=" OH TYR D 232 " model vdw 1.282 2.440 nonbonded pdb=" O2' G 1 308 " pdb=" O5' A 1 309 " model vdw 1.314 2.440 ... (remaining 920823 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 10.270 Check model and map are aligned: 1.140 Set scattering table: 0.740 Process input model: 318.300 Find NCS groups from input model: 2.540 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:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 336.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 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 0.061 115172 Z= 0.401 Angle : 1.043 15.749 169112 Z= 0.706 Chirality : 0.093 0.705 21128 Planarity : 0.004 0.098 11007 Dihedral : 22.626 179.965 61715 Min Nonbonded Distance : 1.123 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 1.26 % Allowed : 6.00 % Favored : 92.74 % Rotamer: Outliers : 3.45 % Allowed : 7.24 % Favored : 89.31 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.16 % 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: -3.33 (0.09), residues: 5785 helix: -2.20 (0.09), residues: 1810 sheet: -2.62 (0.16), residues: 714 loop : -2.12 (0.09), residues: 3261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 155 HIS 0.011 0.001 HIS f 70 PHE 0.018 0.001 PHE G 69 TYR 0.026 0.001 TYR F 224 ARG 0.005 0.001 ARG p 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1711 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1541 time to evaluate : 5.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.8297 (mt0) cc_final: 0.7998 (mt0) REVERT: A 20 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8403 (t) REVERT: A 28 LYS cc_start: 0.7510 (pttt) cc_final: 0.6853 (pttp) REVERT: A 44 MET cc_start: 0.7769 (ttp) cc_final: 0.7200 (ttt) REVERT: A 46 LYS cc_start: 0.7230 (tptm) cc_final: 0.6681 (ttpt) REVERT: A 60 LYS cc_start: 0.7854 (tttt) cc_final: 0.7455 (tttm) REVERT: A 135 ARG cc_start: 0.6927 (ttm170) cc_final: 0.6672 (mtp85) REVERT: A 174 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7378 (mm-30) REVERT: A 196 VAL cc_start: 0.8587 (t) cc_final: 0.8274 (p) REVERT: A 243 ARG cc_start: 0.7147 (mtm180) cc_final: 0.6892 (mtm180) REVERT: B 21 ARG cc_start: 0.8474 (mtt180) cc_final: 0.7743 (mtt180) REVERT: B 53 MET cc_start: 0.8950 (ttt) cc_final: 0.8374 (ttm) REVERT: B 59 ASP cc_start: 0.8172 (t70) cc_final: 0.7284 (t0) REVERT: B 64 ASN cc_start: 0.8201 (t0) cc_final: 0.7832 (t0) REVERT: B 80 GLU cc_start: 0.7618 (tt0) cc_final: 0.7301 (tt0) REVERT: B 89 ILE cc_start: 0.8192 (tt) cc_final: 0.7439 (pt) REVERT: B 92 TYR cc_start: 0.8627 (m-80) cc_final: 0.8250 (m-80) REVERT: B 112 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6029 (pm20) REVERT: B 113 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6757 (pm20) REVERT: B 145 LYS cc_start: 0.6902 (tttt) cc_final: 0.6556 (mttm) REVERT: B 149 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6545 (mm-30) REVERT: B 151 GLN cc_start: 0.7622 (mt0) cc_final: 0.7270 (mt0) REVERT: B 164 GLN cc_start: 0.7069 (mm110) cc_final: 0.6730 (mm-40) REVERT: B 216 ILE cc_start: 0.7333 (tp) cc_final: 0.7062 (pt) REVERT: B 219 LYS cc_start: 0.6945 (mmmt) cc_final: 0.6356 (mptt) REVERT: B 264 ARG cc_start: 0.8248 (ptt180) cc_final: 0.8033 (ptt90) REVERT: B 314 GLU cc_start: 0.6358 (tm-30) cc_final: 0.5766 (tt0) REVERT: B 324 LYS cc_start: 0.8372 (mptt) cc_final: 0.7842 (mmtt) REVERT: B 340 LYS cc_start: 0.6975 (mtmm) cc_final: 0.6452 (mptt) REVERT: B 341 ASP cc_start: 0.8107 (m-30) cc_final: 0.7181 (m-30) REVERT: B 345 MET cc_start: 0.8616 (mtm) cc_final: 0.8380 (mtp) REVERT: B 366 ILE cc_start: 0.7270 (mt) cc_final: 0.6895 (tt) REVERT: B 375 GLU cc_start: 0.7743 (tt0) cc_final: 0.7326 (tp30) REVERT: B 395 LYS cc_start: 0.7439 (pttt) cc_final: 0.6292 (mmmt) REVERT: B 400 LYS cc_start: 0.7562 (tttt) cc_final: 0.7307 (tttm) REVERT: C 23 LYS cc_start: 0.7795 (ptpt) cc_final: 0.7253 (ptpp) REVERT: C 110 ARG cc_start: 0.8517 (mmt-90) cc_final: 0.8028 (mmt180) REVERT: C 140 VAL cc_start: 0.7430 (t) cc_final: 0.7228 (m) REVERT: C 153 ASP cc_start: 0.7450 (t70) cc_final: 0.6893 (t70) REVERT: C 158 ILE cc_start: 0.7017 (mt) cc_final: 0.6811 (mm) REVERT: C 190 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.7245 (mtmm) REVERT: C 202 LYS cc_start: 0.7713 (mttt) cc_final: 0.7413 (mmtm) REVERT: C 225 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7458 (mt-10) REVERT: C 226 THR cc_start: 0.7576 (p) cc_final: 0.7127 (p) REVERT: C 227 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7330 (tp) REVERT: C 265 LYS cc_start: 0.7127 (mmmt) cc_final: 0.6674 (mmtm) REVERT: C 272 SER cc_start: 0.7872 (p) cc_final: 0.7596 (p) REVERT: C 274 MET cc_start: 0.7174 (mtt) cc_final: 0.6807 (mtm) REVERT: C 285 SER cc_start: 0.7240 (m) cc_final: 0.6867 (p) REVERT: C 298 VAL cc_start: 0.8699 (t) cc_final: 0.7912 (p) REVERT: C 303 LYS cc_start: 0.7783 (mttt) cc_final: 0.7287 (pttp) REVERT: C 329 ARG cc_start: 0.7583 (mtt180) cc_final: 0.7326 (mtt-85) REVERT: C 336 ARG cc_start: 0.7488 (ttm170) cc_final: 0.6849 (ttp80) REVERT: C 340 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7464 (tp30) REVERT: C 345 VAL cc_start: 0.7496 (t) cc_final: 0.7277 (p) REVERT: C 360 MET cc_start: 0.7993 (mmt) cc_final: 0.7574 (mmt) REVERT: D 2 SER cc_start: 0.5401 (m) cc_final: 0.5103 (m) REVERT: D 49 ARG cc_start: 0.7617 (ptm-80) cc_final: 0.6985 (ptm-80) REVERT: D 53 ARG cc_start: 0.7191 (mmt90) cc_final: 0.6690 (mmt90) REVERT: D 67 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6978 (mt-10) REVERT: D 88 LYS cc_start: 0.7450 (mttt) cc_final: 0.6679 (ptmm) REVERT: D 111 GLN cc_start: 0.6425 (mt0) cc_final: 0.6145 (mt0) REVERT: D 157 MET cc_start: 0.7884 (ttt) cc_final: 0.7568 (tpp) REVERT: D 223 GLU cc_start: 0.6989 (tt0) cc_final: 0.6653 (pm20) REVERT: D 289 GLU cc_start: 0.5465 (tp30) cc_final: 0.5138 (tp30) REVERT: D 297 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7282 (tm-30) REVERT: E 3 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.6137 (tp30) REVERT: E 16 LYS cc_start: 0.6117 (mmtt) cc_final: 0.5910 (mmmt) REVERT: E 80 GLN cc_start: 0.6550 (mt0) cc_final: 0.6232 (mp10) REVERT: E 86 LYS cc_start: 0.6488 (ttpt) cc_final: 0.6193 (mtpt) REVERT: E 131 VAL cc_start: 0.6709 (t) cc_final: 0.6498 (m) REVERT: E 142 LYS cc_start: 0.6471 (pmtt) cc_final: 0.5779 (ttpp) REVERT: F 17 GLU cc_start: 0.6978 (tp30) cc_final: 0.6486 (tp30) REVERT: F 20 LYS cc_start: 0.6305 (mmmt) cc_final: 0.6015 (mttt) REVERT: F 77 GLU cc_start: 0.7353 (mm-30) cc_final: 0.7010 (mm-30) REVERT: F 79 LYS cc_start: 0.7770 (mmtm) cc_final: 0.7376 (mtmt) REVERT: F 101 HIS cc_start: 0.7558 (t70) cc_final: 0.7334 (m-70) REVERT: F 122 GLU cc_start: 0.7078 (tt0) cc_final: 0.6837 (tt0) REVERT: F 130 GLN cc_start: 0.7964 (mm110) cc_final: 0.6994 (mm-40) REVERT: F 164 GLN cc_start: 0.7934 (tp-100) cc_final: 0.7522 (tp40) REVERT: F 196 ASN cc_start: 0.8208 (t0) cc_final: 0.7725 (t0) REVERT: F 238 MET cc_start: 0.7808 (mmt) cc_final: 0.7515 (mtt) REVERT: G 43 PHE cc_start: 0.7380 (m-80) cc_final: 0.6492 (m-80) REVERT: G 54 ARG cc_start: 0.7611 (tpp-160) cc_final: 0.6950 (mmm160) REVERT: G 58 LYS cc_start: 0.5625 (mttt) cc_final: 0.5372 (mptt) REVERT: G 59 ARG cc_start: 0.7683 (mmt-90) cc_final: 0.7468 (mmt-90) REVERT: G 185 CYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7265 (t) REVERT: G 203 LYS cc_start: 0.7980 (mmmt) cc_final: 0.7401 (tttm) REVERT: G 220 MET cc_start: 0.5986 (mmt) cc_final: 0.4285 (pmm) REVERT: G 230 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6849 (pm20) REVERT: H 8 GLN cc_start: 0.6569 (pt0) cc_final: 0.5756 (pt0) REVERT: H 10 HIS cc_start: 0.7412 (p90) cc_final: 0.7164 (p-80) REVERT: H 21 VAL cc_start: 0.7226 (t) cc_final: 0.6963 (p) REVERT: H 22 LYS cc_start: 0.6798 (tttt) cc_final: 0.6188 (mmtp) REVERT: H 37 LYS cc_start: 0.4919 (tptt) cc_final: 0.4386 (mmtt) REVERT: H 75 ARG cc_start: 0.7838 (mtt180) cc_final: 0.7586 (mtt180) REVERT: H 84 LYS cc_start: 0.7695 (tttm) cc_final: 0.6880 (pttt) REVERT: H 97 LYS cc_start: 0.6748 (tttt) cc_final: 0.6295 (mtpp) REVERT: H 98 MET cc_start: 0.7260 (ptm) cc_final: 0.6570 (ptm) REVERT: H 152 ASN cc_start: 0.6356 (OUTLIER) cc_final: 0.5840 (t0) REVERT: H 196 GLU cc_start: 0.5571 (tt0) cc_final: 0.5336 (pm20) REVERT: I 33 ARG cc_start: 0.7568 (mtt180) cc_final: 0.7153 (mmm160) REVERT: I 51 ARG cc_start: 0.7654 (mtm-85) cc_final: 0.7159 (mtt180) REVERT: I 76 MET cc_start: 0.8067 (mmm) cc_final: 0.7691 (mmm) REVERT: I 77 MET cc_start: 0.6656 (tpp) cc_final: 0.6449 (tpt) REVERT: I 78 LYS cc_start: 0.8088 (tttt) cc_final: 0.7712 (ttpt) REVERT: I 99 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7277 (mt) REVERT: I 102 MET cc_start: 0.7423 (mmm) cc_final: 0.7137 (mmm) REVERT: I 180 GLN cc_start: 0.7947 (mt0) cc_final: 0.7688 (mt0) REVERT: I 196 HIS cc_start: 0.7367 (OUTLIER) cc_final: 0.6617 (p-80) REVERT: I 201 TYR cc_start: 0.6088 (m-80) cc_final: 0.5856 (m-80) REVERT: I 202 ARG cc_start: 0.7038 (ttm-80) cc_final: 0.6795 (mtp180) REVERT: J 30 SER cc_start: 0.7969 (t) cc_final: 0.7726 (m) REVERT: J 39 GLN cc_start: 0.6290 (mt0) cc_final: 0.5987 (mt0) REVERT: J 42 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6837 (tpp) REVERT: J 45 ARG cc_start: 0.6496 (mtt180) cc_final: 0.5439 (mmt90) REVERT: J 50 ILE cc_start: 0.5685 (mt) cc_final: 0.5421 (mt) REVERT: J 55 ILE cc_start: 0.6270 (mt) cc_final: 0.5963 (pt) REVERT: J 56 ARG cc_start: 0.6242 (mmt-90) cc_final: 0.5934 (ptm160) REVERT: J 100 PHE cc_start: 0.8174 (p90) cc_final: 0.7886 (p90) REVERT: J 102 ILE cc_start: 0.5798 (mt) cc_final: 0.5456 (tt) REVERT: J 110 LEU cc_start: 0.5482 (OUTLIER) cc_final: 0.4468 (tt) REVERT: J 116 ILE cc_start: 0.6557 (pt) cc_final: 0.6345 (mp) REVERT: J 132 ASN cc_start: 0.7125 (t0) cc_final: 0.6856 (t0) REVERT: J 133 ARG cc_start: 0.7229 (tpt90) cc_final: 0.6702 (tpt90) REVERT: J 136 ARG cc_start: 0.6872 (mmt-90) cc_final: 0.6346 (mmt90) REVERT: L 55 ARG cc_start: 0.8243 (mtt90) cc_final: 0.7927 (mtt-85) REVERT: L 57 ILE cc_start: 0.8421 (mt) cc_final: 0.8152 (tp) REVERT: L 68 LYS cc_start: 0.7774 (mmtp) cc_final: 0.7094 (mtmt) REVERT: L 80 LEU cc_start: 0.7137 (mt) cc_final: 0.6856 (mp) REVERT: L 91 ARG cc_start: 0.6993 (ttp-110) cc_final: 0.6445 (mtt180) REVERT: L 93 GLN cc_start: 0.6609 (mm110) cc_final: 0.6224 (mt0) REVERT: L 177 GLU cc_start: 0.5827 (mt-10) cc_final: 0.5496 (mm-30) REVERT: M 15 ILE cc_start: 0.7650 (tt) cc_final: 0.7437 (pt) REVERT: M 23 LYS cc_start: 0.7600 (mttp) cc_final: 0.7344 (mttt) REVERT: M 29 ASP cc_start: 0.6961 (t0) cc_final: 0.6532 (t0) REVERT: M 39 ASP cc_start: 0.7947 (t70) cc_final: 0.7353 (t0) REVERT: M 63 LYS cc_start: 0.7956 (ttpt) cc_final: 0.6779 (mmtp) REVERT: M 71 GLU cc_start: 0.5667 (OUTLIER) cc_final: 0.5355 (pp20) REVERT: M 91 LYS cc_start: 0.7153 (mttt) cc_final: 0.6901 (mttt) REVERT: M 116 LYS cc_start: 0.6343 (mttt) cc_final: 0.5855 (mtpt) REVERT: N 25 LEU cc_start: 0.7540 (mt) cc_final: 0.7065 (tp) REVERT: N 51 MET cc_start: 0.8871 (mmm) cc_final: 0.8481 (mmt) REVERT: N 108 LYS cc_start: 0.8263 (ttmt) cc_final: 0.7470 (tttt) REVERT: N 113 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8073 (mp) REVERT: N 117 ASN cc_start: 0.8502 (m-40) cc_final: 0.8054 (t0) REVERT: N 142 ILE cc_start: 0.7925 (mm) cc_final: 0.7713 (mt) REVERT: N 143 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8353 (tp40) REVERT: N 179 HIS cc_start: 0.7493 (OUTLIER) cc_final: 0.6767 (p-80) REVERT: O 30 LYS cc_start: 0.7656 (mttt) cc_final: 0.7376 (mtpp) REVERT: O 85 MET cc_start: 0.8319 (mtt) cc_final: 0.8004 (mtt) REVERT: O 101 GLN cc_start: 0.6455 (OUTLIER) cc_final: 0.6205 (mt0) REVERT: O 103 TYR cc_start: 0.7805 (m-80) cc_final: 0.6982 (m-80) REVERT: O 135 LYS cc_start: 0.7881 (mmtt) cc_final: 0.7667 (mmtm) REVERT: O 164 LYS cc_start: 0.7707 (mmmt) cc_final: 0.7090 (mtmm) REVERT: O 176 ARG cc_start: 0.6099 (ttm-80) cc_final: 0.5561 (tmm-80) REVERT: O 180 ILE cc_start: 0.6753 (mt) cc_final: 0.6465 (mm) REVERT: O 181 GLU cc_start: 0.7447 (tt0) cc_final: 0.6974 (pp20) REVERT: O 182 LYS cc_start: 0.6863 (mtpp) cc_final: 0.6641 (mmtp) REVERT: P 32 GLU cc_start: 0.8098 (tp30) cc_final: 0.7537 (mm-30) REVERT: P 40 MET cc_start: 0.5956 (mtm) cc_final: 0.5469 (mtp) REVERT: P 65 LYS cc_start: 0.8410 (pttt) cc_final: 0.7859 (pttt) REVERT: P 123 ARG cc_start: 0.8141 (mtt180) cc_final: 0.7758 (mtt-85) REVERT: P 131 ARG cc_start: 0.8242 (mtt-85) cc_final: 0.6689 (mtm180) REVERT: P 142 TYR cc_start: 0.8904 (t80) cc_final: 0.8607 (t80) REVERT: Q 24 MET cc_start: 0.8475 (mmm) cc_final: 0.8088 (mmm) REVERT: Q 25 LYS cc_start: 0.7589 (tttt) cc_final: 0.7204 (ttmm) REVERT: Q 26 MET cc_start: 0.6498 (mtp) cc_final: 0.6296 (ttm) REVERT: Q 45 LYS cc_start: 0.6557 (mttt) cc_final: 0.6320 (mtpt) REVERT: Q 80 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8108 (tt) REVERT: Q 117 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6907 (mt-10) REVERT: Q 126 GLN cc_start: 0.7785 (mt0) cc_final: 0.7250 (mm-40) REVERT: Q 147 ASN cc_start: 0.7892 (t0) cc_final: 0.7560 (m-40) REVERT: Q 174 MET cc_start: 0.8491 (mmm) cc_final: 0.8255 (mmt) REVERT: Q 180 LYS cc_start: 0.8184 (ttpt) cc_final: 0.7930 (ttpp) REVERT: R 5 LYS cc_start: 0.8115 (tttm) cc_final: 0.7750 (ttmm) REVERT: R 28 GLU cc_start: 0.6963 (mp0) cc_final: 0.6589 (mp0) REVERT: R 32 ILE cc_start: 0.6813 (mt) cc_final: 0.6346 (mm) REVERT: R 111 LYS cc_start: 0.7928 (mttt) cc_final: 0.7601 (tptt) REVERT: R 114 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7212 (mt-10) REVERT: R 126 LYS cc_start: 0.7251 (mttt) cc_final: 0.6848 (mmtt) REVERT: R 136 ARG cc_start: 0.5942 (ttm170) cc_final: 0.5564 (ttm110) REVERT: S 81 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7176 (tmm-80) REVERT: S 92 GLU cc_start: 0.7738 (pt0) cc_final: 0.7455 (pt0) REVERT: S 147 LYS cc_start: 0.7478 (mttt) cc_final: 0.6695 (mtmm) REVERT: S 164 LYS cc_start: 0.7385 (tttt) cc_final: 0.7043 (pttm) REVERT: T 13 TYR cc_start: 0.7839 (m-80) cc_final: 0.7514 (m-80) REVERT: T 21 LYS cc_start: 0.7326 (mttt) cc_final: 0.6919 (mppt) REVERT: T 29 ILE cc_start: 0.8052 (mt) cc_final: 0.7739 (tt) REVERT: T 36 ILE cc_start: 0.8563 (mt) cc_final: 0.8296 (mt) REVERT: T 52 MET cc_start: 0.8436 (mtt) cc_final: 0.8162 (ttp) REVERT: T 77 LYS cc_start: 0.8433 (mttp) cc_final: 0.7922 (mttt) REVERT: T 110 GLN cc_start: 0.7751 (mt0) cc_final: 0.7345 (mm110) REVERT: T 156 ARG cc_start: 0.6419 (mtt90) cc_final: 0.5732 (mmt90) REVERT: U 23 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6649 (mt-10) REVERT: U 29 GLN cc_start: 0.7585 (mt0) cc_final: 0.7322 (mm110) REVERT: U 34 VAL cc_start: 0.7716 (t) cc_final: 0.7208 (m) REVERT: U 99 ARG cc_start: 0.7710 (mtm-85) cc_final: 0.6659 (ptp-110) REVERT: V 36 ASN cc_start: 0.8158 (m-40) cc_final: 0.7661 (m-40) REVERT: V 43 ARG cc_start: 0.7189 (ttm170) cc_final: 0.6672 (mmm-85) REVERT: V 45 HIS cc_start: 0.7662 (t-90) cc_final: 0.7350 (t70) REVERT: V 83 ARG cc_start: 0.8514 (mtm180) cc_final: 0.8270 (mtm-85) REVERT: V 91 LYS cc_start: 0.6906 (mmmt) cc_final: 0.6642 (mmmt) REVERT: V 123 LYS cc_start: 0.6973 (tttp) cc_final: 0.6017 (ttpt) REVERT: W 41 MET cc_start: 0.6442 (mtt) cc_final: 0.6035 (mmt) REVERT: X 46 LYS cc_start: 0.7241 (tttm) cc_final: 0.6371 (mmtm) REVERT: X 49 LYS cc_start: 0.7826 (mttt) cc_final: 0.7160 (mtpp) REVERT: X 78 ASN cc_start: 0.7799 (t0) cc_final: 0.7404 (t0) REVERT: X 87 LYS cc_start: 0.8466 (mttt) cc_final: 0.7599 (mmmt) REVERT: X 102 LYS cc_start: 0.7891 (mtmm) cc_final: 0.7663 (mmmt) REVERT: X 115 LYS cc_start: 0.8080 (mttt) cc_final: 0.7733 (ptpt) REVERT: Y 23 LYS cc_start: 0.7790 (mttt) cc_final: 0.7364 (pttp) REVERT: Y 55 GLU cc_start: 0.7129 (pt0) cc_final: 0.6916 (pt0) REVERT: Y 57 MET cc_start: 0.6697 (ttp) cc_final: 0.6483 (ptm) REVERT: Y 80 ILE cc_start: 0.7599 (mt) cc_final: 0.7187 (pt) REVERT: Y 95 VAL cc_start: 0.7647 (t) cc_final: 0.6899 (m) REVERT: Y 97 PHE cc_start: 0.6429 (OUTLIER) cc_final: 0.5207 (m-80) REVERT: Y 99 VAL cc_start: 0.8045 (t) cc_final: 0.7432 (m) REVERT: Z 43 MET cc_start: 0.7030 (mmm) cc_final: 0.6561 (mmm) REVERT: Z 47 LYS cc_start: 0.6497 (mttt) cc_final: 0.5810 (tmtt) REVERT: Z 124 LYS cc_start: 0.5465 (mttt) cc_final: 0.5093 (ttpt) REVERT: Z 132 TRP cc_start: 0.7124 (t60) cc_final: 0.6631 (t-100) REVERT: a 22 VAL cc_start: 0.7700 (m) cc_final: 0.7444 (m) REVERT: a 55 LYS cc_start: 0.8565 (tttt) cc_final: 0.8157 (tttm) REVERT: a 97 LYS cc_start: 0.8317 (tttp) cc_final: 0.8086 (ttmm) REVERT: a 122 LYS cc_start: 0.7816 (mttt) cc_final: 0.7375 (tptp) REVERT: a 137 GLU cc_start: 0.7706 (tt0) cc_final: 0.6405 (pt0) REVERT: b 23 LYS cc_start: 0.7534 (tttt) cc_final: 0.6883 (ptpp) REVERT: b 28 LYS cc_start: 0.6318 (ptmt) cc_final: 0.5833 (pttm) REVERT: b 38 LYS cc_start: 0.8023 (ttpt) cc_final: 0.7809 (ttpp) REVERT: c 19 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6909 (tp) REVERT: c 57 SER cc_start: 0.6233 (t) cc_final: 0.5766 (m) REVERT: c 101 SER cc_start: 0.4036 (p) cc_final: 0.2907 (m) REVERT: d 42 LYS cc_start: 0.7070 (tttt) cc_final: 0.6832 (ttmt) REVERT: d 43 MET cc_start: 0.7719 (mmm) cc_final: 0.7492 (mmt) REVERT: d 92 SER cc_start: 0.8345 (p) cc_final: 0.8030 (m) REVERT: e 22 GLN cc_start: 0.8294 (mm-40) cc_final: 0.7688 (mt0) REVERT: e 28 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7302 (ptt180) REVERT: e 67 MET cc_start: 0.8089 (ttm) cc_final: 0.7830 (ttp) REVERT: e 85 MET cc_start: 0.6894 (mmt) cc_final: 0.6690 (ptp) REVERT: e 89 LYS cc_start: 0.7351 (mttt) cc_final: 0.7097 (mttp) REVERT: e 98 SER cc_start: 0.8932 (m) cc_final: 0.8511 (t) REVERT: e 106 GLN cc_start: 0.7179 (tp-100) cc_final: 0.6630 (tp40) REVERT: e 119 GLU cc_start: 0.7627 (tt0) cc_final: 0.6472 (tp30) REVERT: e 126 LYS cc_start: 0.6029 (mtpt) cc_final: 0.5136 (mttt) REVERT: f 48 LYS cc_start: 0.7516 (mtpp) cc_final: 0.6946 (mtmt) REVERT: f 59 GLU cc_start: 0.7225 (tt0) cc_final: 0.6364 (mp0) REVERT: f 81 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6682 (mt-10) REVERT: f 88 MET cc_start: 0.8040 (mmm) cc_final: 0.7769 (mmt) REVERT: f 91 LYS cc_start: 0.6978 (mptt) cc_final: 0.6761 (mmtp) REVERT: g 68 LYS cc_start: 0.6223 (tptt) cc_final: 0.5916 (tptm) REVERT: h 14 ARG cc_start: 0.7141 (ttt-90) cc_final: 0.6711 (ttt90) REVERT: h 43 LYS cc_start: 0.6508 (ttmt) cc_final: 0.6306 (tptt) REVERT: h 67 LYS cc_start: 0.8046 (ttpp) cc_final: 0.7727 (ttmm) REVERT: h 72 LYS cc_start: 0.7114 (ttpp) cc_final: 0.6884 (tttp) REVERT: h 73 TYR cc_start: 0.7294 (m-80) cc_final: 0.6877 (m-80) REVERT: h 85 LYS cc_start: 0.8378 (mtmm) cc_final: 0.7732 (tptp) REVERT: h 109 ARG cc_start: 0.6808 (ttp-170) cc_final: 0.6597 (ttp-170) REVERT: h 115 PHE cc_start: 0.8409 (p90) cc_final: 0.8088 (p90) REVERT: i 71 MET cc_start: 0.7161 (mtp) cc_final: 0.6942 (mmm) REVERT: j 48 ASP cc_start: 0.8122 (m-30) cc_final: 0.7894 (m-30) REVERT: j 64 MET cc_start: 0.8113 (mtm) cc_final: 0.7293 (mtt) REVERT: k 3 LYS cc_start: 0.6626 (mttt) cc_final: 0.6304 (mmtp) REVERT: k 24 LYS cc_start: 0.6844 (mttt) cc_final: 0.6611 (mttm) REVERT: k 27 LYS cc_start: 0.6269 (mmmt) cc_final: 0.5894 (mmtm) REVERT: k 42 TYR cc_start: 0.7867 (m-80) cc_final: 0.7524 (m-80) REVERT: k 49 LYS cc_start: 0.7629 (mttm) cc_final: 0.7383 (mtpt) REVERT: m 95 LYS cc_start: 0.6791 (mttm) cc_final: 0.6518 (mtmm) REVERT: o 22 LYS cc_start: 0.7604 (mtpt) cc_final: 0.7331 (mtpp) REVERT: o 36 LEU cc_start: 0.7854 (tp) cc_final: 0.7580 (tp) REVERT: p 13 LYS cc_start: 0.7825 (pttt) cc_final: 0.7484 (pttt) REVERT: p 32 SER cc_start: 0.7841 (m) cc_final: 0.7168 (p) REVERT: p 37 TYR cc_start: 0.8735 (m-80) cc_final: 0.8506 (m-80) REVERT: p 48 LYS cc_start: 0.7551 (mttt) cc_final: 0.7321 (mttt) outliers start: 170 outliers final: 57 residues processed: 1660 average time/residue: 1.0624 time to fit residues: 2870.9629 Evaluate side-chains 1193 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1113 time to evaluate : 5.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 190 LYS Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 185 CYS Chi-restraints excluded: chain H residue 126 HIS Chi-restraints excluded: chain H residue 152 ASN Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 130 ASN Chi-restraints excluded: chain I residue 196 HIS Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain L residue 6 ASN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 102 MET Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 143 GLN Chi-restraints excluded: chain N residue 179 HIS Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain O residue 101 GLN Chi-restraints excluded: chain O residue 141 THR Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 158 ASN Chi-restraints excluded: chain S residue 81 ARG Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain S residue 95 ASP Chi-restraints excluded: chain S residue 174 CYS Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain V residue 28 CYS Chi-restraints excluded: chain V residue 135 VAL Chi-restraints excluded: chain Y residue 97 PHE Chi-restraints excluded: chain Z residue 104 LEU Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 43 THR Chi-restraints excluded: chain a residue 76 ASN Chi-restraints excluded: chain b residue 8 SER Chi-restraints excluded: chain b residue 11 ASN Chi-restraints excluded: chain c residue 19 LEU Chi-restraints excluded: chain d residue 16 LEU Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 80 ASP Chi-restraints excluded: chain e residue 28 ARG Chi-restraints excluded: chain f residue 26 ASN Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 75 VAL Chi-restraints excluded: chain f residue 81 GLU Chi-restraints excluded: chain h residue 78 LEU Chi-restraints excluded: chain j residue 22 CYS Chi-restraints excluded: chain j residue 40 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 721 optimal weight: 3.9990 chunk 647 optimal weight: 1.9990 chunk 359 optimal weight: 0.9980 chunk 221 optimal weight: 7.9990 chunk 436 optimal weight: 1.9990 chunk 345 optimal weight: 3.9990 chunk 669 optimal weight: 5.9990 chunk 259 optimal weight: 9.9990 chunk 407 optimal weight: 4.9990 chunk 498 optimal weight: 0.0370 chunk 775 optimal weight: 0.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 147 GLN A 207 HIS A 216 HIS B 68 HIS B 195 HIS B 211 ASN B 287 GLN B 292 HIS C 82 ASN C 186 HIS C 220 ASN C 332 GLN ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 ASN D 62 GLN D 228 GLN D 276 HIS D 282 GLN E 70 GLN E 99 GLN E 119 GLN F 37 ASN F 90 ASN F 152 ASN F 163 ASN F 205 HIS G 67 ASN H 30 HIS H 109 HIS H 129 HIS ** H 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 HIS I 73 ASN I 90 ASN I 95 HIS I 132 ASN I 180 GLN I 185 GLN I 187 ASN J 6 ASN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 GLN N 15 GLN N 32 GLN N 87 HIS N 139 HIS O 12 HIS O 24 GLN O 44 GLN O 75 HIS O 199 GLN P 150 GLN Q 28 HIS S 5 GLN S 62 HIS S 85 ASN ** T 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 95 HIS V 36 ASN W 16 HIS Y 5 ASN b 11 ASN ** b 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 22 HIS d 56 ASN f 62 ASN f 72 ASN g 19 ASN g 29 ASN g 34 HIS g 41 ASN g 44 HIS g 70 GLN h 87 GLN j 16 HIS j 24 ASN j 28 HIS o 18 HIS o 33 HIS o 73 GLN Total number of N/Q/H flips: 76 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 115172 Z= 0.188 Angle : 0.645 13.934 169112 Z= 0.340 Chirality : 0.040 0.300 21128 Planarity : 0.005 0.062 11007 Dihedral : 22.786 179.506 49970 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.10 % Favored : 95.40 % Rotamer: Outliers : 4.14 % Allowed : 13.11 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.16 % 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: -2.11 (0.10), residues: 5785 helix: -0.53 (0.11), residues: 1877 sheet: -2.02 (0.16), residues: 833 loop : -1.77 (0.10), residues: 3075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP T 159 HIS 0.010 0.001 HIS H 126 PHE 0.017 0.002 PHE D 19 TYR 0.027 0.001 TYR F 186 ARG 0.007 0.001 ARG I 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1399 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1195 time to evaluate : 5.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.8334 (mt0) cc_final: 0.8001 (mt0) REVERT: A 30 ARG cc_start: 0.7146 (ttm110) cc_final: 0.6809 (ttp-170) REVERT: A 44 MET cc_start: 0.7712 (ttp) cc_final: 0.7116 (ttt) REVERT: A 46 LYS cc_start: 0.7060 (tptm) cc_final: 0.6510 (ttpt) REVERT: A 135 ARG cc_start: 0.7038 (ttm170) cc_final: 0.6540 (mtp85) REVERT: A 172 ARG cc_start: 0.7252 (ptt180) cc_final: 0.7030 (ptt180) REVERT: A 174 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7134 (mm-30) REVERT: A 196 VAL cc_start: 0.8568 (t) cc_final: 0.8315 (p) REVERT: A 243 ARG cc_start: 0.7118 (mtm180) cc_final: 0.6746 (mtm180) REVERT: B 21 ARG cc_start: 0.8447 (mtt180) cc_final: 0.8127 (mtm-85) REVERT: B 53 MET cc_start: 0.8807 (ttt) cc_final: 0.8508 (ttm) REVERT: B 64 ASN cc_start: 0.8346 (t0) cc_final: 0.8051 (t0) REVERT: B 148 GLU cc_start: 0.7602 (tt0) cc_final: 0.7008 (mp0) REVERT: B 151 GLN cc_start: 0.7276 (mt0) cc_final: 0.7032 (mt0) REVERT: B 152 LYS cc_start: 0.7283 (tttm) cc_final: 0.7024 (mttp) REVERT: B 205 ASP cc_start: 0.6728 (t70) cc_final: 0.6372 (t70) REVERT: B 219 LYS cc_start: 0.6879 (mmmt) cc_final: 0.6296 (mptt) REVERT: B 319 SER cc_start: 0.6769 (m) cc_final: 0.6410 (t) REVERT: B 324 LYS cc_start: 0.8453 (mptt) cc_final: 0.8100 (mmmt) REVERT: B 340 LYS cc_start: 0.6755 (mtmm) cc_final: 0.6337 (mptt) REVERT: B 341 ASP cc_start: 0.8064 (m-30) cc_final: 0.7496 (m-30) REVERT: B 345 MET cc_start: 0.8550 (mtm) cc_final: 0.8253 (mtp) REVERT: B 370 ARG cc_start: 0.7383 (mtp180) cc_final: 0.7005 (mtp85) REVERT: B 375 GLU cc_start: 0.7897 (tt0) cc_final: 0.7617 (tp30) REVERT: B 377 ASN cc_start: 0.7422 (OUTLIER) cc_final: 0.6825 (p0) REVERT: B 395 LYS cc_start: 0.7704 (pttt) cc_final: 0.6778 (mmmt) REVERT: C 23 LYS cc_start: 0.7710 (ptpt) cc_final: 0.7275 (ptpp) REVERT: C 36 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6895 (tt0) REVERT: C 82 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7951 (t0) REVERT: C 182 ASP cc_start: 0.6997 (m-30) cc_final: 0.6646 (m-30) REVERT: C 202 LYS cc_start: 0.7896 (mttt) cc_final: 0.7335 (mmmt) REVERT: C 226 THR cc_start: 0.8483 (p) cc_final: 0.8116 (p) REVERT: C 268 SER cc_start: 0.7996 (m) cc_final: 0.7724 (t) REVERT: C 303 LYS cc_start: 0.7554 (mttt) cc_final: 0.7259 (pttm) REVERT: C 329 ARG cc_start: 0.7710 (mtt180) cc_final: 0.7443 (mtt-85) REVERT: C 336 ARG cc_start: 0.7435 (ttm170) cc_final: 0.7062 (ttp80) REVERT: C 340 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7309 (tp30) REVERT: C 345 VAL cc_start: 0.7159 (t) cc_final: 0.6911 (p) REVERT: C 363 GLN cc_start: 0.6945 (tt0) cc_final: 0.6729 (tt0) REVERT: D 53 ARG cc_start: 0.7168 (mmt90) cc_final: 0.6966 (mmt90) REVERT: D 67 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6800 (mt-10) REVERT: D 88 LYS cc_start: 0.7617 (mttt) cc_final: 0.6938 (ptmm) REVERT: D 157 MET cc_start: 0.7763 (ttt) cc_final: 0.7361 (tmm) REVERT: D 158 LYS cc_start: 0.6755 (mttt) cc_final: 0.6296 (tptt) REVERT: D 222 GLU cc_start: 0.6206 (tp30) cc_final: 0.5934 (tp30) REVERT: D 223 GLU cc_start: 0.6789 (tt0) cc_final: 0.6432 (pm20) REVERT: D 233 VAL cc_start: 0.7863 (t) cc_final: 0.7615 (m) REVERT: D 254 ARG cc_start: 0.6636 (mtp85) cc_final: 0.6212 (mtt-85) REVERT: D 266 LYS cc_start: 0.6679 (mtpp) cc_final: 0.6311 (pttp) REVERT: D 279 LYS cc_start: 0.6949 (mmmt) cc_final: 0.6701 (mttp) REVERT: D 280 LYS cc_start: 0.7866 (tptt) cc_final: 0.7366 (tttt) REVERT: E 3 GLU cc_start: 0.6293 (OUTLIER) cc_final: 0.6064 (tp30) REVERT: E 80 GLN cc_start: 0.7027 (mt0) cc_final: 0.6763 (mp10) REVERT: E 121 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6116 (pp20) REVERT: E 142 LYS cc_start: 0.7071 (pmtt) cc_final: 0.6025 (ttpp) REVERT: F 15 ARG cc_start: 0.6478 (ttp-170) cc_final: 0.6175 (ttp-110) REVERT: F 17 GLU cc_start: 0.6204 (tp30) cc_final: 0.5867 (tp30) REVERT: F 79 LYS cc_start: 0.7933 (mmtm) cc_final: 0.7568 (mmmm) REVERT: F 102 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7355 (mp) REVERT: F 122 GLU cc_start: 0.6942 (tt0) cc_final: 0.6432 (tt0) REVERT: F 126 ARG cc_start: 0.7140 (mmt90) cc_final: 0.6769 (mmt-90) REVERT: F 130 GLN cc_start: 0.7856 (mm110) cc_final: 0.7196 (mm-40) REVERT: F 164 GLN cc_start: 0.7966 (tp-100) cc_final: 0.7276 (tp40) REVERT: F 184 GLU cc_start: 0.7989 (tp30) cc_final: 0.7538 (mm-30) REVERT: F 232 ASP cc_start: 0.8110 (m-30) cc_final: 0.7893 (m-30) REVERT: G 54 ARG cc_start: 0.7680 (tpp-160) cc_final: 0.7173 (mmm-85) REVERT: G 57 MET cc_start: 0.6957 (mmm) cc_final: 0.6696 (mmm) REVERT: G 59 ARG cc_start: 0.7285 (mmt-90) cc_final: 0.6941 (mmt-90) REVERT: G 86 GLU cc_start: 0.6412 (tt0) cc_final: 0.5536 (mt-10) REVERT: G 124 GLN cc_start: 0.6986 (pt0) cc_final: 0.6775 (pt0) REVERT: G 143 ILE cc_start: 0.7662 (mt) cc_final: 0.7453 (mt) REVERT: G 185 CYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6346 (t) REVERT: G 220 MET cc_start: 0.5837 (mmt) cc_final: 0.4195 (pmm) REVERT: H 8 GLN cc_start: 0.6344 (pt0) cc_final: 0.5675 (pt0) REVERT: H 9 GLU cc_start: 0.6598 (mt-10) cc_final: 0.6097 (tt0) REVERT: H 21 VAL cc_start: 0.7182 (t) cc_final: 0.6696 (p) REVERT: H 22 LYS cc_start: 0.6789 (tttt) cc_final: 0.6185 (mmtp) REVERT: H 37 LYS cc_start: 0.4655 (tptt) cc_final: 0.4206 (mmtp) REVERT: H 52 PHE cc_start: 0.7641 (m-80) cc_final: 0.7334 (m-80) REVERT: H 84 LYS cc_start: 0.7693 (tttm) cc_final: 0.6945 (pttt) REVERT: H 86 MET cc_start: 0.6299 (mtt) cc_final: 0.6098 (mtt) REVERT: H 97 LYS cc_start: 0.6527 (tttt) cc_final: 0.6076 (ttpp) REVERT: H 154 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.5920 (pm20) REVERT: I 33 ARG cc_start: 0.7611 (mtt180) cc_final: 0.7361 (mmm160) REVERT: I 40 THR cc_start: 0.7992 (OUTLIER) cc_final: 0.7718 (p) REVERT: I 134 GLN cc_start: 0.8611 (pt0) cc_final: 0.8286 (pt0) REVERT: I 170 LYS cc_start: 0.6868 (mtpp) cc_final: 0.6630 (mtpp) REVERT: I 202 ARG cc_start: 0.7274 (ttm-80) cc_final: 0.7039 (mtp180) REVERT: J 34 GLU cc_start: 0.7019 (tm-30) cc_final: 0.6653 (tm-30) REVERT: J 45 ARG cc_start: 0.6058 (mtt180) cc_final: 0.4928 (mmt90) REVERT: J 50 ILE cc_start: 0.5640 (mt) cc_final: 0.5438 (mt) REVERT: J 100 PHE cc_start: 0.7765 (p90) cc_final: 0.7374 (p90) REVERT: J 110 LEU cc_start: 0.5531 (OUTLIER) cc_final: 0.4465 (tt) REVERT: J 116 ILE cc_start: 0.6641 (pt) cc_final: 0.6318 (mp) REVERT: J 136 ARG cc_start: 0.6854 (mmt-90) cc_final: 0.6435 (mpt180) REVERT: L 68 LYS cc_start: 0.7709 (mmtp) cc_final: 0.7009 (mtmt) REVERT: L 91 ARG cc_start: 0.7172 (ttp-110) cc_final: 0.6503 (mtt180) REVERT: L 93 GLN cc_start: 0.6760 (mm110) cc_final: 0.6288 (mt0) REVERT: L 177 GLU cc_start: 0.5836 (mt-10) cc_final: 0.5532 (mm-30) REVERT: M 15 ILE cc_start: 0.7650 (tt) cc_final: 0.7445 (mp) REVERT: M 39 ASP cc_start: 0.7721 (t70) cc_final: 0.7457 (t0) REVERT: M 63 LYS cc_start: 0.8072 (ttpt) cc_final: 0.6970 (mmtp) REVERT: M 116 LYS cc_start: 0.6253 (mttt) cc_final: 0.5985 (mtpt) REVERT: N 51 MET cc_start: 0.8650 (mmm) cc_final: 0.8388 (mmt) REVERT: N 81 TYR cc_start: 0.8729 (m-80) cc_final: 0.8454 (m-80) REVERT: N 108 LYS cc_start: 0.8189 (ttmt) cc_final: 0.7663 (tmmt) REVERT: N 117 ASN cc_start: 0.8662 (m-40) cc_final: 0.8231 (t0) REVERT: N 118 SER cc_start: 0.8962 (p) cc_final: 0.8432 (p) REVERT: N 131 GLU cc_start: 0.8503 (tt0) cc_final: 0.8282 (tt0) REVERT: N 142 ILE cc_start: 0.7769 (mm) cc_final: 0.7528 (mt) REVERT: N 143 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8273 (mm-40) REVERT: N 179 HIS cc_start: 0.7497 (OUTLIER) cc_final: 0.6675 (p-80) REVERT: O 30 LYS cc_start: 0.7715 (mttt) cc_final: 0.7420 (mtpp) REVERT: O 48 THR cc_start: 0.7950 (m) cc_final: 0.7639 (p) REVERT: O 103 TYR cc_start: 0.8042 (m-80) cc_final: 0.7103 (m-80) REVERT: O 104 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6749 (mt-10) REVERT: O 124 CYS cc_start: 0.6907 (m) cc_final: 0.6472 (m) REVERT: O 135 LYS cc_start: 0.7638 (mmtt) cc_final: 0.7359 (mmtt) REVERT: O 164 LYS cc_start: 0.7482 (mmmt) cc_final: 0.6989 (mtmm) REVERT: O 176 ARG cc_start: 0.6223 (ttm-80) cc_final: 0.5704 (tmm-80) REVERT: O 180 ILE cc_start: 0.6528 (mt) cc_final: 0.6307 (mm) REVERT: O 196 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6506 (mm-30) REVERT: P 32 GLU cc_start: 0.7707 (tp30) cc_final: 0.7197 (mm-30) REVERT: P 65 LYS cc_start: 0.8283 (pttt) cc_final: 0.7806 (pttt) REVERT: P 76 GLU cc_start: 0.7296 (pt0) cc_final: 0.6909 (pt0) REVERT: P 94 LYS cc_start: 0.6854 (mttt) cc_final: 0.6144 (ttpp) REVERT: P 131 ARG cc_start: 0.8042 (mtt-85) cc_final: 0.6620 (mtm180) REVERT: Q 13 GLN cc_start: 0.8529 (mt0) cc_final: 0.8243 (mt0) REVERT: Q 24 MET cc_start: 0.7950 (mmm) cc_final: 0.7639 (mmm) REVERT: Q 25 LYS cc_start: 0.7094 (tttt) cc_final: 0.6877 (ttmm) REVERT: Q 26 MET cc_start: 0.6820 (mtp) cc_final: 0.6619 (ttm) REVERT: Q 147 ASN cc_start: 0.7807 (t0) cc_final: 0.7445 (m-40) REVERT: R 5 LYS cc_start: 0.8233 (tttm) cc_final: 0.8007 (ttmm) REVERT: R 28 GLU cc_start: 0.6868 (mp0) cc_final: 0.6545 (mp0) REVERT: R 34 MET cc_start: 0.6947 (mpp) cc_final: 0.6676 (mpp) REVERT: R 36 ASN cc_start: 0.6994 (m-40) cc_final: 0.6229 (p0) REVERT: R 56 LYS cc_start: 0.6034 (tttt) cc_final: 0.5732 (mtmm) REVERT: R 114 GLU cc_start: 0.7434 (mt-10) cc_final: 0.6911 (mp0) REVERT: R 126 LYS cc_start: 0.7118 (mttt) cc_final: 0.6870 (mttt) REVERT: R 136 ARG cc_start: 0.5734 (ttm170) cc_final: 0.5310 (ttm110) REVERT: R 141 HIS cc_start: 0.7400 (OUTLIER) cc_final: 0.6555 (t70) REVERT: S 81 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.6976 (ttp-110) REVERT: S 85 ASN cc_start: 0.6594 (OUTLIER) cc_final: 0.6224 (t0) REVERT: S 125 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8327 (tt) REVERT: S 139 SER cc_start: 0.6733 (t) cc_final: 0.6143 (p) REVERT: S 147 LYS cc_start: 0.7395 (mttt) cc_final: 0.6790 (mtmm) REVERT: S 164 LYS cc_start: 0.7625 (tttt) cc_final: 0.7413 (pttm) REVERT: T 21 LYS cc_start: 0.7222 (mttt) cc_final: 0.6721 (mmtt) REVERT: T 77 LYS cc_start: 0.8663 (mttp) cc_final: 0.8262 (mttt) REVERT: T 156 ARG cc_start: 0.6176 (mtt90) cc_final: 0.5913 (mmt90) REVERT: U 18 PHE cc_start: 0.7325 (OUTLIER) cc_final: 0.6479 (p90) REVERT: U 23 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6813 (mt-10) REVERT: U 99 ARG cc_start: 0.7191 (mtm-85) cc_final: 0.6339 (ptp-170) REVERT: V 16 MET cc_start: 0.7995 (mpp) cc_final: 0.7777 (mtp) REVERT: V 35 LYS cc_start: 0.7790 (mtpp) cc_final: 0.7495 (mtpp) REVERT: V 36 ASN cc_start: 0.8207 (m110) cc_final: 0.7811 (m-40) REVERT: V 43 ARG cc_start: 0.6889 (ttm170) cc_final: 0.6641 (mtt90) REVERT: V 45 HIS cc_start: 0.7658 (t-90) cc_final: 0.7223 (t70) REVERT: V 91 LYS cc_start: 0.6911 (mmmt) cc_final: 0.6632 (mmmt) REVERT: V 123 LYS cc_start: 0.7137 (tttp) cc_final: 0.6922 (tptt) REVERT: X 46 LYS cc_start: 0.7182 (tttm) cc_final: 0.6503 (tppt) REVERT: X 49 LYS cc_start: 0.7889 (mttt) cc_final: 0.7182 (mtpp) REVERT: X 78 ASN cc_start: 0.7816 (t0) cc_final: 0.7480 (t0) REVERT: X 87 LYS cc_start: 0.8408 (mttt) cc_final: 0.7571 (mmmt) REVERT: X 101 TYR cc_start: 0.8157 (m-10) cc_final: 0.7948 (m-80) REVERT: X 104 LYS cc_start: 0.8078 (ttmm) cc_final: 0.7650 (ttpp) REVERT: X 115 LYS cc_start: 0.8069 (mttt) cc_final: 0.7302 (ptpt) REVERT: X 131 MET cc_start: 0.6677 (mtp) cc_final: 0.6338 (mtm) REVERT: Y 23 LYS cc_start: 0.7151 (mttt) cc_final: 0.6604 (pttm) REVERT: Y 88 GLU cc_start: 0.6645 (mt-10) cc_final: 0.6311 (mm-30) REVERT: Y 95 VAL cc_start: 0.7223 (t) cc_final: 0.6833 (m) REVERT: Y 99 VAL cc_start: 0.7972 (t) cc_final: 0.7760 (m) REVERT: Y 124 LEU cc_start: 0.5068 (mt) cc_final: 0.4757 (mt) REVERT: Z 47 LYS cc_start: 0.6488 (mttt) cc_final: 0.5802 (tmtt) REVERT: Z 124 LYS cc_start: 0.5618 (mttt) cc_final: 0.5286 (ttpt) REVERT: Z 132 TRP cc_start: 0.7092 (t60) cc_final: 0.6398 (t-100) REVERT: a 22 VAL cc_start: 0.7906 (m) cc_final: 0.7671 (m) REVERT: a 55 LYS cc_start: 0.8516 (tttt) cc_final: 0.8193 (ttmt) REVERT: a 109 ASN cc_start: 0.8156 (m-40) cc_final: 0.7677 (m110) REVERT: a 122 LYS cc_start: 0.8074 (mttt) cc_final: 0.7384 (tptp) REVERT: a 137 GLU cc_start: 0.7147 (tt0) cc_final: 0.5917 (pt0) REVERT: b 28 LYS cc_start: 0.6575 (ptmt) cc_final: 0.6362 (ptmm) REVERT: b 38 LYS cc_start: 0.7874 (ttpt) cc_final: 0.7617 (ttpp) REVERT: c 56 ARG cc_start: 0.7080 (tpt-90) cc_final: 0.6742 (tpt-90) REVERT: d 44 MET cc_start: 0.7921 (mmp) cc_final: 0.7484 (mmm) REVERT: e 8 LYS cc_start: 0.6679 (mtpp) cc_final: 0.6446 (ttmt) REVERT: e 22 GLN cc_start: 0.8341 (mm-40) cc_final: 0.7908 (mt0) REVERT: e 67 MET cc_start: 0.7800 (ttm) cc_final: 0.7583 (ttp) REVERT: e 98 SER cc_start: 0.9004 (m) cc_final: 0.8677 (t) REVERT: e 119 GLU cc_start: 0.7695 (tt0) cc_final: 0.6742 (tp30) REVERT: e 126 LYS cc_start: 0.5483 (mtpt) cc_final: 0.5200 (ptmt) REVERT: f 48 LYS cc_start: 0.7323 (mtpp) cc_final: 0.6789 (mtmt) REVERT: f 59 GLU cc_start: 0.7248 (tt0) cc_final: 0.6450 (mp0) REVERT: f 81 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6641 (mt-10) REVERT: f 88 MET cc_start: 0.8072 (mmm) cc_final: 0.7721 (mmt) REVERT: f 91 LYS cc_start: 0.6823 (mptt) cc_final: 0.6480 (mmtp) REVERT: f 97 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6758 (pp) REVERT: h 67 LYS cc_start: 0.7752 (ttpp) cc_final: 0.7386 (ttmm) REVERT: h 72 LYS cc_start: 0.7082 (ttpp) cc_final: 0.6556 (tttp) REVERT: h 73 TYR cc_start: 0.7266 (m-80) cc_final: 0.6923 (m-80) REVERT: h 109 ARG cc_start: 0.6904 (ttp-170) cc_final: 0.6500 (ttp-110) REVERT: j 64 MET cc_start: 0.7975 (mtm) cc_final: 0.7683 (mtt) REVERT: k 60 ILE cc_start: 0.7153 (mm) cc_final: 0.6871 (mm) REVERT: o 21 CYS cc_start: 0.8419 (p) cc_final: 0.7748 (p) REVERT: o 22 LYS cc_start: 0.7155 (mtpt) cc_final: 0.6911 (mtpp) REVERT: p 6 LYS cc_start: 0.6498 (mtmt) cc_final: 0.6239 (mtmm) REVERT: p 13 LYS cc_start: 0.7790 (pttt) cc_final: 0.7347 (pttt) REVERT: p 36 LYS cc_start: 0.6957 (OUTLIER) cc_final: 0.6737 (mmtm) outliers start: 204 outliers final: 116 residues processed: 1324 average time/residue: 1.0429 time to fit residues: 2276.4152 Evaluate side-chains 1165 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1030 time to evaluate : 5.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 26 LYS Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 185 CYS Chi-restraints excluded: chain G residue 187 CYS Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 126 HIS Chi-restraints excluded: chain H residue 129 HIS Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 175 LYS Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 130 ASN Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain L residue 6 ASN Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 143 GLN Chi-restraints excluded: chain N residue 179 HIS Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 126 SER Chi-restraints excluded: chain O residue 141 THR Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 151 ILE Chi-restraints excluded: chain Q residue 67 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 145 LEU Chi-restraints excluded: chain R residue 3 SER Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 141 HIS Chi-restraints excluded: chain S residue 2 SER Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 81 ARG Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 98 THR Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain S residue 150 MET Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain V residue 28 CYS Chi-restraints excluded: chain V residue 135 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain Y residue 13 ARG Chi-restraints excluded: chain Y residue 25 ASP Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 104 LEU Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain a residue 43 THR Chi-restraints excluded: chain a residue 86 GLU Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain a residue 105 ASP Chi-restraints excluded: chain a residue 146 VAL Chi-restraints excluded: chain b residue 8 SER Chi-restraints excluded: chain b residue 11 ASN Chi-restraints excluded: chain c residue 18 SER Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 27 ASN Chi-restraints excluded: chain e residue 45 ARG Chi-restraints excluded: chain e residue 83 LEU Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 81 GLU Chi-restraints excluded: chain f residue 97 LEU Chi-restraints excluded: chain g residue 41 ASN Chi-restraints excluded: chain g residue 44 HIS Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain h residue 79 VAL Chi-restraints excluded: chain i residue 19 SER Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 62 LYS Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 22 CYS Chi-restraints excluded: chain k residue 68 VAL Chi-restraints excluded: chain p residue 36 LYS Chi-restraints excluded: chain p residue 42 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 431 optimal weight: 0.5980 chunk 240 optimal weight: 9.9990 chunk 645 optimal weight: 0.4980 chunk 528 optimal weight: 2.9990 chunk 213 optimal weight: 10.0000 chunk 776 optimal weight: 4.9990 chunk 839 optimal weight: 3.9990 chunk 691 optimal weight: 5.9990 chunk 770 optimal weight: 8.9990 chunk 264 optimal weight: 10.0000 chunk 623 optimal weight: 5.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN B 68 HIS B 117 ASN C 47 GLN C 84 ASN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 HIS ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 HIS H 152 ASN H 189 GLN I 169 ASN J 18 ASN J 141 GLN J 148 GLN N 156 HIS O 199 GLN P 70 HIS S 73 ASN S 145 ASN ** T 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 112 ASN W 16 HIS Y 40 GLN Y 103 ASN Z 17 HIS d 15 HIS d 65 ASN g 19 ASN g 70 GLN g 103 GLN g 109 ASN i 32 HIS o 33 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 115172 Z= 0.275 Angle : 0.643 14.841 169112 Z= 0.335 Chirality : 0.040 0.284 21128 Planarity : 0.005 0.077 11007 Dihedral : 22.668 179.811 49882 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.96 % Favored : 94.62 % Rotamer: Outliers : 5.58 % Allowed : 15.48 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.10), residues: 5785 helix: -0.11 (0.11), residues: 1901 sheet: -1.74 (0.16), residues: 832 loop : -1.59 (0.10), residues: 3052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP T 159 HIS 0.023 0.002 HIS H 129 PHE 0.021 0.002 PHE C 267 TYR 0.025 0.002 TYR F 186 ARG 0.009 0.001 ARG I 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1359 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 1084 time to evaluate : 5.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7687 (ttp) cc_final: 0.7152 (ttt) REVERT: A 46 LYS cc_start: 0.7061 (tptm) cc_final: 0.6589 (ttpt) REVERT: A 135 ARG cc_start: 0.6944 (ttm170) cc_final: 0.6566 (mtp85) REVERT: A 172 ARG cc_start: 0.7319 (ptt180) cc_final: 0.7041 (ptt-90) REVERT: A 201 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8192 (mttp) REVERT: B 53 MET cc_start: 0.8763 (ttt) cc_final: 0.8310 (ttm) REVERT: B 64 ASN cc_start: 0.8145 (t0) cc_final: 0.7782 (t0) REVERT: B 146 GLN cc_start: 0.7146 (mt0) cc_final: 0.6725 (mt0) REVERT: B 148 GLU cc_start: 0.7560 (tt0) cc_final: 0.6842 (mm-30) REVERT: B 149 GLU cc_start: 0.7448 (tt0) cc_final: 0.7155 (tm-30) REVERT: B 152 LYS cc_start: 0.7195 (tttm) cc_final: 0.6990 (mtmm) REVERT: B 219 LYS cc_start: 0.6809 (mmmt) cc_final: 0.6185 (mptt) REVERT: B 295 GLU cc_start: 0.8252 (mt-10) cc_final: 0.8039 (mt-10) REVERT: B 319 SER cc_start: 0.6778 (m) cc_final: 0.6422 (t) REVERT: B 324 LYS cc_start: 0.8459 (mptt) cc_final: 0.8018 (mmmt) REVERT: B 340 LYS cc_start: 0.6731 (mtmm) cc_final: 0.6390 (mptt) REVERT: B 345 MET cc_start: 0.8561 (mtm) cc_final: 0.8233 (mtp) REVERT: B 375 GLU cc_start: 0.7973 (tt0) cc_final: 0.7574 (tp30) REVERT: B 377 ASN cc_start: 0.7390 (OUTLIER) cc_final: 0.6768 (p0) REVERT: B 395 LYS cc_start: 0.7754 (pttt) cc_final: 0.6729 (mmmt) REVERT: B 406 LYS cc_start: 0.4181 (OUTLIER) cc_final: 0.3343 (ttmt) REVERT: C 4 GLN cc_start: 0.6391 (pt0) cc_final: 0.5386 (pm20) REVERT: C 15 LYS cc_start: 0.7620 (tttt) cc_final: 0.7405 (tttt) REVERT: C 36 GLU cc_start: 0.7330 (mt-10) cc_final: 0.7096 (tt0) REVERT: C 153 ASP cc_start: 0.7232 (t70) cc_final: 0.6796 (t70) REVERT: C 158 ILE cc_start: 0.7056 (mt) cc_final: 0.6851 (mm) REVERT: C 202 LYS cc_start: 0.7877 (mmtt) cc_final: 0.7395 (mmmt) REVERT: C 226 THR cc_start: 0.8665 (p) cc_final: 0.8361 (p) REVERT: C 268 SER cc_start: 0.7963 (m) cc_final: 0.7644 (t) REVERT: C 303 LYS cc_start: 0.7800 (mttt) cc_final: 0.7293 (pttm) REVERT: C 329 ARG cc_start: 0.7890 (mtt180) cc_final: 0.7392 (mmt-90) REVERT: C 340 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7174 (tp30) REVERT: D 53 ARG cc_start: 0.7031 (mmt90) cc_final: 0.6809 (mmt90) REVERT: D 67 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6764 (mt-10) REVERT: D 88 LYS cc_start: 0.8073 (mttt) cc_final: 0.7473 (ptmm) REVERT: D 157 MET cc_start: 0.8032 (ttt) cc_final: 0.7397 (tmm) REVERT: D 158 LYS cc_start: 0.6794 (mttt) cc_final: 0.6323 (tptt) REVERT: D 223 GLU cc_start: 0.6796 (tt0) cc_final: 0.6442 (pm20) REVERT: D 224 LYS cc_start: 0.7199 (mttt) cc_final: 0.6602 (mtpt) REVERT: D 254 ARG cc_start: 0.6717 (mtp85) cc_final: 0.6294 (mtt-85) REVERT: D 279 LYS cc_start: 0.7002 (mmmt) cc_final: 0.6622 (mttp) REVERT: D 280 LYS cc_start: 0.7972 (tptt) cc_final: 0.7560 (tptm) REVERT: E 73 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.6215 (mtm-85) REVERT: E 80 GLN cc_start: 0.7002 (mt0) cc_final: 0.6756 (mp10) REVERT: E 142 LYS cc_start: 0.7178 (pmtt) cc_final: 0.6126 (ttpp) REVERT: F 24 LEU cc_start: 0.6202 (OUTLIER) cc_final: 0.5982 (mm) REVERT: F 79 LYS cc_start: 0.7941 (mmtm) cc_final: 0.7549 (mtmt) REVERT: F 102 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7116 (mp) REVERT: F 122 GLU cc_start: 0.6942 (tt0) cc_final: 0.6456 (tt0) REVERT: F 130 GLN cc_start: 0.7960 (mm110) cc_final: 0.7462 (mm-40) REVERT: F 164 GLN cc_start: 0.8263 (tp-100) cc_final: 0.7959 (tp40) REVERT: F 228 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7192 (mt-10) REVERT: G 43 PHE cc_start: 0.7061 (m-80) cc_final: 0.6834 (m-80) REVERT: G 54 ARG cc_start: 0.7657 (tpp-160) cc_final: 0.7011 (mmm-85) REVERT: G 59 ARG cc_start: 0.7302 (mmt-90) cc_final: 0.6866 (mmt-90) REVERT: G 67 ASN cc_start: 0.7477 (t160) cc_final: 0.7219 (t0) REVERT: G 86 GLU cc_start: 0.6808 (tt0) cc_final: 0.6066 (mt-10) REVERT: G 137 LYS cc_start: 0.7101 (mttt) cc_final: 0.6599 (mmmt) REVERT: G 169 ILE cc_start: 0.7001 (OUTLIER) cc_final: 0.6472 (mp) REVERT: G 218 GLU cc_start: 0.6985 (tp30) cc_final: 0.6506 (pt0) REVERT: H 8 GLN cc_start: 0.6791 (pt0) cc_final: 0.6240 (pt0) REVERT: H 9 GLU cc_start: 0.6301 (mt-10) cc_final: 0.6043 (tt0) REVERT: H 21 VAL cc_start: 0.7487 (t) cc_final: 0.7102 (p) REVERT: H 22 LYS cc_start: 0.6947 (tttt) cc_final: 0.6474 (mmtp) REVERT: H 37 LYS cc_start: 0.5010 (tptt) cc_final: 0.4373 (mmtt) REVERT: H 84 LYS cc_start: 0.7595 (tttm) cc_final: 0.6873 (pttt) REVERT: H 97 LYS cc_start: 0.6590 (tttt) cc_final: 0.6163 (ttpp) REVERT: H 98 MET cc_start: 0.6253 (ptm) cc_final: 0.5984 (ptm) REVERT: H 152 ASN cc_start: 0.6518 (OUTLIER) cc_final: 0.6012 (t0) REVERT: I 33 ARG cc_start: 0.7624 (mtt180) cc_final: 0.7312 (mmm160) REVERT: I 40 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7917 (p) REVERT: I 156 SER cc_start: 0.8444 (p) cc_final: 0.8185 (p) REVERT: I 192 ASP cc_start: 0.5600 (t0) cc_final: 0.5227 (t0) REVERT: I 202 ARG cc_start: 0.7413 (ttm-80) cc_final: 0.7012 (mtp180) REVERT: J 34 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6766 (tm-30) REVERT: J 45 ARG cc_start: 0.5889 (mtt180) cc_final: 0.4797 (mmt90) REVERT: J 100 PHE cc_start: 0.7681 (p90) cc_final: 0.7471 (p90) REVERT: J 110 LEU cc_start: 0.5375 (OUTLIER) cc_final: 0.4377 (tt) REVERT: J 136 ARG cc_start: 0.6806 (mmt-90) cc_final: 0.6476 (mpt180) REVERT: L 68 LYS cc_start: 0.7581 (mmtp) cc_final: 0.6940 (mtmt) REVERT: L 91 ARG cc_start: 0.7282 (ttp-110) cc_final: 0.6689 (mtt90) REVERT: L 93 GLN cc_start: 0.6987 (mm110) cc_final: 0.6532 (mt0) REVERT: L 110 LYS cc_start: 0.7250 (mttt) cc_final: 0.6885 (mmmt) REVERT: L 145 LYS cc_start: 0.5825 (pttm) cc_final: 0.5405 (ttmm) REVERT: L 177 GLU cc_start: 0.5885 (mt-10) cc_final: 0.5548 (mm-30) REVERT: M 39 ASP cc_start: 0.7682 (t70) cc_final: 0.7468 (t0) REVERT: M 63 LYS cc_start: 0.7991 (ttpt) cc_final: 0.7101 (mmtp) REVERT: M 116 LYS cc_start: 0.6692 (mttt) cc_final: 0.6386 (mtpt) REVERT: N 33 LEU cc_start: 0.7887 (mt) cc_final: 0.7535 (mt) REVERT: N 51 MET cc_start: 0.8546 (mmm) cc_final: 0.8136 (mmt) REVERT: N 59 MET cc_start: 0.8389 (tpp) cc_final: 0.7902 (mtp) REVERT: N 81 TYR cc_start: 0.8715 (m-80) cc_final: 0.8416 (m-80) REVERT: N 108 LYS cc_start: 0.7991 (ttmt) cc_final: 0.7720 (tmmt) REVERT: N 117 ASN cc_start: 0.8564 (m-40) cc_final: 0.8068 (t0) REVERT: N 118 SER cc_start: 0.8979 (p) cc_final: 0.8628 (p) REVERT: N 179 HIS cc_start: 0.7636 (OUTLIER) cc_final: 0.6669 (p-80) REVERT: O 48 THR cc_start: 0.7868 (m) cc_final: 0.7591 (p) REVERT: O 104 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6906 (mt-10) REVERT: O 135 LYS cc_start: 0.7604 (mmtt) cc_final: 0.6732 (mtpt) REVERT: O 176 ARG cc_start: 0.6599 (ttm-80) cc_final: 0.5966 (tmm-80) REVERT: O 180 ILE cc_start: 0.6705 (mt) cc_final: 0.6333 (mm) REVERT: O 196 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6565 (mm-30) REVERT: P 32 GLU cc_start: 0.7673 (tp30) cc_final: 0.7272 (mm-30) REVERT: P 65 LYS cc_start: 0.8355 (pttt) cc_final: 0.7919 (pttt) REVERT: P 76 GLU cc_start: 0.7280 (pt0) cc_final: 0.6622 (pt0) REVERT: P 94 LYS cc_start: 0.6930 (mttt) cc_final: 0.6204 (ttpp) REVERT: P 131 ARG cc_start: 0.8036 (mtt-85) cc_final: 0.6571 (mtm180) REVERT: P 155 GLU cc_start: 0.7896 (tt0) cc_final: 0.7523 (tt0) REVERT: Q 15 GLN cc_start: 0.6600 (tt0) cc_final: 0.5857 (pm20) REVERT: Q 16 GLU cc_start: 0.8045 (pt0) cc_final: 0.7250 (pm20) REVERT: Q 24 MET cc_start: 0.7908 (mmm) cc_final: 0.7482 (mmm) REVERT: Q 26 MET cc_start: 0.6735 (mtp) cc_final: 0.6266 (ttm) REVERT: Q 80 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7788 (tt) REVERT: Q 88 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6573 (mp0) REVERT: Q 95 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7568 (mtpp) REVERT: Q 147 ASN cc_start: 0.8003 (t0) cc_final: 0.7730 (m-40) REVERT: R 5 LYS cc_start: 0.8232 (tttm) cc_final: 0.7990 (ttmm) REVERT: R 28 GLU cc_start: 0.7068 (mp0) cc_final: 0.6531 (mp0) REVERT: R 34 MET cc_start: 0.7025 (mpp) cc_final: 0.6797 (mpp) REVERT: R 36 ASN cc_start: 0.7120 (m-40) cc_final: 0.6572 (p0) REVERT: R 39 GLN cc_start: 0.6953 (mm110) cc_final: 0.6261 (tm-30) REVERT: R 56 LYS cc_start: 0.5896 (tttt) cc_final: 0.5584 (mtmm) REVERT: R 114 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7185 (mp0) REVERT: R 133 ARG cc_start: 0.7430 (ptt-90) cc_final: 0.7117 (ptt-90) REVERT: R 136 ARG cc_start: 0.6248 (ttm170) cc_final: 0.5869 (ttm110) REVERT: R 141 HIS cc_start: 0.7644 (OUTLIER) cc_final: 0.6690 (t70) REVERT: S 16 LYS cc_start: 0.7733 (mttt) cc_final: 0.7362 (tppt) REVERT: S 78 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7754 (pp) REVERT: S 81 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7220 (tmm-80) REVERT: S 85 ASN cc_start: 0.6889 (OUTLIER) cc_final: 0.6196 (t0) REVERT: S 92 GLU cc_start: 0.8029 (pt0) cc_final: 0.7536 (pt0) REVERT: S 116 SER cc_start: 0.7843 (t) cc_final: 0.7423 (p) REVERT: S 147 LYS cc_start: 0.7410 (mttt) cc_final: 0.6858 (mtmm) REVERT: T 21 LYS cc_start: 0.7380 (mttt) cc_final: 0.6848 (mmtt) REVERT: T 77 LYS cc_start: 0.8760 (mttp) cc_final: 0.8377 (mttt) REVERT: T 81 ASN cc_start: 0.6859 (OUTLIER) cc_final: 0.6283 (t0) REVERT: T 156 ARG cc_start: 0.6390 (mtt90) cc_final: 0.6037 (mmt90) REVERT: U 18 PHE cc_start: 0.7142 (OUTLIER) cc_final: 0.6479 (p90) REVERT: U 23 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6832 (mt-10) REVERT: U 32 MET cc_start: 0.7816 (mtt) cc_final: 0.7024 (mtp) REVERT: U 99 ARG cc_start: 0.6852 (mtm-85) cc_final: 0.6096 (ptp-170) REVERT: V 36 ASN cc_start: 0.8072 (m110) cc_final: 0.7676 (m-40) REVERT: V 39 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7269 (pt) REVERT: V 43 ARG cc_start: 0.6807 (ttm170) cc_final: 0.6388 (mtt90) REVERT: V 45 HIS cc_start: 0.7530 (t-90) cc_final: 0.7037 (t70) REVERT: V 75 LYS cc_start: 0.7076 (ttpp) cc_final: 0.6721 (ttpt) REVERT: V 99 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7388 (tp40) REVERT: V 123 LYS cc_start: 0.7282 (tttp) cc_final: 0.6705 (ttpt) REVERT: X 46 LYS cc_start: 0.7104 (tttm) cc_final: 0.6603 (tppt) REVERT: X 49 LYS cc_start: 0.8017 (mttt) cc_final: 0.7243 (mtpp) REVERT: X 71 THR cc_start: 0.6546 (m) cc_final: 0.6231 (p) REVERT: X 78 ASN cc_start: 0.7729 (t0) cc_final: 0.7445 (t0) REVERT: X 87 LYS cc_start: 0.8491 (mttt) cc_final: 0.7657 (mmmt) REVERT: X 101 TYR cc_start: 0.8171 (m-10) cc_final: 0.7837 (m-80) REVERT: X 115 LYS cc_start: 0.8167 (mttt) cc_final: 0.7694 (mtmt) REVERT: Y 23 LYS cc_start: 0.7261 (mttt) cc_final: 0.6691 (pttm) REVERT: Y 57 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.6192 (ptp) REVERT: Y 88 GLU cc_start: 0.6749 (mt-10) cc_final: 0.6307 (mm-30) REVERT: Y 95 VAL cc_start: 0.7108 (t) cc_final: 0.6776 (m) REVERT: Y 99 VAL cc_start: 0.7845 (t) cc_final: 0.7461 (m) REVERT: Y 124 LEU cc_start: 0.5284 (mt) cc_final: 0.4992 (mt) REVERT: Y 127 ASP cc_start: 0.6633 (m-30) cc_final: 0.6302 (t0) REVERT: Z 43 MET cc_start: 0.7382 (ttp) cc_final: 0.7064 (ttp) REVERT: Z 47 LYS cc_start: 0.6447 (mttt) cc_final: 0.5830 (tmtt) REVERT: Z 80 MET cc_start: 0.6292 (ttm) cc_final: 0.5892 (ttm) REVERT: a 22 VAL cc_start: 0.7824 (m) cc_final: 0.7575 (m) REVERT: a 55 LYS cc_start: 0.8487 (tttt) cc_final: 0.8197 (ttmt) REVERT: a 105 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7182 (m-30) REVERT: a 109 ASN cc_start: 0.8371 (m-40) cc_final: 0.7838 (m110) REVERT: a 122 LYS cc_start: 0.8019 (mttt) cc_final: 0.7447 (tptp) REVERT: a 137 GLU cc_start: 0.7156 (tt0) cc_final: 0.5939 (pt0) REVERT: b 23 LYS cc_start: 0.7543 (tttt) cc_final: 0.7056 (pttm) REVERT: c 56 ARG cc_start: 0.7184 (tpt-90) cc_final: 0.6745 (tpt-90) REVERT: e 22 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7829 (mt0) REVERT: e 98 SER cc_start: 0.8971 (m) cc_final: 0.8630 (t) REVERT: e 111 LYS cc_start: 0.7955 (tttt) cc_final: 0.7354 (mmmt) REVERT: e 119 GLU cc_start: 0.7970 (tt0) cc_final: 0.6855 (tp30) REVERT: f 48 LYS cc_start: 0.7539 (mtpp) cc_final: 0.6852 (mtmt) REVERT: f 59 GLU cc_start: 0.7228 (tt0) cc_final: 0.6381 (mp0) REVERT: f 77 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6116 (mtt180) REVERT: f 81 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6554 (mt-10) REVERT: f 88 MET cc_start: 0.8099 (mmm) cc_final: 0.7790 (mmt) REVERT: f 97 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6736 (pp) REVERT: h 34 GLN cc_start: 0.5497 (mt0) cc_final: 0.4978 (tm-30) REVERT: h 72 LYS cc_start: 0.6815 (ttpp) cc_final: 0.6442 (tttp) REVERT: h 78 LEU cc_start: 0.7132 (pp) cc_final: 0.6545 (tp) REVERT: h 109 ARG cc_start: 0.6779 (ttp-170) cc_final: 0.6478 (ttp-110) REVERT: j 50 GLU cc_start: 0.8359 (pt0) cc_final: 0.7858 (pt0) REVERT: j 64 MET cc_start: 0.8038 (mtm) cc_final: 0.7443 (mtt) REVERT: o 20 MET cc_start: 0.6369 (ttm) cc_final: 0.6140 (ttm) REVERT: o 21 CYS cc_start: 0.8557 (p) cc_final: 0.7799 (p) REVERT: o 73 GLN cc_start: 0.7509 (mm110) cc_final: 0.7271 (mm110) REVERT: p 6 LYS cc_start: 0.6305 (mtmt) cc_final: 0.5934 (mtmm) REVERT: p 13 LYS cc_start: 0.7886 (pttt) cc_final: 0.7506 (pttt) REVERT: p 24 LYS cc_start: 0.7056 (OUTLIER) cc_final: 0.6832 (tppt) REVERT: p 34 ARG cc_start: 0.7455 (mtt90) cc_final: 0.7074 (mtt90) outliers start: 275 outliers final: 182 residues processed: 1257 average time/residue: 0.9938 time to fit residues: 2087.1171 Evaluate side-chains 1221 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1011 time to evaluate : 5.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 26 LYS Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 187 CYS Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 64 ARG Chi-restraints excluded: chain H residue 126 HIS Chi-restraints excluded: chain H residue 152 ASN Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 130 ASN Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain L residue 6 ASN Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 179 HIS Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 126 SER Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain O residue 141 THR Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 151 ILE Chi-restraints excluded: chain Q residue 67 THR Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 95 LYS Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 167 SER Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 141 HIS Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain S residue 2 SER Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 81 ARG Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain S residue 121 SER Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain S residue 150 MET Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 81 ASN Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain V residue 28 CYS Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 99 GLN Chi-restraints excluded: chain V residue 112 MET Chi-restraints excluded: chain V residue 135 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain Y residue 2 VAL Chi-restraints excluded: chain Y residue 13 ARG Chi-restraints excluded: chain Y residue 25 ASP Chi-restraints excluded: chain Y residue 31 MET Chi-restraints excluded: chain Y residue 57 MET Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain Z residue 114 LEU Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain a residue 43 THR Chi-restraints excluded: chain a residue 86 GLU Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain a residue 96 LYS Chi-restraints excluded: chain a residue 105 ASP Chi-restraints excluded: chain a residue 146 VAL Chi-restraints excluded: chain b residue 8 SER Chi-restraints excluded: chain b residue 11 ASN Chi-restraints excluded: chain c residue 44 LEU Chi-restraints excluded: chain c residue 101 SER Chi-restraints excluded: chain d residue 16 LEU Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 27 ASN Chi-restraints excluded: chain e residue 70 ASN Chi-restraints excluded: chain e residue 80 LEU Chi-restraints excluded: chain e residue 83 LEU Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 75 VAL Chi-restraints excluded: chain f residue 77 ARG Chi-restraints excluded: chain f residue 81 GLU Chi-restraints excluded: chain f residue 97 LEU Chi-restraints excluded: chain g residue 19 ASN Chi-restraints excluded: chain g residue 57 CYS Chi-restraints excluded: chain g residue 60 THR Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 95 MET Chi-restraints excluded: chain h residue 30 GLU Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 79 VAL Chi-restraints excluded: chain i residue 19 SER Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 22 CYS Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain m residue 84 SER Chi-restraints excluded: chain m residue 92 THR Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain p residue 8 VAL Chi-restraints excluded: chain p residue 24 LYS Chi-restraints excluded: chain p residue 32 SER Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 60 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 767 optimal weight: 4.9990 chunk 584 optimal weight: 0.5980 chunk 403 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 370 optimal weight: 10.0000 chunk 521 optimal weight: 0.0060 chunk 779 optimal weight: 0.8980 chunk 825 optimal weight: 0.4980 chunk 407 optimal weight: 2.9990 chunk 738 optimal weight: 5.9990 chunk 222 optimal weight: 7.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 142 ASN B 68 HIS C 47 GLN C 135 GLN ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 ASN J 6 ASN Q 43 ASN Q 126 GLN T 148 GLN W 29 HIS Y 103 ASN Z 84 HIS f 62 ASN g 19 ASN h 65 GLN o 33 HIS o 45 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 115172 Z= 0.149 Angle : 0.556 12.762 169112 Z= 0.289 Chirality : 0.035 0.281 21128 Planarity : 0.004 0.068 11007 Dihedral : 22.561 179.480 49868 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.18 % Favored : 95.38 % Rotamer: Outliers : 4.38 % Allowed : 17.61 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.10), residues: 5785 helix: 0.40 (0.12), residues: 1909 sheet: -1.44 (0.17), residues: 823 loop : -1.35 (0.10), residues: 3053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP T 159 HIS 0.007 0.001 HIS H 126 PHE 0.011 0.001 PHE l 26 TYR 0.027 0.001 TYR F 186 ARG 0.010 0.000 ARG l 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1295 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1079 time to evaluate : 5.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7659 (ttp) cc_final: 0.7033 (ttt) REVERT: A 46 LYS cc_start: 0.7103 (tptm) cc_final: 0.6549 (ttpt) REVERT: A 135 ARG cc_start: 0.6900 (ttm170) cc_final: 0.6557 (mtp85) REVERT: A 201 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8241 (mttp) REVERT: B 53 MET cc_start: 0.8690 (ttt) cc_final: 0.8409 (ttm) REVERT: B 64 ASN cc_start: 0.8059 (t0) cc_final: 0.7751 (t0) REVERT: B 71 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7537 (mt-10) REVERT: B 84 MET cc_start: 0.7701 (ptm) cc_final: 0.7269 (ptm) REVERT: B 90 ILE cc_start: 0.8237 (mt) cc_final: 0.8002 (tt) REVERT: B 146 GLN cc_start: 0.7061 (mt0) cc_final: 0.6720 (mt0) REVERT: B 149 GLU cc_start: 0.7419 (tt0) cc_final: 0.7182 (tm-30) REVERT: B 151 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7325 (mm-40) REVERT: B 219 LYS cc_start: 0.6847 (mmmt) cc_final: 0.6299 (mptt) REVERT: B 319 SER cc_start: 0.6954 (m) cc_final: 0.6600 (t) REVERT: B 324 LYS cc_start: 0.8433 (mptt) cc_final: 0.7956 (mmmt) REVERT: B 340 LYS cc_start: 0.6521 (mtmm) cc_final: 0.6196 (mptt) REVERT: B 375 GLU cc_start: 0.8010 (tt0) cc_final: 0.7586 (tp30) REVERT: B 377 ASN cc_start: 0.7467 (OUTLIER) cc_final: 0.6837 (p0) REVERT: B 395 LYS cc_start: 0.7724 (pttt) cc_final: 0.6669 (mmmt) REVERT: B 406 LYS cc_start: 0.4322 (OUTLIER) cc_final: 0.3545 (ttmt) REVERT: C 4 GLN cc_start: 0.6521 (pt0) cc_final: 0.5426 (pm20) REVERT: C 36 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7130 (tt0) REVERT: C 158 ILE cc_start: 0.6728 (mt) cc_final: 0.6491 (mm) REVERT: C 202 LYS cc_start: 0.7876 (mmtt) cc_final: 0.7374 (mmmt) REVERT: C 268 SER cc_start: 0.7933 (m) cc_final: 0.7653 (t) REVERT: C 303 LYS cc_start: 0.7881 (mttt) cc_final: 0.7354 (pttm) REVERT: C 329 ARG cc_start: 0.7850 (mtt180) cc_final: 0.7336 (mmt180) REVERT: C 340 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7155 (tp30) REVERT: D 67 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6598 (mt-10) REVERT: D 88 LYS cc_start: 0.7453 (mttt) cc_final: 0.6789 (ptmm) REVERT: D 141 ASP cc_start: 0.8338 (t0) cc_final: 0.8092 (t0) REVERT: D 157 MET cc_start: 0.7907 (ttt) cc_final: 0.7383 (tmm) REVERT: D 158 LYS cc_start: 0.6745 (mttt) cc_final: 0.6368 (tptt) REVERT: D 223 GLU cc_start: 0.6735 (tt0) cc_final: 0.6256 (pm20) REVERT: D 224 LYS cc_start: 0.7105 (mttt) cc_final: 0.6592 (mtpt) REVERT: D 233 VAL cc_start: 0.7877 (t) cc_final: 0.7619 (m) REVERT: D 254 ARG cc_start: 0.6669 (mtp85) cc_final: 0.6270 (mtt-85) REVERT: D 279 LYS cc_start: 0.7022 (mmmt) cc_final: 0.6621 (mttp) REVERT: D 280 LYS cc_start: 0.7995 (tptt) cc_final: 0.7579 (tptm) REVERT: E 73 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.5832 (mtm-85) REVERT: E 80 GLN cc_start: 0.6992 (mt0) cc_final: 0.6719 (mp10) REVERT: E 86 LYS cc_start: 0.7125 (OUTLIER) cc_final: 0.6588 (mtpt) REVERT: E 96 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6429 (mp0) REVERT: E 101 TYR cc_start: 0.7806 (m-80) cc_final: 0.7511 (m-80) REVERT: E 142 LYS cc_start: 0.7553 (pmtt) cc_final: 0.6538 (tttm) REVERT: F 24 LEU cc_start: 0.6283 (OUTLIER) cc_final: 0.6054 (mm) REVERT: F 79 LYS cc_start: 0.7910 (mmtm) cc_final: 0.7345 (mtmt) REVERT: F 102 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7256 (mp) REVERT: F 122 GLU cc_start: 0.6744 (tt0) cc_final: 0.6369 (tt0) REVERT: F 163 ASN cc_start: 0.8222 (m-40) cc_final: 0.7779 (m-40) REVERT: F 164 GLN cc_start: 0.8332 (tp-100) cc_final: 0.7758 (tp40) REVERT: G 48 GLN cc_start: 0.5735 (mt0) cc_final: 0.5493 (mt0) REVERT: G 54 ARG cc_start: 0.7633 (tpp-160) cc_final: 0.6998 (mmm-85) REVERT: G 59 ARG cc_start: 0.7304 (mmt-90) cc_final: 0.6885 (mmt-90) REVERT: G 67 ASN cc_start: 0.7364 (t160) cc_final: 0.7122 (t0) REVERT: G 86 GLU cc_start: 0.6979 (tt0) cc_final: 0.6435 (mt-10) REVERT: G 218 GLU cc_start: 0.7129 (tp30) cc_final: 0.6624 (pt0) REVERT: H 8 GLN cc_start: 0.6619 (pt0) cc_final: 0.6105 (pt0) REVERT: H 9 GLU cc_start: 0.6320 (mt-10) cc_final: 0.6030 (tt0) REVERT: H 21 VAL cc_start: 0.7759 (t) cc_final: 0.7385 (p) REVERT: H 22 LYS cc_start: 0.6930 (tttt) cc_final: 0.6458 (mmtp) REVERT: H 84 LYS cc_start: 0.7662 (tttm) cc_final: 0.6947 (pttt) REVERT: H 97 LYS cc_start: 0.6344 (tttt) cc_final: 0.5886 (ttpp) REVERT: H 98 MET cc_start: 0.6504 (ptm) cc_final: 0.6291 (ptm) REVERT: H 175 LYS cc_start: 0.6164 (OUTLIER) cc_final: 0.5891 (ptpt) REVERT: I 33 ARG cc_start: 0.7570 (mtt180) cc_final: 0.7258 (mmm160) REVERT: I 156 SER cc_start: 0.8471 (p) cc_final: 0.8198 (p) REVERT: I 185 GLN cc_start: 0.7012 (tp40) cc_final: 0.6784 (tm-30) REVERT: I 192 ASP cc_start: 0.5615 (t0) cc_final: 0.5277 (t0) REVERT: I 202 ARG cc_start: 0.7293 (ttm-80) cc_final: 0.6927 (mtp180) REVERT: J 34 GLU cc_start: 0.7130 (tm-30) cc_final: 0.6871 (tm-30) REVERT: J 45 ARG cc_start: 0.5779 (mtt180) cc_final: 0.4822 (mmt90) REVERT: J 100 PHE cc_start: 0.7601 (p90) cc_final: 0.7177 (p90) REVERT: J 110 LEU cc_start: 0.5277 (OUTLIER) cc_final: 0.4217 (tt) REVERT: J 111 LYS cc_start: 0.5409 (mttm) cc_final: 0.5142 (mptt) REVERT: J 136 ARG cc_start: 0.6938 (mmt-90) cc_final: 0.6562 (mpt180) REVERT: L 68 LYS cc_start: 0.7529 (mmtp) cc_final: 0.6973 (mtmt) REVERT: L 91 ARG cc_start: 0.7387 (ttp-110) cc_final: 0.6695 (mtt90) REVERT: L 93 GLN cc_start: 0.6970 (mm110) cc_final: 0.6371 (mt0) REVERT: L 110 LYS cc_start: 0.7357 (mttt) cc_final: 0.6996 (mmmt) REVERT: L 145 LYS cc_start: 0.5871 (pttm) cc_final: 0.5446 (ttmm) REVERT: L 177 GLU cc_start: 0.5834 (mt-10) cc_final: 0.5575 (mm-30) REVERT: M 63 LYS cc_start: 0.8094 (ttpt) cc_final: 0.7209 (mmtp) REVERT: M 116 LYS cc_start: 0.6732 (mttt) cc_final: 0.6391 (mtpt) REVERT: N 33 LEU cc_start: 0.7728 (mt) cc_final: 0.7439 (mt) REVERT: N 37 VAL cc_start: 0.7880 (OUTLIER) cc_final: 0.7661 (m) REVERT: N 51 MET cc_start: 0.8581 (mmm) cc_final: 0.8185 (mmt) REVERT: N 59 MET cc_start: 0.8424 (tpp) cc_final: 0.7676 (mtp) REVERT: N 108 LYS cc_start: 0.7975 (ttmt) cc_final: 0.7720 (tmmt) REVERT: N 117 ASN cc_start: 0.8624 (m-40) cc_final: 0.8204 (t0) REVERT: N 118 SER cc_start: 0.9042 (p) cc_final: 0.8701 (p) REVERT: O 104 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6684 (mt-10) REVERT: O 135 LYS cc_start: 0.7220 (mmtt) cc_final: 0.6606 (mtpt) REVERT: O 176 ARG cc_start: 0.6658 (ttm-80) cc_final: 0.6023 (tmm-80) REVERT: O 180 ILE cc_start: 0.6625 (mt) cc_final: 0.6319 (mm) REVERT: O 196 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6608 (mm-30) REVERT: P 17 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.7852 (mtpp) REVERT: P 24 ARG cc_start: 0.8502 (mtp180) cc_final: 0.8277 (mtm180) REVERT: P 32 GLU cc_start: 0.7632 (tp30) cc_final: 0.7173 (mm-30) REVERT: P 65 LYS cc_start: 0.8267 (pttt) cc_final: 0.7844 (pttt) REVERT: P 76 GLU cc_start: 0.7456 (pt0) cc_final: 0.6745 (pt0) REVERT: P 94 LYS cc_start: 0.6586 (mttt) cc_final: 0.6074 (ttpp) REVERT: P 131 ARG cc_start: 0.7966 (mtt-85) cc_final: 0.6607 (mtm180) REVERT: Q 15 GLN cc_start: 0.6669 (tt0) cc_final: 0.6005 (pm20) REVERT: Q 26 MET cc_start: 0.6790 (mtp) cc_final: 0.5675 (mmt) REVERT: Q 95 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7604 (mtpp) REVERT: Q 147 ASN cc_start: 0.7892 (t0) cc_final: 0.7621 (m-40) REVERT: R 5 LYS cc_start: 0.8203 (tttm) cc_final: 0.7966 (ttmm) REVERT: R 28 GLU cc_start: 0.7054 (mp0) cc_final: 0.6531 (mp0) REVERT: R 34 MET cc_start: 0.6836 (mpp) cc_final: 0.6597 (mpp) REVERT: R 36 ASN cc_start: 0.7127 (m-40) cc_final: 0.6650 (p0) REVERT: R 39 GLN cc_start: 0.6970 (mm110) cc_final: 0.6289 (tm-30) REVERT: R 49 ILE cc_start: 0.8209 (tt) cc_final: 0.7958 (tt) REVERT: R 56 LYS cc_start: 0.5875 (tttt) cc_final: 0.5564 (mtmm) REVERT: R 114 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7214 (mp0) REVERT: R 136 ARG cc_start: 0.6150 (ttm170) cc_final: 0.5787 (ttm110) REVERT: R 141 HIS cc_start: 0.7477 (OUTLIER) cc_final: 0.6618 (t70) REVERT: S 16 LYS cc_start: 0.7739 (mttt) cc_final: 0.7375 (tppt) REVERT: S 81 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.7156 (tmm-80) REVERT: S 85 ASN cc_start: 0.6461 (OUTLIER) cc_final: 0.6025 (t0) REVERT: S 116 SER cc_start: 0.8001 (t) cc_final: 0.7596 (p) REVERT: S 147 LYS cc_start: 0.7405 (mttt) cc_final: 0.6982 (mtmm) REVERT: T 21 LYS cc_start: 0.7266 (mttt) cc_final: 0.6700 (mmtt) REVERT: T 77 LYS cc_start: 0.8643 (mttp) cc_final: 0.7949 (mtpt) REVERT: T 156 ARG cc_start: 0.6315 (mtt90) cc_final: 0.5938 (mmt180) REVERT: U 18 PHE cc_start: 0.7061 (OUTLIER) cc_final: 0.6302 (p90) REVERT: U 23 GLU cc_start: 0.7382 (mt-10) cc_final: 0.6771 (mt-10) REVERT: U 32 MET cc_start: 0.7817 (mtt) cc_final: 0.7082 (mtp) REVERT: U 76 PHE cc_start: 0.7920 (t80) cc_final: 0.7406 (t80) REVERT: V 36 ASN cc_start: 0.8054 (m110) cc_final: 0.7718 (m-40) REVERT: V 39 ILE cc_start: 0.7331 (pt) cc_final: 0.7107 (pt) REVERT: V 43 ARG cc_start: 0.6627 (ttm170) cc_final: 0.6394 (mtt90) REVERT: V 75 LYS cc_start: 0.6903 (ttpp) cc_final: 0.6593 (ttpt) REVERT: V 109 LYS cc_start: 0.6871 (tptp) cc_final: 0.5964 (mmmm) REVERT: V 123 LYS cc_start: 0.7156 (tttp) cc_final: 0.6596 (tttm) REVERT: X 46 LYS cc_start: 0.7078 (tttm) cc_final: 0.6539 (tppt) REVERT: X 49 LYS cc_start: 0.7985 (mttt) cc_final: 0.7268 (mtpp) REVERT: X 66 THR cc_start: 0.7166 (OUTLIER) cc_final: 0.6888 (t) REVERT: X 71 THR cc_start: 0.6574 (m) cc_final: 0.6204 (p) REVERT: X 78 ASN cc_start: 0.7729 (t0) cc_final: 0.7468 (t0) REVERT: X 87 LYS cc_start: 0.8510 (mttt) cc_final: 0.7623 (mmmt) REVERT: X 101 TYR cc_start: 0.8065 (m-10) cc_final: 0.7649 (m-80) REVERT: X 115 LYS cc_start: 0.8125 (mttt) cc_final: 0.7677 (mtmt) REVERT: Y 23 LYS cc_start: 0.7344 (mttt) cc_final: 0.6747 (pttm) REVERT: Y 25 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.6984 (m-30) REVERT: Y 57 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.6369 (ptp) REVERT: Y 80 ILE cc_start: 0.8069 (mt) cc_final: 0.7848 (pt) REVERT: Y 88 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6479 (mm-30) REVERT: Y 95 VAL cc_start: 0.7111 (t) cc_final: 0.6773 (m) REVERT: Z 43 MET cc_start: 0.7425 (ttp) cc_final: 0.7200 (ttp) REVERT: Z 47 LYS cc_start: 0.6473 (mttt) cc_final: 0.5863 (tmtt) REVERT: a 22 VAL cc_start: 0.7854 (OUTLIER) cc_final: 0.7589 (m) REVERT: a 55 LYS cc_start: 0.8466 (tttt) cc_final: 0.8184 (ttmt) REVERT: a 105 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7201 (m-30) REVERT: a 109 ASN cc_start: 0.8324 (m-40) cc_final: 0.7676 (m110) REVERT: a 122 LYS cc_start: 0.7858 (mttt) cc_final: 0.7523 (tptp) REVERT: a 137 GLU cc_start: 0.7059 (tt0) cc_final: 0.6132 (pt0) REVERT: b 23 LYS cc_start: 0.7547 (tttt) cc_final: 0.7056 (pttm) REVERT: c 56 ARG cc_start: 0.6951 (tpt-90) cc_final: 0.6514 (tpt-90) REVERT: d 94 LYS cc_start: 0.6972 (OUTLIER) cc_final: 0.6742 (tptt) REVERT: e 20 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7483 (ttt180) REVERT: e 22 GLN cc_start: 0.8271 (mm-40) cc_final: 0.7837 (mt0) REVERT: e 98 SER cc_start: 0.8909 (m) cc_final: 0.8560 (t) REVERT: e 111 LYS cc_start: 0.7941 (tttt) cc_final: 0.7332 (mmmt) REVERT: e 119 GLU cc_start: 0.7923 (tt0) cc_final: 0.6874 (tp30) REVERT: e 126 LYS cc_start: 0.5815 (mtpt) cc_final: 0.5468 (ptmm) REVERT: f 6 LYS cc_start: 0.6735 (ptmt) cc_final: 0.6327 (mmtt) REVERT: f 47 LYS cc_start: 0.7460 (mmtm) cc_final: 0.7244 (mptt) REVERT: f 48 LYS cc_start: 0.7392 (mtpp) cc_final: 0.6887 (mtmt) REVERT: f 59 GLU cc_start: 0.7225 (tt0) cc_final: 0.6378 (mp0) REVERT: f 81 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6763 (mt-10) REVERT: f 88 MET cc_start: 0.8041 (mmm) cc_final: 0.7800 (mmt) REVERT: f 97 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6738 (pp) REVERT: g 57 CYS cc_start: 0.6301 (OUTLIER) cc_final: 0.5904 (p) REVERT: h 34 GLN cc_start: 0.5716 (mt0) cc_final: 0.5169 (tm-30) REVERT: h 72 LYS cc_start: 0.7069 (ttpp) cc_final: 0.6732 (tttp) REVERT: h 109 ARG cc_start: 0.6713 (ttp-170) cc_final: 0.6449 (ttp-110) REVERT: j 50 GLU cc_start: 0.8398 (pt0) cc_final: 0.7833 (pt0) REVERT: j 64 MET cc_start: 0.7848 (mtm) cc_final: 0.7620 (mtm) REVERT: k 62 GLU cc_start: 0.5580 (OUTLIER) cc_final: 0.5123 (mp0) REVERT: l 37 ARG cc_start: 0.7693 (mtp180) cc_final: 0.7251 (mmm-85) REVERT: o 21 CYS cc_start: 0.8297 (p) cc_final: 0.7645 (p) REVERT: p 6 LYS cc_start: 0.6717 (mtmt) cc_final: 0.6407 (mtmm) REVERT: p 13 LYS cc_start: 0.7820 (pttt) cc_final: 0.7322 (pttt) outliers start: 216 outliers final: 132 residues processed: 1204 average time/residue: 1.0168 time to fit residues: 2037.3957 Evaluate side-chains 1198 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1038 time to evaluate : 5.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 187 CYS Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 64 ARG Chi-restraints excluded: chain H residue 173 LYS Chi-restraints excluded: chain H residue 175 LYS Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain I residue 21 ARG Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 130 ASN Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain L residue 6 ASN Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 126 SER Chi-restraints excluded: chain O residue 141 THR Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain O residue 187 LEU Chi-restraints excluded: chain P residue 17 LYS Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain P residue 151 ILE Chi-restraints excluded: chain Q residue 95 LYS Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 167 SER Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 141 HIS Chi-restraints excluded: chain S residue 2 SER Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 81 ARG Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain S residue 121 SER Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain V residue 112 MET Chi-restraints excluded: chain V residue 117 ILE Chi-restraints excluded: chain V residue 135 VAL Chi-restraints excluded: chain W residue 63 LYS Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain Y residue 2 VAL Chi-restraints excluded: chain Y residue 13 ARG Chi-restraints excluded: chain Y residue 18 SER Chi-restraints excluded: chain Y residue 25 ASP Chi-restraints excluded: chain Y residue 57 MET Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 114 LEU Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain a residue 105 ASP Chi-restraints excluded: chain a residue 146 VAL Chi-restraints excluded: chain b residue 11 ASN Chi-restraints excluded: chain b residue 13 SER Chi-restraints excluded: chain c residue 44 LEU Chi-restraints excluded: chain c residue 101 SER Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 94 LYS Chi-restraints excluded: chain e residue 20 ARG Chi-restraints excluded: chain e residue 27 ASN Chi-restraints excluded: chain e residue 70 ASN Chi-restraints excluded: chain e residue 83 LEU Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 81 GLU Chi-restraints excluded: chain f residue 96 MET Chi-restraints excluded: chain f residue 97 LEU Chi-restraints excluded: chain g residue 19 ASN Chi-restraints excluded: chain g residue 57 CYS Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 95 MET Chi-restraints excluded: chain h residue 30 GLU Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 65 GLN Chi-restraints excluded: chain h residue 79 VAL Chi-restraints excluded: chain h residue 104 THR Chi-restraints excluded: chain i residue 19 SER Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 62 LYS Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 22 CYS Chi-restraints excluded: chain j residue 37 CYS Chi-restraints excluded: chain k residue 62 GLU Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain m residue 84 SER Chi-restraints excluded: chain m residue 92 THR Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain p residue 8 VAL Chi-restraints excluded: chain p residue 32 SER Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 60 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 687 optimal weight: 9.9990 chunk 468 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 614 optimal weight: 0.6980 chunk 340 optimal weight: 6.9990 chunk 704 optimal weight: 0.8980 chunk 570 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 421 optimal weight: 1.9990 chunk 740 optimal weight: 10.0000 chunk 208 optimal weight: 8.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN B 68 HIS B 191 GLN B 200 GLN C 47 GLN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 HIS ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 HIS J 6 ASN M 103 ASN ** N 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 45 HIS g 19 ASN h 65 GLN ** k 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 33 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 115172 Z= 0.245 Angle : 0.598 12.680 169112 Z= 0.309 Chirality : 0.038 0.260 21128 Planarity : 0.005 0.073 11007 Dihedral : 22.543 179.647 49859 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.94 % Favored : 94.64 % Rotamer: Outliers : 5.46 % Allowed : 17.03 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.15 (0.10), residues: 5785 helix: 0.38 (0.12), residues: 1916 sheet: -1.33 (0.17), residues: 813 loop : -1.34 (0.10), residues: 3056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP T 159 HIS 0.009 0.001 HIS H 126 PHE 0.014 0.002 PHE C 267 TYR 0.025 0.002 TYR F 186 ARG 0.007 0.001 ARG g 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1310 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 1041 time to evaluate : 5.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.7424 (ttm110) cc_final: 0.7215 (ttm110) REVERT: A 44 MET cc_start: 0.7587 (ttp) cc_final: 0.6955 (ttt) REVERT: A 46 LYS cc_start: 0.7287 (tptm) cc_final: 0.6664 (ttpt) REVERT: A 135 ARG cc_start: 0.6909 (ttm170) cc_final: 0.6510 (mtp85) REVERT: A 201 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8260 (mttp) REVERT: B 53 MET cc_start: 0.8793 (ttt) cc_final: 0.8339 (ttm) REVERT: B 64 ASN cc_start: 0.8086 (t0) cc_final: 0.7725 (t0) REVERT: B 84 MET cc_start: 0.7827 (ptm) cc_final: 0.7391 (ptm) REVERT: B 146 GLN cc_start: 0.7000 (mt0) cc_final: 0.6577 (mt0) REVERT: B 148 GLU cc_start: 0.7351 (tt0) cc_final: 0.6964 (mm-30) REVERT: B 185 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.7005 (mmmt) REVERT: B 219 LYS cc_start: 0.6924 (mmmt) cc_final: 0.6393 (mptt) REVERT: B 295 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7715 (mt-10) REVERT: B 319 SER cc_start: 0.6892 (m) cc_final: 0.6540 (t) REVERT: B 324 LYS cc_start: 0.8472 (mptt) cc_final: 0.7989 (mmmt) REVERT: B 340 LYS cc_start: 0.6442 (mtmm) cc_final: 0.6040 (mptt) REVERT: B 375 GLU cc_start: 0.7978 (tt0) cc_final: 0.7523 (tp30) REVERT: B 377 ASN cc_start: 0.7387 (OUTLIER) cc_final: 0.6696 (p0) REVERT: B 395 LYS cc_start: 0.7837 (pttt) cc_final: 0.6758 (mmmt) REVERT: B 406 LYS cc_start: 0.4125 (OUTLIER) cc_final: 0.3301 (ttmt) REVERT: C 4 GLN cc_start: 0.6496 (pt0) cc_final: 0.5432 (pm20) REVERT: C 36 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7180 (tt0) REVERT: C 153 ASP cc_start: 0.7324 (t70) cc_final: 0.6889 (t70) REVERT: C 158 ILE cc_start: 0.6722 (mt) cc_final: 0.6498 (mm) REVERT: C 202 LYS cc_start: 0.7842 (mmtt) cc_final: 0.7375 (mmmt) REVERT: C 211 ASP cc_start: 0.7420 (p0) cc_final: 0.7213 (p0) REVERT: C 268 SER cc_start: 0.7949 (m) cc_final: 0.7714 (t) REVERT: C 303 LYS cc_start: 0.7899 (mttt) cc_final: 0.7358 (pttm) REVERT: C 329 ARG cc_start: 0.7859 (mtt180) cc_final: 0.7351 (mmt180) REVERT: C 340 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7113 (tp30) REVERT: D 67 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6890 (mt-10) REVERT: D 88 LYS cc_start: 0.8068 (mttt) cc_final: 0.7594 (ptmt) REVERT: D 157 MET cc_start: 0.8009 (ttt) cc_final: 0.7383 (tmm) REVERT: D 158 LYS cc_start: 0.6808 (mttt) cc_final: 0.6434 (tptt) REVERT: D 223 GLU cc_start: 0.6816 (tt0) cc_final: 0.6313 (pm20) REVERT: D 224 LYS cc_start: 0.7156 (mttt) cc_final: 0.6782 (mttt) REVERT: D 233 VAL cc_start: 0.7908 (t) cc_final: 0.7639 (m) REVERT: D 254 ARG cc_start: 0.6681 (mtp85) cc_final: 0.6241 (mtt-85) REVERT: D 279 LYS cc_start: 0.6978 (mmmt) cc_final: 0.6585 (mttp) REVERT: D 280 LYS cc_start: 0.8023 (tptt) cc_final: 0.7577 (tttt) REVERT: E 73 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.5989 (mtm-85) REVERT: E 80 GLN cc_start: 0.6765 (mt0) cc_final: 0.6539 (mm-40) REVERT: E 86 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6575 (mtpt) REVERT: E 96 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6257 (pm20) REVERT: E 101 TYR cc_start: 0.7813 (m-80) cc_final: 0.7524 (m-80) REVERT: E 142 LYS cc_start: 0.7700 (pmtt) cc_final: 0.6646 (tttm) REVERT: F 24 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.6089 (mm) REVERT: F 79 LYS cc_start: 0.7879 (mmtm) cc_final: 0.7396 (mtmt) REVERT: F 102 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7209 (mp) REVERT: F 122 GLU cc_start: 0.6838 (tt0) cc_final: 0.6413 (tt0) REVERT: F 163 ASN cc_start: 0.8211 (m-40) cc_final: 0.7687 (m-40) REVERT: F 164 GLN cc_start: 0.8360 (tp-100) cc_final: 0.7765 (tp40) REVERT: F 203 LYS cc_start: 0.8220 (mttt) cc_final: 0.7533 (mtmt) REVERT: F 228 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7071 (mt-10) REVERT: G 45 LYS cc_start: 0.7517 (tptp) cc_final: 0.7261 (ttmt) REVERT: G 48 GLN cc_start: 0.6074 (mt0) cc_final: 0.5768 (mt0) REVERT: G 54 ARG cc_start: 0.7720 (tpp-160) cc_final: 0.7058 (mmm-85) REVERT: G 59 ARG cc_start: 0.7334 (mmt-90) cc_final: 0.6844 (mmt-90) REVERT: G 67 ASN cc_start: 0.7472 (t160) cc_final: 0.7160 (t0) REVERT: G 86 GLU cc_start: 0.7105 (tt0) cc_final: 0.6513 (mt-10) REVERT: G 218 GLU cc_start: 0.6842 (tp30) cc_final: 0.6197 (pt0) REVERT: H 8 GLN cc_start: 0.6764 (pt0) cc_final: 0.6488 (pp30) REVERT: H 21 VAL cc_start: 0.7787 (t) cc_final: 0.7216 (p) REVERT: H 22 LYS cc_start: 0.6922 (tttt) cc_final: 0.6426 (mptt) REVERT: H 84 LYS cc_start: 0.7680 (tttm) cc_final: 0.6980 (pttt) REVERT: H 97 LYS cc_start: 0.6444 (tttt) cc_final: 0.6022 (ttpp) REVERT: H 175 LYS cc_start: 0.6272 (OUTLIER) cc_final: 0.5950 (ptpt) REVERT: I 33 ARG cc_start: 0.7668 (mtt180) cc_final: 0.7455 (mmm160) REVERT: I 55 LEU cc_start: 0.7532 (mt) cc_final: 0.7135 (mt) REVERT: I 156 SER cc_start: 0.8529 (p) cc_final: 0.8250 (p) REVERT: I 185 GLN cc_start: 0.6975 (tp40) cc_final: 0.6725 (tm-30) REVERT: I 192 ASP cc_start: 0.5680 (t0) cc_final: 0.5322 (t0) REVERT: J 45 ARG cc_start: 0.5746 (mtt180) cc_final: 0.4888 (mmt90) REVERT: J 100 PHE cc_start: 0.7671 (p90) cc_final: 0.7302 (p90) REVERT: J 110 LEU cc_start: 0.5301 (OUTLIER) cc_final: 0.4467 (tp) REVERT: J 136 ARG cc_start: 0.6847 (mmt-90) cc_final: 0.6459 (mpt180) REVERT: L 11 ASP cc_start: 0.8022 (p0) cc_final: 0.7782 (p0) REVERT: L 44 LYS cc_start: 0.8185 (mttt) cc_final: 0.7982 (mtpp) REVERT: L 68 LYS cc_start: 0.7562 (mmtp) cc_final: 0.6968 (mtmt) REVERT: L 91 ARG cc_start: 0.7366 (ttp-110) cc_final: 0.6561 (mtt90) REVERT: L 93 GLN cc_start: 0.7089 (mm110) cc_final: 0.6588 (mt0) REVERT: L 110 LYS cc_start: 0.7381 (mttt) cc_final: 0.7021 (mmmt) REVERT: L 130 GLU cc_start: 0.6307 (pt0) cc_final: 0.5807 (mp0) REVERT: L 177 GLU cc_start: 0.5837 (mt-10) cc_final: 0.5590 (mm-30) REVERT: M 50 ILE cc_start: 0.6823 (OUTLIER) cc_final: 0.6605 (tt) REVERT: M 63 LYS cc_start: 0.7983 (ttpt) cc_final: 0.7062 (mmtp) REVERT: M 116 LYS cc_start: 0.6768 (mttt) cc_final: 0.6361 (mtpt) REVERT: N 26 ARG cc_start: 0.6001 (mmt90) cc_final: 0.5555 (mtm-85) REVERT: N 33 LEU cc_start: 0.7728 (mt) cc_final: 0.7469 (mt) REVERT: N 37 VAL cc_start: 0.7996 (OUTLIER) cc_final: 0.7688 (m) REVERT: N 51 MET cc_start: 0.8600 (mmm) cc_final: 0.8199 (mmt) REVERT: N 59 MET cc_start: 0.8486 (tpp) cc_final: 0.7646 (mmt) REVERT: N 108 LYS cc_start: 0.8063 (ttmt) cc_final: 0.7829 (tmmt) REVERT: N 117 ASN cc_start: 0.8658 (m-40) cc_final: 0.8195 (t0) REVERT: N 145 ASP cc_start: 0.7771 (t70) cc_final: 0.7457 (t70) REVERT: O 40 GLU cc_start: 0.7459 (pt0) cc_final: 0.6983 (pt0) REVERT: O 104 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6845 (mt-10) REVERT: O 135 LYS cc_start: 0.7501 (mmtt) cc_final: 0.6904 (mtmt) REVERT: O 176 ARG cc_start: 0.6709 (ttm-80) cc_final: 0.6024 (tmm-80) REVERT: O 180 ILE cc_start: 0.6491 (mt) cc_final: 0.6159 (mm) REVERT: O 196 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6488 (mm-30) REVERT: P 17 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.7830 (mtpp) REVERT: P 24 ARG cc_start: 0.8472 (mtp180) cc_final: 0.8223 (mtm180) REVERT: P 32 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7273 (mm-30) REVERT: P 65 LYS cc_start: 0.8330 (pttt) cc_final: 0.7953 (pttt) REVERT: P 76 GLU cc_start: 0.7419 (pt0) cc_final: 0.6708 (pt0) REVERT: P 94 LYS cc_start: 0.6785 (mttt) cc_final: 0.6125 (ttpp) REVERT: P 131 ARG cc_start: 0.8065 (mtt-85) cc_final: 0.6658 (mtm180) REVERT: Q 13 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8168 (mt0) REVERT: Q 16 GLU cc_start: 0.8051 (pt0) cc_final: 0.7348 (pm20) REVERT: Q 26 MET cc_start: 0.7089 (mtp) cc_final: 0.6446 (tpt) REVERT: Q 95 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7694 (mtpp) REVERT: Q 147 ASN cc_start: 0.7953 (t0) cc_final: 0.7713 (m-40) REVERT: R 5 LYS cc_start: 0.8198 (tttm) cc_final: 0.7963 (ttmm) REVERT: R 28 GLU cc_start: 0.7143 (mp0) cc_final: 0.6539 (mp0) REVERT: R 34 MET cc_start: 0.6909 (mpp) cc_final: 0.6700 (mpp) REVERT: R 36 ASN cc_start: 0.7165 (m-40) cc_final: 0.6635 (p0) REVERT: R 39 GLN cc_start: 0.7039 (mm110) cc_final: 0.6490 (tm-30) REVERT: R 114 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7230 (mp0) REVERT: R 136 ARG cc_start: 0.6165 (ttm170) cc_final: 0.5782 (ttm110) REVERT: R 141 HIS cc_start: 0.7570 (OUTLIER) cc_final: 0.6669 (t70) REVERT: S 16 LYS cc_start: 0.7739 (mttt) cc_final: 0.7375 (tppt) REVERT: S 54 HIS cc_start: 0.7903 (OUTLIER) cc_final: 0.7425 (p90) REVERT: S 81 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.7188 (tmm-80) REVERT: S 92 GLU cc_start: 0.8029 (pt0) cc_final: 0.7503 (pt0) REVERT: S 116 SER cc_start: 0.8023 (t) cc_final: 0.7599 (p) REVERT: S 147 LYS cc_start: 0.7415 (mttt) cc_final: 0.6880 (mtmm) REVERT: T 21 LYS cc_start: 0.7419 (mttt) cc_final: 0.6935 (mmtt) REVERT: T 77 LYS cc_start: 0.8747 (mttp) cc_final: 0.7912 (mtpt) REVERT: T 156 ARG cc_start: 0.6584 (mtt90) cc_final: 0.6271 (mmt90) REVERT: U 18 PHE cc_start: 0.7078 (OUTLIER) cc_final: 0.6314 (p90) REVERT: U 23 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6665 (mt-10) REVERT: U 32 MET cc_start: 0.7805 (mtt) cc_final: 0.7498 (ttm) REVERT: U 76 PHE cc_start: 0.7932 (t80) cc_final: 0.7447 (t80) REVERT: U 99 ARG cc_start: 0.6613 (mtp85) cc_final: 0.5849 (ptp-170) REVERT: V 123 LYS cc_start: 0.7101 (tttp) cc_final: 0.6816 (tptt) REVERT: X 46 LYS cc_start: 0.7047 (tttm) cc_final: 0.6579 (mmtm) REVERT: X 49 LYS cc_start: 0.8001 (mttt) cc_final: 0.7308 (mtpp) REVERT: X 66 THR cc_start: 0.7168 (OUTLIER) cc_final: 0.6906 (t) REVERT: X 71 THR cc_start: 0.6781 (m) cc_final: 0.6463 (p) REVERT: X 78 ASN cc_start: 0.7769 (t0) cc_final: 0.7499 (t0) REVERT: X 87 LYS cc_start: 0.8498 (mttt) cc_final: 0.7665 (mmmt) REVERT: X 115 LYS cc_start: 0.8160 (mttt) cc_final: 0.7694 (mtmt) REVERT: Y 23 LYS cc_start: 0.7141 (mttt) cc_final: 0.6567 (pttm) REVERT: Y 57 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.6490 (ptp) REVERT: Y 80 ILE cc_start: 0.8129 (mt) cc_final: 0.7780 (pt) REVERT: Y 95 VAL cc_start: 0.7109 (t) cc_final: 0.6811 (m) REVERT: Z 43 MET cc_start: 0.7386 (ttp) cc_final: 0.7170 (ttp) REVERT: Z 47 LYS cc_start: 0.6531 (mttt) cc_final: 0.5898 (tmtt) REVERT: a 22 VAL cc_start: 0.8010 (OUTLIER) cc_final: 0.7792 (m) REVERT: a 55 LYS cc_start: 0.8471 (tttt) cc_final: 0.8174 (ttmt) REVERT: a 105 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7168 (m-30) REVERT: a 109 ASN cc_start: 0.8351 (m-40) cc_final: 0.7705 (m110) REVERT: a 122 LYS cc_start: 0.7932 (mttt) cc_final: 0.7598 (tptp) REVERT: a 137 GLU cc_start: 0.7081 (tt0) cc_final: 0.5867 (pt0) REVERT: b 23 LYS cc_start: 0.7589 (tttt) cc_final: 0.7098 (pttm) REVERT: c 47 PHE cc_start: 0.7537 (m-80) cc_final: 0.7042 (m-80) REVERT: c 56 ARG cc_start: 0.6917 (tpt-90) cc_final: 0.6636 (tpt-90) REVERT: d 42 LYS cc_start: 0.7124 (tttt) cc_final: 0.6824 (ttmt) REVERT: d 43 MET cc_start: 0.7467 (tpp) cc_final: 0.7224 (tpp) REVERT: d 94 LYS cc_start: 0.6987 (OUTLIER) cc_final: 0.6776 (tptt) REVERT: e 20 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7397 (ttt180) REVERT: e 22 GLN cc_start: 0.8326 (mm-40) cc_final: 0.7840 (mt0) REVERT: e 25 LEU cc_start: 0.7937 (mp) cc_final: 0.7619 (mm) REVERT: e 98 SER cc_start: 0.8888 (m) cc_final: 0.8534 (t) REVERT: e 104 LYS cc_start: 0.7019 (tttm) cc_final: 0.6515 (mmmt) REVERT: e 111 LYS cc_start: 0.7945 (tttt) cc_final: 0.7383 (mmmt) REVERT: e 119 GLU cc_start: 0.7885 (tt0) cc_final: 0.7000 (tp30) REVERT: f 6 LYS cc_start: 0.6894 (ptmt) cc_final: 0.6544 (mmtt) REVERT: f 48 LYS cc_start: 0.7577 (mtpp) cc_final: 0.7023 (mtmt) REVERT: f 59 GLU cc_start: 0.7218 (tt0) cc_final: 0.6490 (mp0) REVERT: f 81 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6559 (mt-10) REVERT: f 88 MET cc_start: 0.8030 (mmm) cc_final: 0.7795 (mmt) REVERT: f 97 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7000 (pp) REVERT: g 39 ARG cc_start: 0.8127 (mmm160) cc_final: 0.7418 (mtp180) REVERT: h 34 GLN cc_start: 0.5579 (mt0) cc_final: 0.5081 (tm-30) REVERT: h 46 GLU cc_start: 0.7177 (tt0) cc_final: 0.6863 (mt-10) REVERT: h 65 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7430 (tt0) REVERT: h 69 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.6481 (tt) REVERT: h 72 LYS cc_start: 0.7115 (ttpp) cc_final: 0.6785 (tttp) REVERT: j 50 GLU cc_start: 0.8367 (pt0) cc_final: 0.7811 (pt0) REVERT: j 64 MET cc_start: 0.7903 (mtm) cc_final: 0.7571 (mtt) REVERT: o 21 CYS cc_start: 0.8371 (p) cc_final: 0.7733 (p) REVERT: p 13 LYS cc_start: 0.7873 (pttt) cc_final: 0.7365 (pttt) REVERT: p 24 LYS cc_start: 0.7088 (tttt) cc_final: 0.6880 (ttmt) REVERT: p 34 ARG cc_start: 0.7216 (mtt90) cc_final: 0.6918 (mtt90) outliers start: 269 outliers final: 204 residues processed: 1202 average time/residue: 1.0075 time to fit residues: 2028.1872 Evaluate side-chains 1245 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1009 time to evaluate : 6.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 187 CYS Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 64 ARG Chi-restraints excluded: chain H residue 173 LYS Chi-restraints excluded: chain H residue 175 LYS Chi-restraints excluded: chain H residue 176 ASP Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain I residue 21 ARG Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 130 ASN Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain I residue 193 CYS Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain L residue 6 ASN Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 126 SER Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 141 THR Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain P residue 17 LYS Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 32 GLU Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 132 ILE Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain P residue 151 ILE Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain Q residue 67 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 95 LYS Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 141 HIS Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain S residue 2 SER Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 54 HIS Chi-restraints excluded: chain S residue 81 ARG Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain S residue 121 SER Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain S residue 150 MET Chi-restraints excluded: chain S residue 151 LEU Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain V residue 28 CYS Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain V residue 112 MET Chi-restraints excluded: chain V residue 117 ILE Chi-restraints excluded: chain V residue 135 VAL Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 137 ILE Chi-restraints excluded: chain Y residue 2 VAL Chi-restraints excluded: chain Y residue 13 ARG Chi-restraints excluded: chain Y residue 25 ASP Chi-restraints excluded: chain Y residue 31 MET Chi-restraints excluded: chain Y residue 57 MET Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 104 LEU Chi-restraints excluded: chain Z residue 114 LEU Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 43 THR Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 86 GLU Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain a residue 96 LYS Chi-restraints excluded: chain a residue 105 ASP Chi-restraints excluded: chain b residue 11 ASN Chi-restraints excluded: chain b residue 13 SER Chi-restraints excluded: chain c residue 18 SER Chi-restraints excluded: chain c residue 44 LEU Chi-restraints excluded: chain c residue 101 SER Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 94 LYS Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 15 THR Chi-restraints excluded: chain e residue 20 ARG Chi-restraints excluded: chain e residue 27 ASN Chi-restraints excluded: chain e residue 70 ASN Chi-restraints excluded: chain e residue 83 LEU Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 30 LEU Chi-restraints excluded: chain f residue 81 GLU Chi-restraints excluded: chain f residue 96 MET Chi-restraints excluded: chain f residue 97 LEU Chi-restraints excluded: chain g residue 19 ASN Chi-restraints excluded: chain g residue 57 CYS Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 95 MET Chi-restraints excluded: chain h residue 30 GLU Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 65 GLN Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 78 LEU Chi-restraints excluded: chain h residue 79 VAL Chi-restraints excluded: chain h residue 104 THR Chi-restraints excluded: chain i residue 19 SER Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 62 LYS Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 22 CYS Chi-restraints excluded: chain k residue 32 ASN Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 51 ILE Chi-restraints excluded: chain m residue 84 SER Chi-restraints excluded: chain m residue 92 THR Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain o residue 62 THR Chi-restraints excluded: chain o residue 92 THR Chi-restraints excluded: chain p residue 8 VAL Chi-restraints excluded: chain p residue 32 SER Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 60 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 277 optimal weight: 20.0000 chunk 743 optimal weight: 0.8980 chunk 163 optimal weight: 10.0000 chunk 484 optimal weight: 0.9990 chunk 203 optimal weight: 7.9990 chunk 826 optimal weight: 0.0470 chunk 685 optimal weight: 0.9990 chunk 382 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 273 optimal weight: 10.0000 chunk 433 optimal weight: 2.9990 overall best weight: 1.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 142 ASN B 68 HIS C 4 GLN C 47 GLN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 ASN ** N 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 23 GLN ** S 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 140 HIS T 148 GLN a 66 ASN g 19 ASN h 65 GLN ** k 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 33 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 115172 Z= 0.157 Angle : 0.555 12.641 169112 Z= 0.288 Chirality : 0.035 0.249 21128 Planarity : 0.004 0.070 11007 Dihedral : 22.533 179.818 49859 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.49 % Favored : 95.06 % Rotamer: Outliers : 5.30 % Allowed : 18.16 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.11), residues: 5785 helix: 0.56 (0.12), residues: 1918 sheet: -1.21 (0.17), residues: 822 loop : -1.25 (0.11), residues: 3045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP T 159 HIS 0.019 0.001 HIS T 140 PHE 0.013 0.001 PHE E 28 TYR 0.025 0.001 TYR F 186 ARG 0.011 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1306 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1045 time to evaluate : 5.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7481 (ttp) cc_final: 0.6782 (ttt) REVERT: A 46 LYS cc_start: 0.7266 (tptm) cc_final: 0.6637 (ttpt) REVERT: A 135 ARG cc_start: 0.6839 (ttm170) cc_final: 0.6516 (mtp85) REVERT: A 174 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7364 (mt-10) REVERT: A 201 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8239 (mttp) REVERT: B 53 MET cc_start: 0.8688 (ttt) cc_final: 0.8460 (ttm) REVERT: B 64 ASN cc_start: 0.8065 (t0) cc_final: 0.7707 (t0) REVERT: B 71 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7772 (mt-10) REVERT: B 84 MET cc_start: 0.7688 (ptm) cc_final: 0.7331 (ptm) REVERT: B 89 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7507 (mt) REVERT: B 146 GLN cc_start: 0.6931 (mt0) cc_final: 0.6548 (mt0) REVERT: B 148 GLU cc_start: 0.7277 (tt0) cc_final: 0.6831 (mm-30) REVERT: B 219 LYS cc_start: 0.6750 (mmmt) cc_final: 0.6257 (mptt) REVERT: B 228 THR cc_start: 0.7230 (m) cc_final: 0.6893 (p) REVERT: B 295 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7629 (mt-10) REVERT: B 319 SER cc_start: 0.6862 (m) cc_final: 0.6520 (t) REVERT: B 324 LYS cc_start: 0.8462 (mptt) cc_final: 0.7987 (mmmt) REVERT: B 340 LYS cc_start: 0.6483 (mtmm) cc_final: 0.6142 (mptt) REVERT: B 345 MET cc_start: 0.8367 (ttp) cc_final: 0.7778 (ttm) REVERT: B 375 GLU cc_start: 0.7727 (tt0) cc_final: 0.7511 (tp30) REVERT: B 377 ASN cc_start: 0.7384 (OUTLIER) cc_final: 0.6692 (p0) REVERT: B 395 LYS cc_start: 0.7788 (pttt) cc_final: 0.6683 (mmmt) REVERT: B 406 LYS cc_start: 0.3851 (OUTLIER) cc_final: 0.3293 (ttmt) REVERT: C 4 GLN cc_start: 0.6397 (pt0) cc_final: 0.5364 (pm20) REVERT: C 11 GLN cc_start: 0.6392 (tt0) cc_final: 0.5706 (mt0) REVERT: C 153 ASP cc_start: 0.7332 (t70) cc_final: 0.6904 (t70) REVERT: C 202 LYS cc_start: 0.7853 (mmtt) cc_final: 0.7383 (mmmt) REVERT: C 265 LYS cc_start: 0.6455 (mmmt) cc_final: 0.6045 (mmtt) REVERT: C 268 SER cc_start: 0.7985 (m) cc_final: 0.7718 (t) REVERT: C 303 LYS cc_start: 0.7982 (mttt) cc_final: 0.7427 (pttm) REVERT: C 329 ARG cc_start: 0.7865 (mtt180) cc_final: 0.7332 (mmt180) REVERT: C 340 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7097 (tp30) REVERT: D 4 LYS cc_start: 0.6883 (mttt) cc_final: 0.6225 (mppt) REVERT: D 67 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6825 (mt-10) REVERT: D 88 LYS cc_start: 0.7656 (mttt) cc_final: 0.7206 (ptmt) REVERT: D 157 MET cc_start: 0.8038 (ttt) cc_final: 0.7458 (tmm) REVERT: D 158 LYS cc_start: 0.6745 (mttt) cc_final: 0.6338 (tptt) REVERT: D 223 GLU cc_start: 0.6782 (tt0) cc_final: 0.6260 (pm20) REVERT: D 224 LYS cc_start: 0.7082 (mttt) cc_final: 0.6685 (mttt) REVERT: D 233 VAL cc_start: 0.7907 (t) cc_final: 0.7637 (m) REVERT: D 254 ARG cc_start: 0.6648 (mtp85) cc_final: 0.6239 (mtt-85) REVERT: D 279 LYS cc_start: 0.6989 (mmmt) cc_final: 0.6594 (mttp) REVERT: D 280 LYS cc_start: 0.8032 (tptt) cc_final: 0.7623 (tptm) REVERT: D 308 LYS cc_start: 0.4998 (ttpt) cc_final: 0.4749 (ttpt) REVERT: E 73 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7774 (mmt90) REVERT: E 80 GLN cc_start: 0.6760 (mt0) cc_final: 0.6533 (mm-40) REVERT: E 86 LYS cc_start: 0.7119 (OUTLIER) cc_final: 0.6585 (mtpt) REVERT: E 96 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.6261 (pm20) REVERT: E 101 TYR cc_start: 0.7810 (m-80) cc_final: 0.7509 (m-80) REVERT: E 142 LYS cc_start: 0.7684 (pmtt) cc_final: 0.6581 (tttm) REVERT: F 24 LEU cc_start: 0.6201 (OUTLIER) cc_final: 0.5996 (mt) REVERT: F 26 LYS cc_start: 0.6203 (ttmm) cc_final: 0.5839 (ttmm) REVERT: F 79 LYS cc_start: 0.7949 (mmtm) cc_final: 0.7351 (mtmt) REVERT: F 102 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7234 (mp) REVERT: F 122 GLU cc_start: 0.6829 (tt0) cc_final: 0.6420 (tt0) REVERT: F 163 ASN cc_start: 0.8134 (m-40) cc_final: 0.7672 (m-40) REVERT: F 164 GLN cc_start: 0.8344 (tp-100) cc_final: 0.7789 (tp40) REVERT: F 203 LYS cc_start: 0.8212 (mttt) cc_final: 0.7547 (mtmt) REVERT: G 48 GLN cc_start: 0.5826 (mt0) cc_final: 0.5517 (mt0) REVERT: G 54 ARG cc_start: 0.7717 (tpp-160) cc_final: 0.7053 (mmm-85) REVERT: G 59 ARG cc_start: 0.7308 (mmt-90) cc_final: 0.6849 (mmt-90) REVERT: G 67 ASN cc_start: 0.7403 (t160) cc_final: 0.7064 (t0) REVERT: G 86 GLU cc_start: 0.7069 (tt0) cc_final: 0.6464 (mt-10) REVERT: G 218 GLU cc_start: 0.6868 (tp30) cc_final: 0.6173 (pt0) REVERT: H 8 GLN cc_start: 0.6639 (pt0) cc_final: 0.6391 (pt0) REVERT: H 22 LYS cc_start: 0.6913 (tttt) cc_final: 0.6411 (mptt) REVERT: H 84 LYS cc_start: 0.7599 (tttm) cc_final: 0.6947 (pttt) REVERT: H 113 GLU cc_start: 0.5753 (pm20) cc_final: 0.5226 (pm20) REVERT: H 128 GLU cc_start: 0.5212 (tp30) cc_final: 0.4811 (tp30) REVERT: H 175 LYS cc_start: 0.6223 (OUTLIER) cc_final: 0.5895 (ptpt) REVERT: I 55 LEU cc_start: 0.7358 (mt) cc_final: 0.7029 (mt) REVERT: I 156 SER cc_start: 0.8524 (p) cc_final: 0.8239 (p) REVERT: I 185 GLN cc_start: 0.6918 (tp40) cc_final: 0.6643 (tm-30) REVERT: I 192 ASP cc_start: 0.5903 (t0) cc_final: 0.5660 (t0) REVERT: J 45 ARG cc_start: 0.5764 (mtt180) cc_final: 0.4906 (mmt90) REVERT: J 100 PHE cc_start: 0.7597 (p90) cc_final: 0.7214 (p90) REVERT: J 110 LEU cc_start: 0.5116 (OUTLIER) cc_final: 0.4337 (tp) REVERT: J 136 ARG cc_start: 0.6740 (mmt-90) cc_final: 0.6417 (mpt180) REVERT: L 11 ASP cc_start: 0.8139 (p0) cc_final: 0.7913 (p0) REVERT: L 68 LYS cc_start: 0.7572 (mmtp) cc_final: 0.6974 (mtmt) REVERT: L 91 ARG cc_start: 0.7407 (ttp-110) cc_final: 0.6601 (mtt90) REVERT: L 93 GLN cc_start: 0.7024 (mm110) cc_final: 0.6523 (mt0) REVERT: L 110 LYS cc_start: 0.7443 (mttt) cc_final: 0.7056 (mmmt) REVERT: L 130 GLU cc_start: 0.6455 (pt0) cc_final: 0.5649 (mp0) REVERT: L 177 GLU cc_start: 0.5864 (mt-10) cc_final: 0.5622 (mm-30) REVERT: M 48 GLN cc_start: 0.7914 (pm20) cc_final: 0.7410 (pm20) REVERT: M 63 LYS cc_start: 0.7989 (ttpt) cc_final: 0.7141 (mmtp) REVERT: M 116 LYS cc_start: 0.6771 (mttt) cc_final: 0.6409 (mtpt) REVERT: N 26 ARG cc_start: 0.5994 (OUTLIER) cc_final: 0.5671 (mtm-85) REVERT: N 33 LEU cc_start: 0.7649 (mt) cc_final: 0.7380 (mt) REVERT: N 37 VAL cc_start: 0.7896 (OUTLIER) cc_final: 0.7680 (m) REVERT: N 51 MET cc_start: 0.8615 (mmm) cc_final: 0.8228 (mmt) REVERT: N 59 MET cc_start: 0.8429 (tpp) cc_final: 0.7862 (mtp) REVERT: N 108 LYS cc_start: 0.8052 (ttmt) cc_final: 0.7818 (tmmt) REVERT: N 117 ASN cc_start: 0.8579 (m-40) cc_final: 0.8189 (t0) REVERT: N 177 VAL cc_start: 0.7913 (t) cc_final: 0.7632 (m) REVERT: O 40 GLU cc_start: 0.7397 (pt0) cc_final: 0.6952 (pt0) REVERT: O 104 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6751 (mt-10) REVERT: O 176 ARG cc_start: 0.6719 (ttm-80) cc_final: 0.5998 (tmm-80) REVERT: O 180 ILE cc_start: 0.6425 (mt) cc_final: 0.6093 (mm) REVERT: O 196 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6491 (mm-30) REVERT: P 17 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.7839 (mtpp) REVERT: P 24 ARG cc_start: 0.8340 (mtp180) cc_final: 0.8005 (mtm180) REVERT: P 32 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7289 (mm-30) REVERT: P 65 LYS cc_start: 0.8313 (pttt) cc_final: 0.7946 (pttt) REVERT: P 76 GLU cc_start: 0.7412 (pt0) cc_final: 0.6634 (pt0) REVERT: P 94 LYS cc_start: 0.6743 (mttt) cc_final: 0.6108 (ttpp) REVERT: P 131 ARG cc_start: 0.8046 (mtt-85) cc_final: 0.6676 (mtm180) REVERT: Q 13 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8186 (mt0) REVERT: Q 26 MET cc_start: 0.7195 (mtp) cc_final: 0.6470 (tpt) REVERT: Q 95 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7589 (mtpp) REVERT: Q 147 ASN cc_start: 0.7920 (t0) cc_final: 0.7700 (m-40) REVERT: Q 162 ARG cc_start: 0.7868 (mtp85) cc_final: 0.7516 (tpp80) REVERT: R 5 LYS cc_start: 0.8193 (tttm) cc_final: 0.7960 (ttmm) REVERT: R 28 GLU cc_start: 0.7093 (mp0) cc_final: 0.6526 (mp0) REVERT: R 36 ASN cc_start: 0.7348 (m-40) cc_final: 0.6719 (p0) REVERT: R 39 GLN cc_start: 0.6889 (mm110) cc_final: 0.6299 (tm-30) REVERT: R 114 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7239 (mp0) REVERT: R 136 ARG cc_start: 0.6191 (ttm170) cc_final: 0.5848 (ttm110) REVERT: R 141 HIS cc_start: 0.7537 (OUTLIER) cc_final: 0.6692 (t70) REVERT: S 16 LYS cc_start: 0.7729 (mttt) cc_final: 0.7391 (tppt) REVERT: S 81 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7146 (tmm-80) REVERT: S 85 ASN cc_start: 0.6602 (OUTLIER) cc_final: 0.6035 (t0) REVERT: S 92 GLU cc_start: 0.8018 (pt0) cc_final: 0.7529 (pt0) REVERT: S 116 SER cc_start: 0.8006 (t) cc_final: 0.7574 (p) REVERT: S 147 LYS cc_start: 0.7384 (mttt) cc_final: 0.6880 (mtmm) REVERT: T 21 LYS cc_start: 0.7396 (mttt) cc_final: 0.6947 (mmtt) REVERT: T 77 LYS cc_start: 0.8596 (mttp) cc_final: 0.7881 (mtpt) REVERT: T 156 ARG cc_start: 0.6553 (mtt90) cc_final: 0.6255 (mmt90) REVERT: U 18 PHE cc_start: 0.6997 (OUTLIER) cc_final: 0.6243 (p90) REVERT: U 23 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6615 (mt-10) REVERT: U 32 MET cc_start: 0.7803 (mtt) cc_final: 0.7502 (ttm) REVERT: U 76 PHE cc_start: 0.7897 (t80) cc_final: 0.7433 (t80) REVERT: U 99 ARG cc_start: 0.6694 (mtp180) cc_final: 0.6050 (ptp-170) REVERT: V 14 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.7230 (m-80) REVERT: V 36 ASN cc_start: 0.8144 (m110) cc_final: 0.7796 (m-40) REVERT: V 43 ARG cc_start: 0.6852 (ttm170) cc_final: 0.6628 (mmm-85) REVERT: V 96 ILE cc_start: 0.7052 (OUTLIER) cc_final: 0.6780 (tt) REVERT: V 123 LYS cc_start: 0.7080 (tttp) cc_final: 0.6508 (tttm) REVERT: X 46 LYS cc_start: 0.7174 (tttm) cc_final: 0.6605 (mmtm) REVERT: X 49 LYS cc_start: 0.7939 (mttt) cc_final: 0.7212 (mtpp) REVERT: X 66 THR cc_start: 0.7147 (OUTLIER) cc_final: 0.6893 (t) REVERT: X 71 THR cc_start: 0.6759 (m) cc_final: 0.6429 (p) REVERT: X 78 ASN cc_start: 0.7728 (t0) cc_final: 0.7456 (t0) REVERT: X 87 LYS cc_start: 0.8485 (mttt) cc_final: 0.7648 (mmmt) REVERT: X 115 LYS cc_start: 0.8155 (mttt) cc_final: 0.7698 (mtmt) REVERT: Y 23 LYS cc_start: 0.7282 (mttt) cc_final: 0.6685 (pttm) REVERT: Y 57 MET cc_start: 0.6755 (OUTLIER) cc_final: 0.6504 (ptp) REVERT: Y 80 ILE cc_start: 0.8168 (mt) cc_final: 0.7917 (pt) REVERT: Y 95 VAL cc_start: 0.7038 (t) cc_final: 0.6784 (m) REVERT: Z 47 LYS cc_start: 0.6349 (mttt) cc_final: 0.5747 (tmtt) REVERT: Z 56 MET cc_start: 0.5592 (tpt) cc_final: 0.5121 (ttm) REVERT: a 22 VAL cc_start: 0.7821 (OUTLIER) cc_final: 0.7565 (m) REVERT: a 55 LYS cc_start: 0.8447 (tttt) cc_final: 0.8162 (ttmt) REVERT: a 105 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7184 (m-30) REVERT: a 109 ASN cc_start: 0.8332 (m-40) cc_final: 0.7690 (m110) REVERT: a 122 LYS cc_start: 0.7923 (mttt) cc_final: 0.7534 (mmmt) REVERT: a 137 GLU cc_start: 0.6973 (tt0) cc_final: 0.6023 (pt0) REVERT: c 47 PHE cc_start: 0.7499 (m-80) cc_final: 0.7045 (m-80) REVERT: c 56 ARG cc_start: 0.6859 (tpt-90) cc_final: 0.6513 (tpt-90) REVERT: d 42 LYS cc_start: 0.7129 (tttt) cc_final: 0.6812 (ttmt) REVERT: d 43 MET cc_start: 0.7509 (tpp) cc_final: 0.7242 (tpp) REVERT: e 20 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7511 (ttt180) REVERT: e 22 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7866 (mt0) REVERT: e 25 LEU cc_start: 0.7964 (mp) cc_final: 0.7649 (mp) REVERT: e 65 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7645 (ttp-170) REVERT: e 98 SER cc_start: 0.8866 (m) cc_final: 0.8527 (t) REVERT: e 104 LYS cc_start: 0.7024 (tttm) cc_final: 0.6499 (mmmt) REVERT: e 111 LYS cc_start: 0.7941 (tttt) cc_final: 0.7373 (mmmt) REVERT: e 119 GLU cc_start: 0.7878 (tt0) cc_final: 0.7010 (tp30) REVERT: e 126 LYS cc_start: 0.5851 (mtpt) cc_final: 0.5447 (ptmm) REVERT: f 6 LYS cc_start: 0.6907 (ptmt) cc_final: 0.6610 (mmtt) REVERT: f 48 LYS cc_start: 0.7537 (mtpp) cc_final: 0.6961 (mtmt) REVERT: f 59 GLU cc_start: 0.7196 (tt0) cc_final: 0.6475 (mp0) REVERT: f 81 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6566 (mt-10) REVERT: f 88 MET cc_start: 0.7986 (mmm) cc_final: 0.7769 (mmt) REVERT: f 97 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7061 (pp) REVERT: g 39 ARG cc_start: 0.8114 (mmm160) cc_final: 0.7467 (mtp180) REVERT: h 34 GLN cc_start: 0.5617 (mt0) cc_final: 0.5102 (tm-30) REVERT: h 46 GLU cc_start: 0.7172 (tt0) cc_final: 0.6862 (mt-10) REVERT: h 65 GLN cc_start: 0.7909 (tt0) cc_final: 0.7591 (tm-30) REVERT: h 72 LYS cc_start: 0.6920 (ttpp) cc_final: 0.6661 (tttp) REVERT: j 50 GLU cc_start: 0.8399 (pt0) cc_final: 0.7821 (pt0) REVERT: j 64 MET cc_start: 0.7852 (mtm) cc_final: 0.7245 (mtt) REVERT: k 62 GLU cc_start: 0.5561 (OUTLIER) cc_final: 0.4993 (mp0) REVERT: l 37 ARG cc_start: 0.8095 (mtp180) cc_final: 0.7494 (mmm-85) REVERT: o 21 CYS cc_start: 0.8330 (p) cc_final: 0.7711 (p) REVERT: p 6 LYS cc_start: 0.6521 (mtmt) cc_final: 0.6200 (mtmm) REVERT: p 13 LYS cc_start: 0.7868 (pttt) cc_final: 0.7488 (pttt) REVERT: p 34 ARG cc_start: 0.7065 (mtt90) cc_final: 0.6785 (mtt90) outliers start: 261 outliers final: 192 residues processed: 1196 average time/residue: 1.0166 time to fit residues: 2028.1989 Evaluate side-chains 1241 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1017 time to evaluate : 5.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 187 CYS Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 64 ARG Chi-restraints excluded: chain H residue 175 LYS Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain I residue 21 ARG Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 130 ASN Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain I residue 193 CYS Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain L residue 6 ASN Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 26 ARG Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 126 SER Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 141 THR Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain P residue 17 LYS Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 32 GLU Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 151 ILE Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain Q residue 67 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 95 LYS Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 167 SER Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 141 HIS Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain S residue 2 SER Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 81 ARG Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 97 THR Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain S residue 121 SER Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain S residue 150 MET Chi-restraints excluded: chain S residue 151 LEU Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 20 GLN Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain V residue 14 PHE Chi-restraints excluded: chain V residue 28 CYS Chi-restraints excluded: chain V residue 96 ILE Chi-restraints excluded: chain V residue 112 MET Chi-restraints excluded: chain V residue 117 ILE Chi-restraints excluded: chain V residue 135 VAL Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain X residue 137 ILE Chi-restraints excluded: chain Y residue 2 VAL Chi-restraints excluded: chain Y residue 13 ARG Chi-restraints excluded: chain Y residue 18 SER Chi-restraints excluded: chain Y residue 25 ASP Chi-restraints excluded: chain Y residue 57 MET Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 58 THR Chi-restraints excluded: chain Z residue 104 LEU Chi-restraints excluded: chain Z residue 114 LEU Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 43 THR Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain a residue 96 LYS Chi-restraints excluded: chain a residue 105 ASP Chi-restraints excluded: chain b residue 10 HIS Chi-restraints excluded: chain b residue 11 ASN Chi-restraints excluded: chain c residue 18 SER Chi-restraints excluded: chain c residue 44 LEU Chi-restraints excluded: chain c residue 101 SER Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 15 THR Chi-restraints excluded: chain e residue 20 ARG Chi-restraints excluded: chain e residue 27 ASN Chi-restraints excluded: chain e residue 61 ASP Chi-restraints excluded: chain e residue 65 ARG Chi-restraints excluded: chain e residue 70 ASN Chi-restraints excluded: chain e residue 83 LEU Chi-restraints excluded: chain f residue 7 LEU Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 52 VAL Chi-restraints excluded: chain f residue 81 GLU Chi-restraints excluded: chain f residue 96 MET Chi-restraints excluded: chain f residue 97 LEU Chi-restraints excluded: chain g residue 57 CYS Chi-restraints excluded: chain g residue 60 THR Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 95 MET Chi-restraints excluded: chain h residue 30 GLU Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 78 LEU Chi-restraints excluded: chain h residue 79 VAL Chi-restraints excluded: chain i residue 19 SER Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 62 LYS Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 22 CYS Chi-restraints excluded: chain j residue 37 CYS Chi-restraints excluded: chain k residue 9 LYS Chi-restraints excluded: chain k residue 30 ASP Chi-restraints excluded: chain k residue 32 ASN Chi-restraints excluded: chain k residue 62 GLU Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 51 ILE Chi-restraints excluded: chain m residue 84 SER Chi-restraints excluded: chain m residue 92 THR Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain o residue 92 THR Chi-restraints excluded: chain p residue 8 VAL Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 60 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 796 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 470 optimal weight: 0.7980 chunk 603 optimal weight: 0.9980 chunk 467 optimal weight: 2.9990 chunk 695 optimal weight: 7.9990 chunk 461 optimal weight: 10.0000 chunk 823 optimal weight: 0.6980 chunk 515 optimal weight: 0.4980 chunk 501 optimal weight: 20.0000 chunk 380 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 147 GLN B 68 HIS B 162 HIS C 47 GLN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN D 76 GLN ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 HIS J 6 ASN ** N 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 140 HIS U 29 GLN f 62 ASN i 38 GLN ** k 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 33 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 115172 Z= 0.135 Angle : 0.543 11.892 169112 Z= 0.282 Chirality : 0.034 0.244 21128 Planarity : 0.004 0.072 11007 Dihedral : 22.516 179.820 49857 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.75 % Favored : 94.85 % Rotamer: Outliers : 5.05 % Allowed : 18.85 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.11), residues: 5785 helix: 0.70 (0.12), residues: 1913 sheet: -1.08 (0.17), residues: 824 loop : -1.20 (0.11), residues: 3048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP T 159 HIS 0.020 0.001 HIS T 140 PHE 0.019 0.001 PHE H 123 TYR 0.024 0.001 TYR F 186 ARG 0.008 0.000 ARG l 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1281 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 1032 time to evaluate : 5.556 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: A 8 GLN cc_start: 0.8319 (mt0) cc_final: 0.8046 (mt0) REVERT: A 30 ARG cc_start: 0.7247 (ttp-110) cc_final: 0.7006 (ttp-170) REVERT: A 44 MET cc_start: 0.7442 (ttp) cc_final: 0.6791 (ttt) REVERT: A 46 LYS cc_start: 0.7265 (tptm) cc_final: 0.6627 (ttpt) REVERT: A 135 ARG cc_start: 0.6826 (ttm170) cc_final: 0.6509 (mtp85) REVERT: A 201 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8199 (mttp) REVERT: B 53 MET cc_start: 0.8667 (ttt) cc_final: 0.8452 (ttm) REVERT: B 64 ASN cc_start: 0.8045 (t0) cc_final: 0.7723 (t0) REVERT: B 71 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7810 (mt-10) REVERT: B 84 MET cc_start: 0.7607 (ptm) cc_final: 0.7373 (ptm) REVERT: B 146 GLN cc_start: 0.6900 (mt0) cc_final: 0.6529 (mt0) REVERT: B 148 GLU cc_start: 0.7254 (tt0) cc_final: 0.6829 (mm-30) REVERT: B 181 LYS cc_start: 0.5600 (OUTLIER) cc_final: 0.5281 (pttt) REVERT: B 219 LYS cc_start: 0.6708 (mmmt) cc_final: 0.6196 (mptt) REVERT: B 228 THR cc_start: 0.7237 (m) cc_final: 0.6900 (p) REVERT: B 319 SER cc_start: 0.6819 (m) cc_final: 0.6510 (t) REVERT: B 324 LYS cc_start: 0.8396 (mptt) cc_final: 0.7938 (mmmt) REVERT: B 340 LYS cc_start: 0.6525 (mtmm) cc_final: 0.6181 (mptt) REVERT: B 345 MET cc_start: 0.8506 (ttp) cc_final: 0.8092 (ttm) REVERT: B 377 ASN cc_start: 0.7388 (OUTLIER) cc_final: 0.6690 (p0) REVERT: B 395 LYS cc_start: 0.7792 (pttt) cc_final: 0.6690 (mmmt) REVERT: B 406 LYS cc_start: 0.3997 (OUTLIER) cc_final: 0.3444 (ttmt) REVERT: C 4 GLN cc_start: 0.6439 (pt0) cc_final: 0.5354 (pm20) REVERT: C 202 LYS cc_start: 0.7806 (mmtt) cc_final: 0.7342 (mmmt) REVERT: C 210 GLU cc_start: 0.6452 (mt-10) cc_final: 0.6093 (pt0) REVERT: C 225 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7316 (mp0) REVERT: C 265 LYS cc_start: 0.6436 (mmmt) cc_final: 0.6033 (mmtt) REVERT: C 268 SER cc_start: 0.7970 (m) cc_final: 0.7686 (t) REVERT: C 303 LYS cc_start: 0.7979 (mttt) cc_final: 0.7424 (pttm) REVERT: C 329 ARG cc_start: 0.7726 (mtt180) cc_final: 0.7256 (mmt180) REVERT: C 340 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7093 (tp30) REVERT: D 4 LYS cc_start: 0.6875 (mttt) cc_final: 0.6216 (mppt) REVERT: D 67 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6707 (mt-10) REVERT: D 88 LYS cc_start: 0.7596 (mttt) cc_final: 0.7077 (ptmt) REVERT: D 157 MET cc_start: 0.7949 (ttt) cc_final: 0.7548 (tmm) REVERT: D 158 LYS cc_start: 0.6689 (mttt) cc_final: 0.6256 (tptt) REVERT: D 223 GLU cc_start: 0.6757 (tt0) cc_final: 0.6329 (pm20) REVERT: D 224 LYS cc_start: 0.7068 (mttt) cc_final: 0.6560 (mtpt) REVERT: D 233 VAL cc_start: 0.7902 (t) cc_final: 0.7631 (m) REVERT: D 254 ARG cc_start: 0.6642 (mtp85) cc_final: 0.6234 (mtt-85) REVERT: D 279 LYS cc_start: 0.6931 (mmmt) cc_final: 0.6519 (mttp) REVERT: D 280 LYS cc_start: 0.8038 (tptt) cc_final: 0.7629 (tptm) REVERT: E 73 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7771 (mmt90) REVERT: E 80 GLN cc_start: 0.6760 (mt0) cc_final: 0.6527 (mm-40) REVERT: E 86 LYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6580 (mtpt) REVERT: E 96 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6256 (pm20) REVERT: E 101 TYR cc_start: 0.7798 (m-80) cc_final: 0.7500 (m-80) REVERT: E 142 LYS cc_start: 0.7674 (pmtt) cc_final: 0.6575 (tttm) REVERT: F 24 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5995 (mt) REVERT: F 26 LYS cc_start: 0.6214 (ttmm) cc_final: 0.5849 (ttmm) REVERT: F 79 LYS cc_start: 0.7936 (mmtm) cc_final: 0.7323 (mtmt) REVERT: F 102 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7222 (mp) REVERT: F 122 GLU cc_start: 0.6899 (tt0) cc_final: 0.6409 (tt0) REVERT: F 163 ASN cc_start: 0.8112 (m-40) cc_final: 0.7654 (m-40) REVERT: F 164 GLN cc_start: 0.8335 (tp-100) cc_final: 0.7799 (tp40) REVERT: F 203 LYS cc_start: 0.8207 (mttt) cc_final: 0.7545 (mtmt) REVERT: G 45 LYS cc_start: 0.7495 (tptp) cc_final: 0.7220 (ttmt) REVERT: G 54 ARG cc_start: 0.7706 (tpp-160) cc_final: 0.7047 (mmm-85) REVERT: G 59 ARG cc_start: 0.7304 (mmt-90) cc_final: 0.6837 (mmt-90) REVERT: G 67 ASN cc_start: 0.7394 (t160) cc_final: 0.7082 (t0) REVERT: G 86 GLU cc_start: 0.7058 (tt0) cc_final: 0.6465 (mt-10) REVERT: G 218 GLU cc_start: 0.6864 (tp30) cc_final: 0.6160 (pt0) REVERT: G 219 GLU cc_start: 0.5129 (mm-30) cc_final: 0.4629 (pt0) REVERT: H 8 GLN cc_start: 0.6838 (pt0) cc_final: 0.6623 (pt0) REVERT: H 22 LYS cc_start: 0.6903 (tttt) cc_final: 0.6402 (mptt) REVERT: H 30 HIS cc_start: 0.6746 (t70) cc_final: 0.6325 (t-90) REVERT: H 84 LYS cc_start: 0.7596 (tttm) cc_final: 0.6943 (pttt) REVERT: H 99 HIS cc_start: 0.7027 (p-80) cc_final: 0.5704 (p-80) REVERT: H 175 LYS cc_start: 0.6276 (OUTLIER) cc_final: 0.5928 (ptpt) REVERT: I 55 LEU cc_start: 0.7371 (mt) cc_final: 0.7045 (mt) REVERT: I 156 SER cc_start: 0.8524 (p) cc_final: 0.8242 (p) REVERT: I 185 GLN cc_start: 0.6887 (tp40) cc_final: 0.6598 (tm-30) REVERT: I 192 ASP cc_start: 0.5906 (t0) cc_final: 0.5639 (t0) REVERT: J 45 ARG cc_start: 0.5928 (mtt180) cc_final: 0.5096 (mmt90) REVERT: J 100 PHE cc_start: 0.7588 (p90) cc_final: 0.7213 (p90) REVERT: J 110 LEU cc_start: 0.5094 (OUTLIER) cc_final: 0.4276 (tp) REVERT: J 136 ARG cc_start: 0.6883 (mmt-90) cc_final: 0.6551 (mpt180) REVERT: L 11 ASP cc_start: 0.8109 (p0) cc_final: 0.7878 (p0) REVERT: L 58 VAL cc_start: 0.8071 (OUTLIER) cc_final: 0.7775 (m) REVERT: L 68 LYS cc_start: 0.7606 (mmtp) cc_final: 0.6990 (mtmt) REVERT: L 91 ARG cc_start: 0.7419 (ttp-110) cc_final: 0.6561 (mtt180) REVERT: L 93 GLN cc_start: 0.7007 (mm110) cc_final: 0.6508 (mt0) REVERT: L 110 LYS cc_start: 0.7436 (mttt) cc_final: 0.7046 (mmmt) REVERT: L 166 LYS cc_start: 0.5327 (mttt) cc_final: 0.5058 (mmmt) REVERT: L 177 GLU cc_start: 0.5854 (mt-10) cc_final: 0.5622 (mm-30) REVERT: M 63 LYS cc_start: 0.7988 (ttpt) cc_final: 0.7150 (mmtp) REVERT: M 116 LYS cc_start: 0.6771 (mttt) cc_final: 0.6410 (mtpt) REVERT: N 26 ARG cc_start: 0.5972 (OUTLIER) cc_final: 0.5628 (mtm-85) REVERT: N 33 LEU cc_start: 0.7591 (mt) cc_final: 0.7311 (mt) REVERT: N 51 MET cc_start: 0.8622 (mmm) cc_final: 0.8252 (mmt) REVERT: N 59 MET cc_start: 0.8486 (tpp) cc_final: 0.7644 (mtp) REVERT: N 108 LYS cc_start: 0.8051 (ttmt) cc_final: 0.7828 (tmmt) REVERT: N 117 ASN cc_start: 0.8579 (m-40) cc_final: 0.8201 (t0) REVERT: N 177 VAL cc_start: 0.8117 (t) cc_final: 0.7825 (m) REVERT: O 40 GLU cc_start: 0.7225 (pt0) cc_final: 0.6785 (pt0) REVERT: O 104 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6725 (mt-10) REVERT: O 176 ARG cc_start: 0.6720 (ttm-80) cc_final: 0.5996 (tmm-80) REVERT: O 180 ILE cc_start: 0.6407 (mt) cc_final: 0.6078 (mm) REVERT: O 196 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6491 (mm-30) REVERT: P 17 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.7853 (mtpp) REVERT: P 24 ARG cc_start: 0.8360 (mtp180) cc_final: 0.8061 (mtm180) REVERT: P 32 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7204 (mm-30) REVERT: P 65 LYS cc_start: 0.8328 (pttt) cc_final: 0.7979 (pttt) REVERT: P 76 GLU cc_start: 0.7344 (pt0) cc_final: 0.6554 (pt0) REVERT: P 94 LYS cc_start: 0.6664 (mttt) cc_final: 0.6091 (ttpp) REVERT: P 131 ARG cc_start: 0.8066 (mtt-85) cc_final: 0.6670 (mtm180) REVERT: Q 13 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8176 (mt0) REVERT: Q 26 MET cc_start: 0.7038 (mtp) cc_final: 0.6473 (tpt) REVERT: Q 95 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7571 (mtpp) REVERT: Q 147 ASN cc_start: 0.7891 (t0) cc_final: 0.7662 (m-40) REVERT: Q 162 ARG cc_start: 0.7844 (mtp85) cc_final: 0.7515 (tpp80) REVERT: R 5 LYS cc_start: 0.8165 (tttm) cc_final: 0.7936 (ttmm) REVERT: R 28 GLU cc_start: 0.7091 (mp0) cc_final: 0.6580 (mp0) REVERT: R 36 ASN cc_start: 0.7383 (m-40) cc_final: 0.6719 (p0) REVERT: R 39 GLN cc_start: 0.6866 (mm110) cc_final: 0.6298 (tm-30) REVERT: R 114 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7244 (mp0) REVERT: R 136 ARG cc_start: 0.6164 (ttm170) cc_final: 0.5851 (ttm110) REVERT: R 141 HIS cc_start: 0.7511 (OUTLIER) cc_final: 0.6709 (t70) REVERT: S 16 LYS cc_start: 0.7730 (mttt) cc_final: 0.7390 (tppt) REVERT: S 54 HIS cc_start: 0.7893 (OUTLIER) cc_final: 0.7345 (p90) REVERT: S 81 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.7039 (tmm-80) REVERT: S 85 ASN cc_start: 0.6544 (OUTLIER) cc_final: 0.6076 (t0) REVERT: S 92 GLU cc_start: 0.7981 (pt0) cc_final: 0.7573 (pt0) REVERT: S 116 SER cc_start: 0.7998 (t) cc_final: 0.7649 (p) REVERT: S 147 LYS cc_start: 0.7361 (mttt) cc_final: 0.6868 (mtmm) REVERT: T 21 LYS cc_start: 0.7286 (mttt) cc_final: 0.6849 (mmtt) REVERT: T 77 LYS cc_start: 0.8589 (mttp) cc_final: 0.7876 (mtpt) REVERT: T 156 ARG cc_start: 0.6566 (mtt90) cc_final: 0.6261 (mmt180) REVERT: U 18 PHE cc_start: 0.7083 (OUTLIER) cc_final: 0.6360 (p90) REVERT: U 23 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6606 (mt-10) REVERT: U 32 MET cc_start: 0.7798 (mtt) cc_final: 0.7493 (ttm) REVERT: U 76 PHE cc_start: 0.7883 (t80) cc_final: 0.7425 (t80) REVERT: U 99 ARG cc_start: 0.6768 (mtp180) cc_final: 0.6171 (ptp-170) REVERT: V 14 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.7209 (m-80) REVERT: V 36 ASN cc_start: 0.8182 (m110) cc_final: 0.7828 (m-40) REVERT: V 43 ARG cc_start: 0.6825 (ttm170) cc_final: 0.6452 (mtt90) REVERT: V 96 ILE cc_start: 0.7028 (OUTLIER) cc_final: 0.6758 (tt) REVERT: V 123 LYS cc_start: 0.7030 (tttp) cc_final: 0.6474 (tttm) REVERT: X 39 ARG cc_start: 0.5043 (ptp90) cc_final: 0.4040 (mtp180) REVERT: X 46 LYS cc_start: 0.7161 (tttm) cc_final: 0.6599 (mmtm) REVERT: X 49 LYS cc_start: 0.7943 (mttt) cc_final: 0.7192 (mtpp) REVERT: X 66 THR cc_start: 0.7345 (OUTLIER) cc_final: 0.7013 (t) REVERT: X 71 THR cc_start: 0.6749 (m) cc_final: 0.6421 (p) REVERT: X 78 ASN cc_start: 0.7674 (t0) cc_final: 0.7399 (t0) REVERT: X 87 LYS cc_start: 0.8481 (mttt) cc_final: 0.7643 (mmmt) REVERT: X 115 LYS cc_start: 0.8147 (mttt) cc_final: 0.7691 (mtmt) REVERT: Y 23 LYS cc_start: 0.7262 (mttt) cc_final: 0.6667 (pttm) REVERT: Y 57 MET cc_start: 0.6762 (OUTLIER) cc_final: 0.6562 (ptp) REVERT: Y 80 ILE cc_start: 0.8197 (mt) cc_final: 0.7897 (pt) REVERT: Y 95 VAL cc_start: 0.7035 (t) cc_final: 0.6787 (m) REVERT: Z 47 LYS cc_start: 0.6369 (mttt) cc_final: 0.5760 (tmtt) REVERT: a 22 VAL cc_start: 0.7873 (OUTLIER) cc_final: 0.7585 (m) REVERT: a 55 LYS cc_start: 0.8442 (tttt) cc_final: 0.8174 (ttmt) REVERT: a 105 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7148 (m-30) REVERT: a 109 ASN cc_start: 0.8198 (m-40) cc_final: 0.7565 (m110) REVERT: a 122 LYS cc_start: 0.7924 (mttt) cc_final: 0.7455 (mmmt) REVERT: a 137 GLU cc_start: 0.7066 (tt0) cc_final: 0.6324 (pt0) REVERT: c 47 PHE cc_start: 0.7599 (m-80) cc_final: 0.7132 (m-80) REVERT: c 56 ARG cc_start: 0.6855 (tpt-90) cc_final: 0.6509 (tpt-90) REVERT: d 42 LYS cc_start: 0.7130 (tttt) cc_final: 0.6808 (ttmt) REVERT: e 20 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7540 (ttt180) REVERT: e 22 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7863 (mt0) REVERT: e 25 LEU cc_start: 0.7975 (mp) cc_final: 0.7663 (mp) REVERT: e 96 MET cc_start: 0.7967 (ttt) cc_final: 0.7393 (ttt) REVERT: e 98 SER cc_start: 0.8853 (m) cc_final: 0.8531 (t) REVERT: e 104 LYS cc_start: 0.7024 (tttm) cc_final: 0.6497 (mmmt) REVERT: e 111 LYS cc_start: 0.7937 (tttt) cc_final: 0.7368 (mmmt) REVERT: e 119 GLU cc_start: 0.7893 (tt0) cc_final: 0.7055 (tp30) REVERT: e 126 LYS cc_start: 0.5843 (mtpt) cc_final: 0.5438 (ptmm) REVERT: f 6 LYS cc_start: 0.6907 (ptmt) cc_final: 0.6614 (mmtt) REVERT: f 48 LYS cc_start: 0.7470 (mtpp) cc_final: 0.6883 (mtmt) REVERT: f 59 GLU cc_start: 0.7181 (tt0) cc_final: 0.6465 (mp0) REVERT: f 81 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6581 (mt-10) REVERT: f 97 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7050 (pp) REVERT: g 39 ARG cc_start: 0.8127 (mmm160) cc_final: 0.7517 (mtp180) REVERT: h 46 GLU cc_start: 0.7168 (tt0) cc_final: 0.6859 (mt-10) REVERT: h 71 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6631 (mt-10) REVERT: h 72 LYS cc_start: 0.6901 (ttpp) cc_final: 0.6611 (tttp) REVERT: i 83 GLU cc_start: 0.5898 (tp30) cc_final: 0.5652 (tm-30) REVERT: j 50 GLU cc_start: 0.8408 (pt0) cc_final: 0.7856 (pt0) REVERT: j 64 MET cc_start: 0.7811 (mtm) cc_final: 0.7236 (mtt) REVERT: k 62 GLU cc_start: 0.5553 (OUTLIER) cc_final: 0.4989 (mp0) REVERT: l 37 ARG cc_start: 0.8090 (mtp180) cc_final: 0.7490 (mmm-85) REVERT: o 21 CYS cc_start: 0.8303 (p) cc_final: 0.7688 (p) REVERT: p 6 LYS cc_start: 0.6495 (mtmt) cc_final: 0.6170 (mtmt) REVERT: p 13 LYS cc_start: 0.7847 (pttt) cc_final: 0.7378 (pttt) REVERT: p 34 ARG cc_start: 0.6985 (mtt90) cc_final: 0.6713 (mtt90) outliers start: 249 outliers final: 180 residues processed: 1175 average time/residue: 1.0008 time to fit residues: 1957.0238 Evaluate side-chains 1230 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1018 time to evaluate : 5.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 187 CYS Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 64 ARG Chi-restraints excluded: chain H residue 175 LYS Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain I residue 21 ARG Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 130 ASN Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain I residue 193 CYS Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 138 LYS Chi-restraints excluded: chain L residue 6 ASN Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 26 ARG Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain O residue 38 GLU Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 126 SER Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 141 THR Chi-restraints excluded: chain O residue 195 LEU Chi-restraints excluded: chain P residue 17 LYS Chi-restraints excluded: chain P residue 32 GLU Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 151 ILE Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain Q residue 95 LYS Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 141 HIS Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain S residue 2 SER Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 54 HIS Chi-restraints excluded: chain S residue 81 ARG Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain S residue 150 MET Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain T residue 137 ARG Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 20 GLN Chi-restraints excluded: chain U residue 21 LEU Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain V residue 14 PHE Chi-restraints excluded: chain V residue 28 CYS Chi-restraints excluded: chain V residue 96 ILE Chi-restraints excluded: chain V residue 112 MET Chi-restraints excluded: chain V residue 117 ILE Chi-restraints excluded: chain V residue 135 VAL Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Y residue 2 VAL Chi-restraints excluded: chain Y residue 13 ARG Chi-restraints excluded: chain Y residue 25 ASP Chi-restraints excluded: chain Y residue 57 MET Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Z residue 104 LEU Chi-restraints excluded: chain Z residue 114 LEU Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 77 VAL Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain a residue 105 ASP Chi-restraints excluded: chain b residue 10 HIS Chi-restraints excluded: chain b residue 11 ASN Chi-restraints excluded: chain c residue 18 SER Chi-restraints excluded: chain c residue 44 LEU Chi-restraints excluded: chain c residue 101 SER Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 15 THR Chi-restraints excluded: chain e residue 20 ARG Chi-restraints excluded: chain e residue 27 ASN Chi-restraints excluded: chain e residue 70 ASN Chi-restraints excluded: chain e residue 80 LEU Chi-restraints excluded: chain e residue 83 LEU Chi-restraints excluded: chain e residue 90 ASN Chi-restraints excluded: chain f residue 7 LEU Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 81 GLU Chi-restraints excluded: chain f residue 96 MET Chi-restraints excluded: chain f residue 97 LEU Chi-restraints excluded: chain g residue 57 CYS Chi-restraints excluded: chain g residue 60 THR Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 95 MET Chi-restraints excluded: chain h residue 30 GLU Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 78 LEU Chi-restraints excluded: chain h residue 79 VAL Chi-restraints excluded: chain h residue 104 THR Chi-restraints excluded: chain i residue 19 SER Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 62 LYS Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 22 CYS Chi-restraints excluded: chain j residue 37 CYS Chi-restraints excluded: chain k residue 32 ASN Chi-restraints excluded: chain k residue 62 GLU Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain m residue 84 SER Chi-restraints excluded: chain m residue 92 THR Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain o residue 62 THR Chi-restraints excluded: chain o residue 92 THR Chi-restraints excluded: chain p residue 32 SER Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 60 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 509 optimal weight: 0.9990 chunk 328 optimal weight: 3.9990 chunk 491 optimal weight: 9.9990 chunk 247 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 523 optimal weight: 8.9990 chunk 560 optimal weight: 0.7980 chunk 406 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 646 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 142 ASN B 68 HIS C 47 GLN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN D 76 GLN ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 HIS H 126 HIS ** N 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 36 ASN ** S 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 81 ASN T 140 HIS W 16 HIS f 62 ASN ** g 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 65 GLN k 32 ASN o 33 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 115172 Z= 0.303 Angle : 0.635 13.166 169112 Z= 0.325 Chirality : 0.039 0.301 21128 Planarity : 0.005 0.070 11007 Dihedral : 22.510 179.884 49856 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.43 % Favored : 94.14 % Rotamer: Outliers : 5.76 % Allowed : 18.71 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.11), residues: 5785 helix: 0.46 (0.12), residues: 1903 sheet: -1.02 (0.18), residues: 813 loop : -1.32 (0.11), residues: 3069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP T 159 HIS 0.014 0.001 HIS T 140 PHE 0.021 0.002 PHE H 123 TYR 0.025 0.002 TYR p 83 ARG 0.008 0.001 ARG l 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1329 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 1045 time to evaluate : 5.603 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: A 30 ARG cc_start: 0.7374 (ttp-110) cc_final: 0.7132 (ttp-110) REVERT: A 44 MET cc_start: 0.7446 (ttp) cc_final: 0.6754 (ttt) REVERT: A 46 LYS cc_start: 0.7365 (tptm) cc_final: 0.6733 (ttpt) REVERT: A 135 ARG cc_start: 0.6873 (ttm170) cc_final: 0.6547 (mtp85) REVERT: A 179 LYS cc_start: 0.7509 (mtmt) cc_final: 0.7097 (mtmt) REVERT: A 201 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8347 (mttp) REVERT: B 53 MET cc_start: 0.8774 (ttt) cc_final: 0.8234 (ttm) REVERT: B 64 ASN cc_start: 0.8326 (t0) cc_final: 0.7890 (t0) REVERT: B 84 MET cc_start: 0.7739 (ptm) cc_final: 0.7307 (ptm) REVERT: B 89 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7592 (mt) REVERT: B 144 GLU cc_start: 0.6945 (mm-30) cc_final: 0.5863 (tt0) REVERT: B 146 GLN cc_start: 0.6980 (mt0) cc_final: 0.6632 (mt0) REVERT: B 148 GLU cc_start: 0.7315 (tt0) cc_final: 0.6862 (mm-30) REVERT: B 219 LYS cc_start: 0.6782 (mmmt) cc_final: 0.6437 (mptt) REVERT: B 295 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7678 (mt-10) REVERT: B 319 SER cc_start: 0.6827 (m) cc_final: 0.6516 (t) REVERT: B 324 LYS cc_start: 0.8497 (mptt) cc_final: 0.8006 (mmmt) REVERT: B 340 LYS cc_start: 0.6548 (mtmm) cc_final: 0.6153 (mptt) REVERT: B 345 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.7762 (ttm) REVERT: B 395 LYS cc_start: 0.7795 (pttt) cc_final: 0.6705 (mmmt) REVERT: B 406 LYS cc_start: 0.4050 (OUTLIER) cc_final: 0.3215 (ttmt) REVERT: C 4 GLN cc_start: 0.6527 (pt0) cc_final: 0.5594 (pm20) REVERT: C 11 GLN cc_start: 0.6312 (tt0) cc_final: 0.5780 (mt0) REVERT: C 153 ASP cc_start: 0.7308 (t70) cc_final: 0.6900 (t70) REVERT: C 202 LYS cc_start: 0.7900 (mmtt) cc_final: 0.7416 (mmmt) REVERT: C 268 SER cc_start: 0.8164 (m) cc_final: 0.7944 (t) REVERT: C 296 LYS cc_start: 0.7564 (mtmm) cc_final: 0.7355 (mtmm) REVERT: C 303 LYS cc_start: 0.7953 (mttt) cc_final: 0.7465 (mtmm) REVERT: C 329 ARG cc_start: 0.7727 (mtt180) cc_final: 0.7271 (mmt180) REVERT: C 340 GLU cc_start: 0.7637 (mt-10) cc_final: 0.6996 (tp30) REVERT: D 88 LYS cc_start: 0.7962 (mttt) cc_final: 0.7621 (ptmt) REVERT: D 157 MET cc_start: 0.8125 (ttt) cc_final: 0.7647 (tmm) REVERT: D 158 LYS cc_start: 0.6850 (mttt) cc_final: 0.6457 (tptt) REVERT: D 223 GLU cc_start: 0.6868 (tt0) cc_final: 0.6265 (pm20) REVERT: D 224 LYS cc_start: 0.7188 (mttt) cc_final: 0.6659 (mtpt) REVERT: D 232 TYR cc_start: 0.7339 (m-80) cc_final: 0.5778 (m-80) REVERT: D 233 VAL cc_start: 0.7945 (t) cc_final: 0.7676 (m) REVERT: D 254 ARG cc_start: 0.6334 (mtp85) cc_final: 0.5952 (mtt-85) REVERT: D 279 LYS cc_start: 0.6973 (mmmt) cc_final: 0.6610 (mttp) REVERT: D 280 LYS cc_start: 0.8013 (tptt) cc_final: 0.7550 (tttt) REVERT: E 53 ARG cc_start: 0.6791 (ttp-170) cc_final: 0.6543 (ttp-170) REVERT: E 73 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7865 (mmt90) REVERT: E 80 GLN cc_start: 0.6771 (mt0) cc_final: 0.6509 (mm-40) REVERT: E 86 LYS cc_start: 0.7107 (OUTLIER) cc_final: 0.6533 (mtpt) REVERT: E 96 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6210 (pm20) REVERT: E 101 TYR cc_start: 0.7754 (m-80) cc_final: 0.7432 (m-80) REVERT: E 142 LYS cc_start: 0.7585 (pmtt) cc_final: 0.6472 (tttm) REVERT: F 24 LEU cc_start: 0.6224 (OUTLIER) cc_final: 0.5998 (mm) REVERT: F 26 LYS cc_start: 0.6214 (ttmm) cc_final: 0.5866 (ttmm) REVERT: F 79 LYS cc_start: 0.7895 (mmtm) cc_final: 0.7480 (mtmt) REVERT: F 102 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7230 (mp) REVERT: F 122 GLU cc_start: 0.6970 (tt0) cc_final: 0.6511 (tt0) REVERT: F 163 ASN cc_start: 0.8117 (m-40) cc_final: 0.7606 (m-40) REVERT: F 164 GLN cc_start: 0.8340 (tp-100) cc_final: 0.8096 (tp40) REVERT: F 203 LYS cc_start: 0.8233 (mttt) cc_final: 0.7545 (mtmt) REVERT: F 211 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.6031 (p90) REVERT: F 228 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7065 (mt-10) REVERT: G 45 LYS cc_start: 0.7494 (tptp) cc_final: 0.7177 (ttmt) REVERT: G 48 GLN cc_start: 0.6160 (mt0) cc_final: 0.5833 (mt0) REVERT: G 54 ARG cc_start: 0.7738 (tpp-160) cc_final: 0.7077 (mmm-85) REVERT: G 59 ARG cc_start: 0.7321 (mmt-90) cc_final: 0.6970 (mmt-90) REVERT: G 67 ASN cc_start: 0.7449 (t160) cc_final: 0.7118 (t0) REVERT: G 86 GLU cc_start: 0.7065 (tt0) cc_final: 0.6484 (mt-10) REVERT: G 218 GLU cc_start: 0.6900 (tp30) cc_final: 0.6169 (pt0) REVERT: H 8 GLN cc_start: 0.6763 (pt0) cc_final: 0.6477 (pt0) REVERT: H 22 LYS cc_start: 0.7009 (tttt) cc_final: 0.6477 (mptt) REVERT: H 84 LYS cc_start: 0.7626 (tttm) cc_final: 0.6966 (pttt) REVERT: H 113 GLU cc_start: 0.5779 (pm20) cc_final: 0.5399 (pm20) REVERT: H 128 GLU cc_start: 0.5397 (tp30) cc_final: 0.4971 (tp30) REVERT: H 175 LYS cc_start: 0.6255 (OUTLIER) cc_final: 0.5863 (ptpt) REVERT: I 156 SER cc_start: 0.8588 (p) cc_final: 0.8299 (p) REVERT: I 192 ASP cc_start: 0.6028 (t0) cc_final: 0.5741 (t0) REVERT: J 45 ARG cc_start: 0.5771 (mtt180) cc_final: 0.4870 (mmt90) REVERT: J 52 LYS cc_start: 0.7429 (tptt) cc_final: 0.7036 (tptp) REVERT: J 100 PHE cc_start: 0.7691 (p90) cc_final: 0.7312 (p90) REVERT: J 110 LEU cc_start: 0.5017 (OUTLIER) cc_final: 0.4276 (tp) REVERT: J 136 ARG cc_start: 0.6830 (mmt-90) cc_final: 0.5910 (mmt90) REVERT: L 11 ASP cc_start: 0.8391 (p0) cc_final: 0.8126 (p0) REVERT: L 68 LYS cc_start: 0.7653 (mmtp) cc_final: 0.6942 (mtmt) REVERT: L 91 ARG cc_start: 0.7369 (ttp-110) cc_final: 0.6549 (mtt90) REVERT: L 93 GLN cc_start: 0.7207 (mm110) cc_final: 0.6456 (mt0) REVERT: L 110 LYS cc_start: 0.7337 (mttt) cc_final: 0.6935 (mmmt) REVERT: L 130 GLU cc_start: 0.6823 (pt0) cc_final: 0.6113 (mp0) REVERT: L 166 LYS cc_start: 0.5344 (mttt) cc_final: 0.5114 (mmmt) REVERT: L 177 GLU cc_start: 0.5883 (mt-10) cc_final: 0.5628 (mm-30) REVERT: M 63 LYS cc_start: 0.7963 (ttpt) cc_final: 0.7155 (mmtp) REVERT: M 116 LYS cc_start: 0.6782 (mttt) cc_final: 0.6425 (mtpt) REVERT: N 33 LEU cc_start: 0.7774 (mt) cc_final: 0.7500 (mt) REVERT: N 51 MET cc_start: 0.8545 (mmm) cc_final: 0.8275 (mmt) REVERT: N 59 MET cc_start: 0.8491 (tpp) cc_final: 0.7911 (mtp) REVERT: N 108 LYS cc_start: 0.8082 (ttmt) cc_final: 0.7843 (tmmt) REVERT: N 117 ASN cc_start: 0.8603 (m-40) cc_final: 0.8165 (t0) REVERT: N 177 VAL cc_start: 0.8008 (t) cc_final: 0.7742 (m) REVERT: O 40 GLU cc_start: 0.7500 (pt0) cc_final: 0.6985 (pt0) REVERT: O 104 GLU cc_start: 0.7392 (mt-10) cc_final: 0.6932 (mt-10) REVERT: O 135 LYS cc_start: 0.7533 (mmtt) cc_final: 0.7016 (mtmt) REVERT: O 176 ARG cc_start: 0.6752 (ttm-80) cc_final: 0.5985 (tmm-80) REVERT: O 185 LYS cc_start: 0.7305 (mttm) cc_final: 0.7037 (mppt) REVERT: O 196 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6490 (mm-30) REVERT: P 17 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.7813 (mtpp) REVERT: P 24 ARG cc_start: 0.8372 (mtp180) cc_final: 0.8032 (mtm180) REVERT: P 32 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7345 (mm-30) REVERT: P 41 LYS cc_start: 0.6451 (mttp) cc_final: 0.6094 (mtpp) REVERT: P 53 MET cc_start: 0.7422 (mtt) cc_final: 0.7136 (mtt) REVERT: P 65 LYS cc_start: 0.8339 (pttt) cc_final: 0.7991 (pttt) REVERT: P 76 GLU cc_start: 0.7184 (pt0) cc_final: 0.6463 (pt0) REVERT: P 94 LYS cc_start: 0.6764 (mttt) cc_final: 0.6107 (ttpp) REVERT: P 131 ARG cc_start: 0.8197 (mtt-85) cc_final: 0.6765 (mtm180) REVERT: Q 13 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8191 (mt0) REVERT: Q 16 GLU cc_start: 0.8199 (pt0) cc_final: 0.7425 (pm20) REVERT: Q 26 MET cc_start: 0.6756 (mtp) cc_final: 0.6368 (tpt) REVERT: Q 95 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7697 (mtpp) REVERT: Q 147 ASN cc_start: 0.7973 (t0) cc_final: 0.7708 (m-40) REVERT: R 5 LYS cc_start: 0.8196 (tttm) cc_final: 0.7983 (ttmm) REVERT: R 28 GLU cc_start: 0.7134 (mp0) cc_final: 0.6556 (mp0) REVERT: R 36 ASN cc_start: 0.7422 (m110) cc_final: 0.6881 (p0) REVERT: R 39 GLN cc_start: 0.7031 (mm110) cc_final: 0.6482 (tm-30) REVERT: R 136 ARG cc_start: 0.6100 (ttm170) cc_final: 0.5680 (ttm110) REVERT: R 141 HIS cc_start: 0.7599 (OUTLIER) cc_final: 0.6697 (t70) REVERT: S 16 LYS cc_start: 0.7776 (mttt) cc_final: 0.7437 (tppt) REVERT: S 54 HIS cc_start: 0.7955 (OUTLIER) cc_final: 0.7458 (p90) REVERT: S 78 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7768 (pp) REVERT: S 81 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.7069 (tmm-80) REVERT: S 116 SER cc_start: 0.8044 (t) cc_final: 0.7587 (p) REVERT: S 147 LYS cc_start: 0.7408 (mttt) cc_final: 0.6965 (mtmm) REVERT: T 21 LYS cc_start: 0.7308 (mttt) cc_final: 0.6848 (mmtt) REVERT: T 77 LYS cc_start: 0.8719 (mttp) cc_final: 0.7927 (mtmt) REVERT: T 148 GLN cc_start: 0.7134 (tt0) cc_final: 0.6744 (tt0) REVERT: T 156 ARG cc_start: 0.6642 (mtt90) cc_final: 0.6335 (mmt90) REVERT: U 18 PHE cc_start: 0.7074 (OUTLIER) cc_final: 0.6272 (p90) REVERT: U 23 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6626 (mt-10) REVERT: U 29 GLN cc_start: 0.7561 (mt0) cc_final: 0.6842 (mm110) REVERT: U 32 MET cc_start: 0.7762 (mtt) cc_final: 0.7466 (ttm) REVERT: U 76 PHE cc_start: 0.7923 (t80) cc_final: 0.7459 (t80) REVERT: U 99 ARG cc_start: 0.6930 (mtp180) cc_final: 0.6191 (ptp-170) REVERT: V 10 GLN cc_start: 0.5216 (mt0) cc_final: 0.4990 (mt0) REVERT: V 14 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7232 (m-80) REVERT: V 96 ILE cc_start: 0.7259 (OUTLIER) cc_final: 0.7008 (tt) REVERT: V 123 LYS cc_start: 0.7103 (tttp) cc_final: 0.6522 (tttm) REVERT: X 39 ARG cc_start: 0.5552 (ptp90) cc_final: 0.4296 (mtp85) REVERT: X 46 LYS cc_start: 0.7075 (tttm) cc_final: 0.6619 (mmtm) REVERT: X 49 LYS cc_start: 0.7925 (mttt) cc_final: 0.7217 (mtpp) REVERT: X 71 THR cc_start: 0.6782 (m) cc_final: 0.6486 (p) REVERT: X 78 ASN cc_start: 0.7715 (t0) cc_final: 0.7415 (t0) REVERT: X 87 LYS cc_start: 0.8473 (mttt) cc_final: 0.7663 (mmmt) REVERT: X 115 LYS cc_start: 0.8182 (mttt) cc_final: 0.7724 (mtmt) REVERT: Y 23 LYS cc_start: 0.7160 (mttt) cc_final: 0.6573 (pttm) REVERT: Y 57 MET cc_start: 0.6621 (OUTLIER) cc_final: 0.6320 (ptp) REVERT: Y 79 ARG cc_start: 0.7253 (mtt180) cc_final: 0.5825 (mtm180) REVERT: Y 80 ILE cc_start: 0.8178 (mt) cc_final: 0.7615 (pt) REVERT: Y 95 VAL cc_start: 0.7123 (t) cc_final: 0.6581 (m) REVERT: Y 97 PHE cc_start: 0.6952 (OUTLIER) cc_final: 0.6086 (m-80) REVERT: Y 123 ARG cc_start: 0.5617 (ttm170) cc_final: 0.4911 (ttt180) REVERT: Z 47 LYS cc_start: 0.6365 (mttt) cc_final: 0.5651 (tmtt) REVERT: Z 56 MET cc_start: 0.5632 (tpt) cc_final: 0.5092 (ttm) REVERT: a 22 VAL cc_start: 0.8153 (OUTLIER) cc_final: 0.7936 (m) REVERT: a 55 LYS cc_start: 0.8459 (tttt) cc_final: 0.8174 (ttmt) REVERT: a 105 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7085 (m-30) REVERT: a 109 ASN cc_start: 0.8158 (m-40) cc_final: 0.7577 (m110) REVERT: a 122 LYS cc_start: 0.8048 (mttt) cc_final: 0.7503 (mmmt) REVERT: a 137 GLU cc_start: 0.7100 (tt0) cc_final: 0.5863 (pt0) REVERT: b 23 LYS cc_start: 0.7633 (tttt) cc_final: 0.7100 (ptpp) REVERT: c 56 ARG cc_start: 0.6889 (tpt-90) cc_final: 0.6621 (tpt-90) REVERT: c 89 ARG cc_start: 0.6722 (mtt180) cc_final: 0.6410 (ptp90) REVERT: d 42 LYS cc_start: 0.6841 (tttt) cc_final: 0.6542 (ttmt) REVERT: e 20 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7416 (ttt180) REVERT: e 22 GLN cc_start: 0.8328 (mm-40) cc_final: 0.7845 (mt0) REVERT: e 25 LEU cc_start: 0.7756 (mp) cc_final: 0.7491 (mp) REVERT: e 65 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7602 (ttt90) REVERT: e 98 SER cc_start: 0.8857 (m) cc_final: 0.8517 (t) REVERT: e 104 LYS cc_start: 0.7064 (tttm) cc_final: 0.6571 (mmmt) REVERT: e 111 LYS cc_start: 0.7910 (tttt) cc_final: 0.7366 (mmmt) REVERT: e 119 GLU cc_start: 0.7866 (tt0) cc_final: 0.7075 (tp30) REVERT: e 126 LYS cc_start: 0.5960 (mtpt) cc_final: 0.5538 (ptmm) REVERT: f 6 LYS cc_start: 0.6875 (ptmt) cc_final: 0.6515 (mmtt) REVERT: f 48 LYS cc_start: 0.7621 (mtpp) cc_final: 0.7005 (mtmt) REVERT: f 59 GLU cc_start: 0.7219 (tt0) cc_final: 0.6470 (mp0) REVERT: f 77 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6707 (mtm180) REVERT: f 81 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6837 (mt-10) REVERT: f 97 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7030 (pp) REVERT: g 39 ARG cc_start: 0.8113 (mmm160) cc_final: 0.7534 (mtp180) REVERT: h 72 LYS cc_start: 0.7209 (ttpp) cc_final: 0.6722 (tttp) REVERT: h 73 TYR cc_start: 0.7497 (m-80) cc_final: 0.7130 (m-80) REVERT: h 93 ASN cc_start: 0.7676 (m-40) cc_final: 0.7420 (m-40) REVERT: j 50 GLU cc_start: 0.8376 (pt0) cc_final: 0.7777 (pt0) REVERT: j 64 MET cc_start: 0.7922 (mtm) cc_final: 0.7606 (mtt) REVERT: k 62 GLU cc_start: 0.5571 (OUTLIER) cc_final: 0.5026 (mp0) REVERT: l 37 ARG cc_start: 0.8142 (mtp180) cc_final: 0.7409 (mmm-85) REVERT: o 21 CYS cc_start: 0.8342 (p) cc_final: 0.7729 (p) REVERT: p 6 LYS cc_start: 0.6584 (mtmt) cc_final: 0.6238 (mtmm) REVERT: p 13 LYS cc_start: 0.7905 (pttt) cc_final: 0.7501 (pttt) REVERT: p 30 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7702 (mm-30) outliers start: 284 outliers final: 221 residues processed: 1216 average time/residue: 1.0141 time to fit residues: 2058.2935 Evaluate side-chains 1275 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1020 time to evaluate : 4.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 211 TYR Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 187 CYS Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 64 ARG Chi-restraints excluded: chain H residue 129 HIS Chi-restraints excluded: chain H residue 175 LYS Chi-restraints excluded: chain H residue 176 ASP Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain I residue 21 ARG Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 130 ASN Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain I residue 193 CYS Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 138 LYS Chi-restraints excluded: chain L residue 6 ASN Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 102 MET Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 26 ARG Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain O residue 38 GLU Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 126 SER Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 141 THR Chi-restraints excluded: chain O residue 142 THR Chi-restraints excluded: chain O residue 187 LEU Chi-restraints excluded: chain O residue 195 LEU Chi-restraints excluded: chain P residue 17 LYS Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 32 GLU Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 151 ILE Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain Q residue 67 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 95 LYS Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 167 SER Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 141 HIS Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain S residue 2 SER Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 54 HIS Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 81 ARG Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 97 THR Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain S residue 150 MET Chi-restraints excluded: chain S residue 151 LEU Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain T residue 81 ASN Chi-restraints excluded: chain T residue 137 ARG Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 21 LEU Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain V residue 14 PHE Chi-restraints excluded: chain V residue 28 CYS Chi-restraints excluded: chain V residue 96 ILE Chi-restraints excluded: chain V residue 112 MET Chi-restraints excluded: chain V residue 117 ILE Chi-restraints excluded: chain V residue 135 VAL Chi-restraints excluded: chain W residue 61 HIS Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 100 LEU Chi-restraints excluded: chain X residue 137 ILE Chi-restraints excluded: chain Y residue 2 VAL Chi-restraints excluded: chain Y residue 13 ARG Chi-restraints excluded: chain Y residue 25 ASP Chi-restraints excluded: chain Y residue 57 MET Chi-restraints excluded: chain Y residue 97 PHE Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 58 THR Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 104 LEU Chi-restraints excluded: chain Z residue 114 LEU Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 43 THR Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 77 VAL Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain a residue 96 LYS Chi-restraints excluded: chain a residue 105 ASP Chi-restraints excluded: chain b residue 11 ASN Chi-restraints excluded: chain c residue 18 SER Chi-restraints excluded: chain c residue 44 LEU Chi-restraints excluded: chain c residue 101 SER Chi-restraints excluded: chain d residue 16 LEU Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 15 THR Chi-restraints excluded: chain e residue 20 ARG Chi-restraints excluded: chain e residue 27 ASN Chi-restraints excluded: chain e residue 65 ARG Chi-restraints excluded: chain e residue 70 ASN Chi-restraints excluded: chain e residue 80 LEU Chi-restraints excluded: chain e residue 83 LEU Chi-restraints excluded: chain e residue 90 ASN Chi-restraints excluded: chain f residue 7 LEU Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 52 VAL Chi-restraints excluded: chain f residue 77 ARG Chi-restraints excluded: chain f residue 81 GLU Chi-restraints excluded: chain f residue 96 MET Chi-restraints excluded: chain f residue 97 LEU Chi-restraints excluded: chain g residue 57 CYS Chi-restraints excluded: chain g residue 60 THR Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 95 MET Chi-restraints excluded: chain h residue 30 GLU Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 78 LEU Chi-restraints excluded: chain h residue 79 VAL Chi-restraints excluded: chain h residue 104 THR Chi-restraints excluded: chain i residue 19 SER Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain i residue 62 LYS Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 22 CYS Chi-restraints excluded: chain j residue 37 CYS Chi-restraints excluded: chain k residue 30 ASP Chi-restraints excluded: chain k residue 32 ASN Chi-restraints excluded: chain k residue 62 GLU Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain m residue 84 SER Chi-restraints excluded: chain m residue 92 THR Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain o residue 62 THR Chi-restraints excluded: chain o residue 92 THR Chi-restraints excluded: chain p residue 8 VAL Chi-restraints excluded: chain p residue 32 SER Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 60 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 748 optimal weight: 6.9990 chunk 788 optimal weight: 0.5980 chunk 719 optimal weight: 10.0000 chunk 767 optimal weight: 3.9990 chunk 461 optimal weight: 2.9990 chunk 334 optimal weight: 0.0970 chunk 602 optimal weight: 1.9990 chunk 235 optimal weight: 8.9990 chunk 693 optimal weight: 0.9980 chunk 725 optimal weight: 0.0470 chunk 764 optimal weight: 2.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 142 ASN A 147 GLN B 68 HIS B 377 ASN C 47 GLN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN D 76 GLN ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 HIS ** S 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 62 ASN ** g 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 75 ASN o 3 HIS o 33 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.085 115172 Z= 0.140 Angle : 0.557 12.274 169112 Z= 0.288 Chirality : 0.035 0.238 21128 Planarity : 0.004 0.072 11007 Dihedral : 22.505 179.936 49856 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.56 % Favored : 95.06 % Rotamer: Outliers : 4.44 % Allowed : 19.97 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.11), residues: 5785 helix: 0.68 (0.12), residues: 1904 sheet: -0.98 (0.18), residues: 813 loop : -1.22 (0.11), residues: 3068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP T 159 HIS 0.008 0.001 HIS G 71 PHE 0.031 0.001 PHE H 123 TYR 0.029 0.001 TYR F 186 ARG 0.016 0.000 ARG T 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1244 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1025 time to evaluate : 5.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.8273 (mt0) cc_final: 0.8016 (mt0) REVERT: A 30 ARG cc_start: 0.7340 (ttp-110) cc_final: 0.7056 (ttp-170) REVERT: A 44 MET cc_start: 0.7387 (ttp) cc_final: 0.6911 (ttt) REVERT: A 46 LYS cc_start: 0.7456 (tptm) cc_final: 0.6757 (ttpt) REVERT: A 135 ARG cc_start: 0.6873 (ttm170) cc_final: 0.6556 (mtp85) REVERT: A 201 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8283 (mttp) REVERT: B 40 LYS cc_start: 0.6651 (mmtt) cc_final: 0.6423 (mmmt) REVERT: B 53 MET cc_start: 0.8697 (ttt) cc_final: 0.8460 (ttm) REVERT: B 64 ASN cc_start: 0.8241 (t0) cc_final: 0.7800 (t0) REVERT: B 66 ARG cc_start: 0.8124 (mtp85) cc_final: 0.7633 (mtp85) REVERT: B 71 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7788 (mt-10) REVERT: B 89 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7552 (mt) REVERT: B 146 GLN cc_start: 0.6916 (mt0) cc_final: 0.6553 (mt0) REVERT: B 148 GLU cc_start: 0.7302 (tt0) cc_final: 0.6863 (mm-30) REVERT: B 181 LYS cc_start: 0.5786 (OUTLIER) cc_final: 0.5558 (pttt) REVERT: B 219 LYS cc_start: 0.6881 (mmmt) cc_final: 0.6415 (mptt) REVERT: B 228 THR cc_start: 0.7159 (m) cc_final: 0.6845 (p) REVERT: B 319 SER cc_start: 0.6909 (m) cc_final: 0.6571 (t) REVERT: B 324 LYS cc_start: 0.8497 (mptt) cc_final: 0.8002 (mmmt) REVERT: B 340 LYS cc_start: 0.6434 (mtmm) cc_final: 0.6101 (mptt) REVERT: B 345 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8034 (ttm) REVERT: B 395 LYS cc_start: 0.7789 (pttt) cc_final: 0.6680 (mmmt) REVERT: B 406 LYS cc_start: 0.3925 (OUTLIER) cc_final: 0.3394 (ttmt) REVERT: C 4 GLN cc_start: 0.6485 (pt0) cc_final: 0.5380 (pm20) REVERT: C 11 GLN cc_start: 0.6260 (tt0) cc_final: 0.5750 (mt0) REVERT: C 153 ASP cc_start: 0.7365 (t70) cc_final: 0.6915 (t70) REVERT: C 202 LYS cc_start: 0.7818 (mmtt) cc_final: 0.7342 (mmmt) REVERT: C 265 LYS cc_start: 0.6491 (mmmt) cc_final: 0.5998 (mmtt) REVERT: C 268 SER cc_start: 0.7980 (m) cc_final: 0.7695 (t) REVERT: C 296 LYS cc_start: 0.7451 (mtmm) cc_final: 0.7243 (mtmm) REVERT: C 303 LYS cc_start: 0.8002 (mttt) cc_final: 0.7529 (mtmm) REVERT: C 329 ARG cc_start: 0.7674 (mtt180) cc_final: 0.7286 (mmt180) REVERT: C 340 GLU cc_start: 0.7604 (mt-10) cc_final: 0.6997 (tp30) REVERT: D 4 LYS cc_start: 0.6873 (mttt) cc_final: 0.6212 (mppt) REVERT: D 88 LYS cc_start: 0.7969 (mttt) cc_final: 0.7619 (ptmt) REVERT: D 157 MET cc_start: 0.8055 (ttt) cc_final: 0.7668 (tmm) REVERT: D 158 LYS cc_start: 0.6759 (mttt) cc_final: 0.6371 (tptt) REVERT: D 223 GLU cc_start: 0.6770 (tt0) cc_final: 0.6223 (pm20) REVERT: D 224 LYS cc_start: 0.7194 (mttt) cc_final: 0.6770 (mttt) REVERT: D 233 VAL cc_start: 0.7912 (t) cc_final: 0.7639 (m) REVERT: D 254 ARG cc_start: 0.6280 (mtp85) cc_final: 0.5882 (mtt-85) REVERT: D 279 LYS cc_start: 0.6922 (mmmt) cc_final: 0.6516 (mttp) REVERT: D 280 LYS cc_start: 0.8020 (tptt) cc_final: 0.7591 (tptm) REVERT: E 53 ARG cc_start: 0.6740 (ttp-170) cc_final: 0.6533 (ttp-170) REVERT: E 80 GLN cc_start: 0.6764 (mt0) cc_final: 0.6549 (mm-40) REVERT: E 96 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.6251 (pm20) REVERT: E 101 TYR cc_start: 0.7755 (m-80) cc_final: 0.7454 (m-80) REVERT: E 142 LYS cc_start: 0.7544 (pmtt) cc_final: 0.6390 (tttm) REVERT: F 24 LEU cc_start: 0.6209 (OUTLIER) cc_final: 0.6005 (mt) REVERT: F 79 LYS cc_start: 0.7863 (mmtm) cc_final: 0.7385 (mtmt) REVERT: F 102 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7255 (mp) REVERT: F 122 GLU cc_start: 0.6948 (tt0) cc_final: 0.6465 (tt0) REVERT: F 163 ASN cc_start: 0.8039 (m-40) cc_final: 0.7588 (m-40) REVERT: F 164 GLN cc_start: 0.8331 (tp-100) cc_final: 0.7767 (tp40) REVERT: F 203 LYS cc_start: 0.8218 (mttt) cc_final: 0.7541 (mtmt) REVERT: F 211 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.6142 (p90) REVERT: F 228 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7032 (mt-10) REVERT: G 45 LYS cc_start: 0.7482 (tptp) cc_final: 0.7166 (ttmt) REVERT: G 48 GLN cc_start: 0.6103 (mt0) cc_final: 0.5774 (mt0) REVERT: G 54 ARG cc_start: 0.7655 (tpp-160) cc_final: 0.7040 (mmm-85) REVERT: G 59 ARG cc_start: 0.7272 (mmt-90) cc_final: 0.6817 (mmt-90) REVERT: G 67 ASN cc_start: 0.7773 (t160) cc_final: 0.7352 (t0) REVERT: G 86 GLU cc_start: 0.7027 (tt0) cc_final: 0.6471 (mt-10) REVERT: G 213 LEU cc_start: 0.7241 (tp) cc_final: 0.6745 (mt) REVERT: G 218 GLU cc_start: 0.6888 (tp30) cc_final: 0.6128 (pt0) REVERT: H 8 GLN cc_start: 0.6541 (pt0) cc_final: 0.6270 (pt0) REVERT: H 22 LYS cc_start: 0.6999 (tttt) cc_final: 0.6470 (mptt) REVERT: H 84 LYS cc_start: 0.7597 (tttm) cc_final: 0.6944 (pttt) REVERT: H 124 MET cc_start: 0.6185 (mmt) cc_final: 0.5771 (tpp) REVERT: H 175 LYS cc_start: 0.6242 (pttt) cc_final: 0.5875 (ptpt) REVERT: I 156 SER cc_start: 0.8568 (p) cc_final: 0.8271 (p) REVERT: I 192 ASP cc_start: 0.5956 (t0) cc_final: 0.5645 (t0) REVERT: J 25 GLN cc_start: 0.5091 (mm-40) cc_final: 0.4884 (mm-40) REVERT: J 45 ARG cc_start: 0.5927 (mtt180) cc_final: 0.5043 (mmt90) REVERT: J 100 PHE cc_start: 0.7666 (p90) cc_final: 0.7380 (p90) REVERT: J 110 LEU cc_start: 0.4982 (OUTLIER) cc_final: 0.4225 (tp) REVERT: J 136 ARG cc_start: 0.6872 (mmt-90) cc_final: 0.5982 (mmt90) REVERT: L 11 ASP cc_start: 0.8166 (p0) cc_final: 0.7936 (p0) REVERT: L 68 LYS cc_start: 0.7635 (mmtp) cc_final: 0.6935 (mtmt) REVERT: L 91 ARG cc_start: 0.7403 (ttp-110) cc_final: 0.6526 (mtt180) REVERT: L 93 GLN cc_start: 0.7156 (mm110) cc_final: 0.6583 (mt0) REVERT: L 110 LYS cc_start: 0.7437 (mttt) cc_final: 0.7026 (mmmt) REVERT: L 130 GLU cc_start: 0.6787 (pt0) cc_final: 0.6125 (mp0) REVERT: L 166 LYS cc_start: 0.5265 (mttt) cc_final: 0.5057 (mmmt) REVERT: L 177 GLU cc_start: 0.5887 (mt-10) cc_final: 0.5643 (mm-30) REVERT: M 63 LYS cc_start: 0.7969 (ttpt) cc_final: 0.7223 (mmtp) REVERT: M 116 LYS cc_start: 0.6774 (mttt) cc_final: 0.6357 (mtpt) REVERT: N 26 ARG cc_start: 0.6029 (OUTLIER) cc_final: 0.5720 (mtm-85) REVERT: N 33 LEU cc_start: 0.7593 (mt) cc_final: 0.7312 (mt) REVERT: N 51 MET cc_start: 0.8584 (mmm) cc_final: 0.8184 (mmt) REVERT: N 59 MET cc_start: 0.8464 (tpp) cc_final: 0.7628 (mtp) REVERT: N 108 LYS cc_start: 0.8070 (ttmt) cc_final: 0.7848 (tmmt) REVERT: N 117 ASN cc_start: 0.8555 (m-40) cc_final: 0.8157 (t0) REVERT: N 177 VAL cc_start: 0.8128 (t) cc_final: 0.7789 (m) REVERT: O 40 GLU cc_start: 0.7397 (pt0) cc_final: 0.6936 (pt0) REVERT: O 104 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6831 (mt-10) REVERT: O 176 ARG cc_start: 0.6697 (ttm-80) cc_final: 0.6060 (tmm-80) REVERT: O 185 LYS cc_start: 0.7278 (mttm) cc_final: 0.7014 (mppt) REVERT: O 196 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6531 (mm-30) REVERT: P 17 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.7833 (mtpp) REVERT: P 24 ARG cc_start: 0.8354 (mtp180) cc_final: 0.8142 (mtp180) REVERT: P 32 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7391 (mm-30) REVERT: P 76 GLU cc_start: 0.7166 (pt0) cc_final: 0.6425 (pt0) REVERT: P 94 LYS cc_start: 0.6644 (mttt) cc_final: 0.6064 (ttpp) REVERT: P 131 ARG cc_start: 0.8082 (mtt-85) cc_final: 0.6685 (mtm180) REVERT: Q 26 MET cc_start: 0.7015 (mtp) cc_final: 0.6506 (tpt) REVERT: Q 95 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7616 (mtpp) REVERT: Q 147 ASN cc_start: 0.7922 (t0) cc_final: 0.7687 (m-40) REVERT: Q 162 ARG cc_start: 0.7749 (mtp85) cc_final: 0.7469 (tpp80) REVERT: R 5 LYS cc_start: 0.8200 (tttm) cc_final: 0.7986 (ttmm) REVERT: R 28 GLU cc_start: 0.7127 (mp0) cc_final: 0.6568 (mp0) REVERT: R 36 ASN cc_start: 0.7441 (m110) cc_final: 0.6918 (p0) REVERT: R 39 GLN cc_start: 0.7087 (mm110) cc_final: 0.6514 (tm-30) REVERT: R 136 ARG cc_start: 0.6107 (ttm170) cc_final: 0.5768 (ttm110) REVERT: R 141 HIS cc_start: 0.7550 (OUTLIER) cc_final: 0.6724 (t70) REVERT: S 16 LYS cc_start: 0.7773 (mttt) cc_final: 0.7415 (tppt) REVERT: S 54 HIS cc_start: 0.7859 (OUTLIER) cc_final: 0.7333 (p90) REVERT: S 81 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7152 (tmm-80) REVERT: S 92 GLU cc_start: 0.7969 (pt0) cc_final: 0.7392 (pt0) REVERT: S 116 SER cc_start: 0.8025 (t) cc_final: 0.7660 (p) REVERT: S 147 LYS cc_start: 0.7399 (mttt) cc_final: 0.6893 (mtmm) REVERT: T 21 LYS cc_start: 0.7283 (mttt) cc_final: 0.6819 (mmtt) REVERT: T 31 LEU cc_start: 0.8316 (mt) cc_final: 0.8005 (mp) REVERT: T 77 LYS cc_start: 0.8580 (mttp) cc_final: 0.7922 (mtmt) REVERT: T 81 ASN cc_start: 0.6690 (OUTLIER) cc_final: 0.6270 (t0) REVERT: T 148 GLN cc_start: 0.7143 (tt0) cc_final: 0.6761 (tt0) REVERT: T 156 ARG cc_start: 0.6495 (mtt90) cc_final: 0.6082 (mmt90) REVERT: U 18 PHE cc_start: 0.7206 (OUTLIER) cc_final: 0.6424 (p90) REVERT: U 23 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6584 (mt-10) REVERT: U 29 GLN cc_start: 0.7548 (mt0) cc_final: 0.7180 (mm110) REVERT: U 32 MET cc_start: 0.7759 (mtt) cc_final: 0.7468 (ttm) REVERT: U 76 PHE cc_start: 0.7888 (t80) cc_final: 0.7440 (t80) REVERT: U 99 ARG cc_start: 0.6747 (mtp180) cc_final: 0.6180 (ptp-170) REVERT: V 14 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7374 (m-80) REVERT: V 96 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6961 (tt) REVERT: V 123 LYS cc_start: 0.7074 (tttp) cc_final: 0.6773 (tptt) REVERT: X 39 ARG cc_start: 0.5515 (ptp90) cc_final: 0.4320 (mtp85) REVERT: X 46 LYS cc_start: 0.6969 (tttm) cc_final: 0.6539 (mmtm) REVERT: X 49 LYS cc_start: 0.7764 (mttt) cc_final: 0.7114 (mtpp) REVERT: X 71 THR cc_start: 0.6748 (m) cc_final: 0.6437 (p) REVERT: X 78 ASN cc_start: 0.7644 (t0) cc_final: 0.7343 (t0) REVERT: X 87 LYS cc_start: 0.8461 (mttt) cc_final: 0.7642 (mmmt) REVERT: X 115 LYS cc_start: 0.8137 (mttt) cc_final: 0.7701 (mtmt) REVERT: Y 23 LYS cc_start: 0.7093 (mttt) cc_final: 0.6511 (pttm) REVERT: Y 80 ILE cc_start: 0.8092 (mt) cc_final: 0.7600 (pt) REVERT: Y 95 VAL cc_start: 0.7132 (t) cc_final: 0.6596 (m) REVERT: Y 97 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6138 (m-80) REVERT: Z 43 MET cc_start: 0.7335 (ttp) cc_final: 0.6953 (tmm) REVERT: Z 47 LYS cc_start: 0.6459 (mttt) cc_final: 0.5761 (tmtt) REVERT: Z 56 MET cc_start: 0.5592 (tpt) cc_final: 0.5087 (ttp) REVERT: a 22 VAL cc_start: 0.7877 (OUTLIER) cc_final: 0.7593 (m) REVERT: a 55 LYS cc_start: 0.8422 (tttt) cc_final: 0.8147 (ttmt) REVERT: a 105 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7080 (m-30) REVERT: a 109 ASN cc_start: 0.8148 (m-40) cc_final: 0.7571 (m110) REVERT: a 122 LYS cc_start: 0.8031 (mttt) cc_final: 0.7514 (mmmt) REVERT: a 137 GLU cc_start: 0.6959 (tt0) cc_final: 0.6009 (pt0) REVERT: b 23 LYS cc_start: 0.7607 (tttt) cc_final: 0.7107 (pttm) REVERT: c 56 ARG cc_start: 0.6993 (tpt-90) cc_final: 0.6726 (tpt-90) REVERT: c 89 ARG cc_start: 0.6826 (mtt180) cc_final: 0.6472 (ptp90) REVERT: d 42 LYS cc_start: 0.6951 (tttt) cc_final: 0.6637 (ttmt) REVERT: e 20 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7442 (ttt180) REVERT: e 22 GLN cc_start: 0.8320 (mm-40) cc_final: 0.7875 (mt0) REVERT: e 25 LEU cc_start: 0.7643 (mp) cc_final: 0.7381 (mp) REVERT: e 80 LEU cc_start: 0.7538 (tp) cc_final: 0.7256 (tt) REVERT: e 98 SER cc_start: 0.8841 (m) cc_final: 0.8514 (t) REVERT: e 104 LYS cc_start: 0.7018 (tttm) cc_final: 0.6529 (mmmt) REVERT: e 111 LYS cc_start: 0.7937 (tttt) cc_final: 0.7300 (mmmt) REVERT: e 119 GLU cc_start: 0.7871 (tt0) cc_final: 0.7100 (tp30) REVERT: e 126 LYS cc_start: 0.5883 (mtpt) cc_final: 0.5453 (ptmm) REVERT: f 6 LYS cc_start: 0.6902 (ptmt) cc_final: 0.6594 (mmtt) REVERT: f 48 LYS cc_start: 0.7594 (mtpp) cc_final: 0.6964 (mtmt) REVERT: f 59 GLU cc_start: 0.7186 (tt0) cc_final: 0.6453 (mp0) REVERT: f 81 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6679 (mt-10) REVERT: f 97 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.6998 (pp) REVERT: g 39 ARG cc_start: 0.8116 (mmm160) cc_final: 0.7555 (mtp180) REVERT: g 97 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.6032 (tm-30) REVERT: h 71 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6848 (pt0) REVERT: h 72 LYS cc_start: 0.7184 (ttpp) cc_final: 0.6809 (tttp) REVERT: h 73 TYR cc_start: 0.7549 (m-80) cc_final: 0.7164 (m-80) REVERT: h 103 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7348 (mp) REVERT: j 50 GLU cc_start: 0.8413 (pt0) cc_final: 0.7768 (pt0) REVERT: j 64 MET cc_start: 0.7839 (mtm) cc_final: 0.7273 (mtt) REVERT: k 32 ASN cc_start: 0.6850 (OUTLIER) cc_final: 0.6575 (m-40) REVERT: k 62 GLU cc_start: 0.5495 (OUTLIER) cc_final: 0.5064 (mp0) REVERT: l 37 ARG cc_start: 0.8099 (mtp180) cc_final: 0.7500 (mmm-85) REVERT: o 21 CYS cc_start: 0.8349 (p) cc_final: 0.7747 (p) REVERT: p 6 LYS cc_start: 0.6540 (mtmt) cc_final: 0.6165 (mtmm) REVERT: p 13 LYS cc_start: 0.7866 (pttt) cc_final: 0.7419 (pttt) REVERT: p 30 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7544 (mm-30) outliers start: 219 outliers final: 171 residues processed: 1148 average time/residue: 1.0127 time to fit residues: 1933.6887 Evaluate side-chains 1203 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1000 time to evaluate : 5.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 211 TYR Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 187 CYS Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 64 ARG Chi-restraints excluded: chain H residue 129 HIS Chi-restraints excluded: chain I residue 21 ARG Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 130 ASN Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain I residue 193 CYS Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 138 LYS Chi-restraints excluded: chain L residue 6 ASN Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 26 ARG Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain O residue 38 GLU Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 126 SER Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 141 THR Chi-restraints excluded: chain O residue 195 LEU Chi-restraints excluded: chain P residue 17 LYS Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 32 GLU Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 151 ILE Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 95 LYS Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 167 SER Chi-restraints excluded: chain R residue 24 MET Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 141 HIS Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain S residue 2 SER Chi-restraints excluded: chain S residue 54 HIS Chi-restraints excluded: chain S residue 81 ARG Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 97 THR Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain S residue 151 LEU Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain T residue 81 ASN Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain V residue 14 PHE Chi-restraints excluded: chain V residue 28 CYS Chi-restraints excluded: chain V residue 96 ILE Chi-restraints excluded: chain V residue 112 MET Chi-restraints excluded: chain V residue 117 ILE Chi-restraints excluded: chain V residue 135 VAL Chi-restraints excluded: chain W residue 31 MET Chi-restraints excluded: chain X residue 100 LEU Chi-restraints excluded: chain X residue 137 ILE Chi-restraints excluded: chain Y residue 2 VAL Chi-restraints excluded: chain Y residue 13 ARG Chi-restraints excluded: chain Y residue 25 ASP Chi-restraints excluded: chain Y residue 97 PHE Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 58 THR Chi-restraints excluded: chain Z residue 104 LEU Chi-restraints excluded: chain Z residue 114 LEU Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 43 THR Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 77 VAL Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain a residue 96 LYS Chi-restraints excluded: chain a residue 105 ASP Chi-restraints excluded: chain b residue 10 HIS Chi-restraints excluded: chain b residue 11 ASN Chi-restraints excluded: chain c residue 44 LEU Chi-restraints excluded: chain c residue 101 SER Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 15 THR Chi-restraints excluded: chain e residue 20 ARG Chi-restraints excluded: chain e residue 27 ASN Chi-restraints excluded: chain e residue 70 ASN Chi-restraints excluded: chain e residue 83 LEU Chi-restraints excluded: chain f residue 7 LEU Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 81 GLU Chi-restraints excluded: chain f residue 96 MET Chi-restraints excluded: chain f residue 97 LEU Chi-restraints excluded: chain g residue 60 THR Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 95 MET Chi-restraints excluded: chain g residue 97 GLU Chi-restraints excluded: chain h residue 30 GLU Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 78 LEU Chi-restraints excluded: chain h residue 79 VAL Chi-restraints excluded: chain h residue 103 LEU Chi-restraints excluded: chain h residue 104 THR Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 62 LYS Chi-restraints excluded: chain j residue 22 CYS Chi-restraints excluded: chain j residue 37 CYS Chi-restraints excluded: chain k residue 30 ASP Chi-restraints excluded: chain k residue 32 ASN Chi-restraints excluded: chain k residue 62 GLU Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain m residue 84 SER Chi-restraints excluded: chain m residue 92 THR Chi-restraints excluded: chain m residue 122 LYS Chi-restraints excluded: chain o residue 92 THR Chi-restraints excluded: chain p residue 8 VAL Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 60 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 503 optimal weight: 0.9990 chunk 811 optimal weight: 4.9990 chunk 495 optimal weight: 0.9990 chunk 384 optimal weight: 0.6980 chunk 563 optimal weight: 0.7980 chunk 850 optimal weight: 0.3980 chunk 783 optimal weight: 1.9990 chunk 677 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 523 optimal weight: 6.9990 chunk 415 optimal weight: 6.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 147 GLN B 68 HIS C 47 GLN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 81 ASN a 109 ASN ** g 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 33 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 115172 Z= 0.137 Angle : 0.538 11.514 169112 Z= 0.277 Chirality : 0.034 0.281 21128 Planarity : 0.004 0.066 11007 Dihedral : 22.423 179.939 49852 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.84 % Favored : 94.80 % Rotamer: Outliers : 4.00 % Allowed : 20.52 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.11), residues: 5785 helix: 0.81 (0.12), residues: 1909 sheet: -0.91 (0.17), residues: 837 loop : -1.12 (0.11), residues: 3039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP T 159 HIS 0.009 0.001 HIS H 126 PHE 0.024 0.001 PHE H 123 TYR 0.028 0.001 TYR F 186 ARG 0.010 0.000 ARG l 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11570 Ramachandran restraints generated. 5785 Oldfield, 0 Emsley, 5785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1237 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1040 time to evaluate : 5.653 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: A 8 GLN cc_start: 0.8269 (mt0) cc_final: 0.8005 (mt0) REVERT: A 44 MET cc_start: 0.7357 (ttp) cc_final: 0.6866 (ttt) REVERT: A 46 LYS cc_start: 0.7445 (tptm) cc_final: 0.6745 (ttpt) REVERT: A 135 ARG cc_start: 0.6770 (ttm170) cc_final: 0.6475 (mtp85) REVERT: A 179 LYS cc_start: 0.7443 (mtmt) cc_final: 0.7101 (mtmt) REVERT: A 201 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8276 (mttp) REVERT: B 53 MET cc_start: 0.8685 (ttt) cc_final: 0.8483 (ttm) REVERT: B 64 ASN cc_start: 0.8229 (t0) cc_final: 0.7816 (t0) REVERT: B 71 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7763 (mt-10) REVERT: B 84 MET cc_start: 0.7632 (ptm) cc_final: 0.7419 (ptm) REVERT: B 89 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7536 (mt) REVERT: B 146 GLN cc_start: 0.6873 (mt0) cc_final: 0.6512 (mt0) REVERT: B 148 GLU cc_start: 0.7284 (tt0) cc_final: 0.6849 (mm-30) REVERT: B 181 LYS cc_start: 0.5703 (OUTLIER) cc_final: 0.5490 (pttt) REVERT: B 219 LYS cc_start: 0.6824 (mmmt) cc_final: 0.6341 (mptt) REVERT: B 228 THR cc_start: 0.7156 (m) cc_final: 0.6824 (p) REVERT: B 319 SER cc_start: 0.6871 (m) cc_final: 0.6534 (t) REVERT: B 324 LYS cc_start: 0.8447 (mptt) cc_final: 0.7981 (mmmt) REVERT: B 340 LYS cc_start: 0.6383 (mtmm) cc_final: 0.6155 (mptt) REVERT: B 345 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7944 (ttm) REVERT: B 395 LYS cc_start: 0.7801 (pttt) cc_final: 0.6702 (mmmt) REVERT: C 4 GLN cc_start: 0.6331 (pt0) cc_final: 0.5290 (pm20) REVERT: C 11 GLN cc_start: 0.6434 (tt0) cc_final: 0.5925 (mt0) REVERT: C 54 MET cc_start: 0.8042 (ttp) cc_final: 0.7814 (ttm) REVERT: C 153 ASP cc_start: 0.7248 (t70) cc_final: 0.6859 (t70) REVERT: C 202 LYS cc_start: 0.7801 (mmtt) cc_final: 0.7303 (mmmt) REVERT: C 265 LYS cc_start: 0.6590 (mmmt) cc_final: 0.6130 (mmtt) REVERT: C 303 LYS cc_start: 0.8003 (mttt) cc_final: 0.7443 (pttm) REVERT: C 340 GLU cc_start: 0.7520 (mt-10) cc_final: 0.6886 (tp30) REVERT: D 4 LYS cc_start: 0.6862 (mttt) cc_final: 0.6201 (mppt) REVERT: D 88 LYS cc_start: 0.7798 (mttt) cc_final: 0.7472 (ptmt) REVERT: D 157 MET cc_start: 0.7939 (ttt) cc_final: 0.7571 (tmm) REVERT: D 158 LYS cc_start: 0.6729 (mttt) cc_final: 0.6299 (tptt) REVERT: D 223 GLU cc_start: 0.6678 (tt0) cc_final: 0.6193 (pm20) REVERT: D 224 LYS cc_start: 0.7057 (mttt) cc_final: 0.6667 (mttt) REVERT: D 233 VAL cc_start: 0.7913 (t) cc_final: 0.7655 (m) REVERT: D 254 ARG cc_start: 0.6673 (mtp85) cc_final: 0.6300 (mtt-85) REVERT: D 279 LYS cc_start: 0.6921 (mmmt) cc_final: 0.6512 (mttp) REVERT: D 280 LYS cc_start: 0.8031 (tptt) cc_final: 0.7604 (tptm) REVERT: E 96 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6312 (pm20) REVERT: E 101 TYR cc_start: 0.7760 (m-80) cc_final: 0.7462 (m-80) REVERT: E 142 LYS cc_start: 0.7520 (pmtt) cc_final: 0.6349 (tttm) REVERT: F 24 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5986 (mt) REVERT: F 63 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6756 (tm-30) REVERT: F 79 LYS cc_start: 0.7862 (mmtm) cc_final: 0.7375 (mtmt) REVERT: F 102 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7244 (mp) REVERT: F 122 GLU cc_start: 0.6928 (tt0) cc_final: 0.6437 (tt0) REVERT: F 163 ASN cc_start: 0.7922 (m-40) cc_final: 0.7524 (m-40) REVERT: F 164 GLN cc_start: 0.8304 (tp-100) cc_final: 0.7787 (tp40) REVERT: F 203 LYS cc_start: 0.8216 (mttt) cc_final: 0.7548 (mtmt) REVERT: F 211 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.6007 (p90) REVERT: F 228 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7132 (mt-10) REVERT: G 45 LYS cc_start: 0.7536 (tptp) cc_final: 0.7256 (ttmt) REVERT: G 48 GLN cc_start: 0.6074 (mt0) cc_final: 0.5748 (mt0) REVERT: G 54 ARG cc_start: 0.7635 (tpp-160) cc_final: 0.6992 (mmm160) REVERT: G 59 ARG cc_start: 0.7249 (mmt-90) cc_final: 0.6883 (mmt-90) REVERT: G 67 ASN cc_start: 0.7755 (t160) cc_final: 0.7270 (t0) REVERT: G 86 GLU cc_start: 0.6983 (tt0) cc_final: 0.6593 (mt-10) REVERT: G 213 LEU cc_start: 0.7089 (tp) cc_final: 0.6592 (mt) REVERT: G 218 GLU cc_start: 0.6888 (tp30) cc_final: 0.6112 (pt0) REVERT: H 8 GLN cc_start: 0.6532 (pt0) cc_final: 0.6099 (pt0) REVERT: H 22 LYS cc_start: 0.6983 (tttt) cc_final: 0.6427 (mmtp) REVERT: H 84 LYS cc_start: 0.7590 (tttm) cc_final: 0.6935 (pttt) REVERT: H 104 HIS cc_start: 0.6303 (t-90) cc_final: 0.6087 (t70) REVERT: H 113 GLU cc_start: 0.5927 (pm20) cc_final: 0.5597 (pm20) REVERT: H 128 GLU cc_start: 0.5362 (tp30) cc_final: 0.4831 (tp30) REVERT: H 175 LYS cc_start: 0.6204 (pttt) cc_final: 0.5843 (ptpt) REVERT: I 30 ARG cc_start: 0.5884 (mmm-85) cc_final: 0.5340 (mmm160) REVERT: I 156 SER cc_start: 0.8574 (p) cc_final: 0.8278 (p) REVERT: I 192 ASP cc_start: 0.6036 (t0) cc_final: 0.5753 (t0) REVERT: J 4 LYS cc_start: 0.5407 (ttpt) cc_final: 0.5002 (mtmm) REVERT: J 45 ARG cc_start: 0.5900 (mtt180) cc_final: 0.5023 (mmt90) REVERT: J 100 PHE cc_start: 0.7515 (p90) cc_final: 0.7268 (p90) REVERT: J 110 LEU cc_start: 0.4954 (OUTLIER) cc_final: 0.4229 (tp) REVERT: J 136 ARG cc_start: 0.7193 (mmt-90) cc_final: 0.6206 (mmt90) REVERT: L 11 ASP cc_start: 0.8093 (p0) cc_final: 0.7865 (p0) REVERT: L 68 LYS cc_start: 0.7702 (mmtp) cc_final: 0.6994 (mtmt) REVERT: L 91 ARG cc_start: 0.7427 (ttp-110) cc_final: 0.6521 (mtt180) REVERT: L 93 GLN cc_start: 0.7138 (mm110) cc_final: 0.6564 (mt0) REVERT: L 110 LYS cc_start: 0.7428 (mttt) cc_final: 0.7015 (mmmt) REVERT: L 130 GLU cc_start: 0.6476 (pt0) cc_final: 0.6004 (mp0) REVERT: L 166 LYS cc_start: 0.5327 (mttt) cc_final: 0.5056 (mmmt) REVERT: L 177 GLU cc_start: 0.6069 (mt-10) cc_final: 0.5778 (mm-30) REVERT: M 8 GLU cc_start: 0.7724 (tt0) cc_final: 0.7334 (mt-10) REVERT: M 63 LYS cc_start: 0.7961 (ttpt) cc_final: 0.7181 (mmtp) REVERT: M 116 LYS cc_start: 0.6778 (mttt) cc_final: 0.6412 (mtpt) REVERT: N 33 LEU cc_start: 0.7530 (mt) cc_final: 0.7223 (mt) REVERT: N 51 MET cc_start: 0.8585 (mmm) cc_final: 0.8204 (mmt) REVERT: N 59 MET cc_start: 0.8430 (tpp) cc_final: 0.7653 (mtp) REVERT: N 108 LYS cc_start: 0.8077 (ttmt) cc_final: 0.7848 (tmmt) REVERT: N 117 ASN cc_start: 0.8522 (m-40) cc_final: 0.8129 (m-40) REVERT: N 177 VAL cc_start: 0.8110 (t) cc_final: 0.7805 (m) REVERT: O 32 VAL cc_start: 0.8276 (t) cc_final: 0.7969 (p) REVERT: O 34 VAL cc_start: 0.7730 (m) cc_final: 0.7494 (m) REVERT: O 40 GLU cc_start: 0.7212 (pt0) cc_final: 0.6742 (pt0) REVERT: O 104 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6934 (mt-10) REVERT: O 176 ARG cc_start: 0.6724 (ttm-80) cc_final: 0.6033 (tmm-80) REVERT: O 185 LYS cc_start: 0.7343 (mttm) cc_final: 0.7054 (mppt) REVERT: O 196 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6526 (mm-30) REVERT: P 17 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.7885 (mtpp) REVERT: P 24 ARG cc_start: 0.8403 (mtp180) cc_final: 0.8147 (mtm180) REVERT: P 32 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7322 (mm-30) REVERT: P 76 GLU cc_start: 0.7227 (pt0) cc_final: 0.6495 (pt0) REVERT: P 94 LYS cc_start: 0.6524 (mttt) cc_final: 0.6024 (ttpp) REVERT: P 131 ARG cc_start: 0.8142 (mtt-85) cc_final: 0.6735 (mtm180) REVERT: Q 13 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8084 (mt0) REVERT: Q 26 MET cc_start: 0.7005 (mtp) cc_final: 0.6488 (tpt) REVERT: Q 95 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7602 (mtpp) REVERT: Q 147 ASN cc_start: 0.7874 (t0) cc_final: 0.7634 (m-40) REVERT: Q 162 ARG cc_start: 0.7798 (mtp85) cc_final: 0.7499 (tpp80) REVERT: R 5 LYS cc_start: 0.8184 (tttm) cc_final: 0.7967 (ttmm) REVERT: R 28 GLU cc_start: 0.7125 (mp0) cc_final: 0.6629 (mp0) REVERT: R 36 ASN cc_start: 0.7436 (m110) cc_final: 0.6930 (p0) REVERT: R 39 GLN cc_start: 0.7066 (mm110) cc_final: 0.6530 (tm-30) REVERT: R 114 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7410 (mt-10) REVERT: R 136 ARG cc_start: 0.6120 (ttm170) cc_final: 0.5780 (ttm110) REVERT: R 141 HIS cc_start: 0.7484 (OUTLIER) cc_final: 0.6737 (t70) REVERT: S 16 LYS cc_start: 0.7675 (mttt) cc_final: 0.7325 (tppt) REVERT: S 81 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6947 (tmm-80) REVERT: S 85 ASN cc_start: 0.6495 (OUTLIER) cc_final: 0.6039 (t0) REVERT: S 92 GLU cc_start: 0.7985 (pt0) cc_final: 0.7464 (pt0) REVERT: S 116 SER cc_start: 0.7971 (t) cc_final: 0.7618 (p) REVERT: S 147 LYS cc_start: 0.7412 (mttt) cc_final: 0.6873 (mtmm) REVERT: T 21 LYS cc_start: 0.7298 (mttt) cc_final: 0.6822 (mmtt) REVERT: T 52 MET cc_start: 0.8414 (mtp) cc_final: 0.8142 (ttp) REVERT: T 77 LYS cc_start: 0.8574 (mttp) cc_final: 0.7906 (mtmt) REVERT: T 156 ARG cc_start: 0.6471 (mtt90) cc_final: 0.6100 (mmt90) REVERT: U 18 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.6253 (p90) REVERT: U 20 GLN cc_start: 0.5859 (mt0) cc_final: 0.5452 (tt0) REVERT: U 23 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6553 (mt-10) REVERT: U 26 GLU cc_start: 0.7826 (tt0) cc_final: 0.7450 (tp30) REVERT: U 29 GLN cc_start: 0.7415 (mt0) cc_final: 0.7088 (mm110) REVERT: U 32 MET cc_start: 0.7727 (mtt) cc_final: 0.7451 (ttm) REVERT: U 76 PHE cc_start: 0.7861 (t80) cc_final: 0.7515 (t80) REVERT: V 14 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7053 (m-80) REVERT: V 96 ILE cc_start: 0.7058 (OUTLIER) cc_final: 0.6840 (tt) REVERT: V 123 LYS cc_start: 0.7046 (tttp) cc_final: 0.6736 (tptt) REVERT: X 39 ARG cc_start: 0.5439 (ptp90) cc_final: 0.4298 (mtp85) REVERT: X 46 LYS cc_start: 0.7073 (tttm) cc_final: 0.6570 (mmtm) REVERT: X 49 LYS cc_start: 0.7753 (mttt) cc_final: 0.7044 (mtpp) REVERT: X 78 ASN cc_start: 0.7502 (t0) cc_final: 0.7226 (t0) REVERT: X 87 LYS cc_start: 0.8453 (mttt) cc_final: 0.7621 (mmmt) REVERT: X 115 LYS cc_start: 0.8134 (mttt) cc_final: 0.7668 (mtmt) REVERT: Y 23 LYS cc_start: 0.7258 (mttt) cc_final: 0.6653 (pttm) REVERT: Y 80 ILE cc_start: 0.8109 (mt) cc_final: 0.7683 (pt) REVERT: Y 95 VAL cc_start: 0.7135 (t) cc_final: 0.6616 (m) REVERT: Y 97 PHE cc_start: 0.7005 (OUTLIER) cc_final: 0.6315 (m-80) REVERT: Z 43 MET cc_start: 0.8119 (ttp) cc_final: 0.7848 (tmm) REVERT: Z 47 LYS cc_start: 0.6462 (mttt) cc_final: 0.5773 (tmtt) REVERT: Z 56 MET cc_start: 0.5567 (tpt) cc_final: 0.5091 (ttm) REVERT: a 16 SER cc_start: 0.9022 (m) cc_final: 0.8811 (t) REVERT: a 22 VAL cc_start: 0.7901 (OUTLIER) cc_final: 0.7610 (m) REVERT: a 55 LYS cc_start: 0.8437 (tttt) cc_final: 0.8161 (ttmt) REVERT: a 105 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7033 (m-30) REVERT: a 109 ASN cc_start: 0.8164 (m110) cc_final: 0.7623 (m110) REVERT: a 122 LYS cc_start: 0.8020 (mttt) cc_final: 0.7504 (mmmt) REVERT: a 137 GLU cc_start: 0.6917 (tt0) cc_final: 0.5986 (pt0) REVERT: b 23 LYS cc_start: 0.7600 (tttt) cc_final: 0.7088 (pttm) REVERT: c 56 ARG cc_start: 0.7018 (tpt-90) cc_final: 0.6714 (tpt-90) REVERT: c 89 ARG cc_start: 0.6796 (mtt180) cc_final: 0.6434 (ptp90) REVERT: d 42 LYS cc_start: 0.6955 (tttt) cc_final: 0.6614 (ttmt) REVERT: e 20 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7417 (ttt180) REVERT: e 22 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7839 (mt0) REVERT: e 25 LEU cc_start: 0.7654 (mp) cc_final: 0.7380 (mp) REVERT: e 65 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7582 (ttt90) REVERT: e 80 LEU cc_start: 0.7543 (tp) cc_final: 0.7262 (tt) REVERT: e 98 SER cc_start: 0.8852 (m) cc_final: 0.8573 (t) REVERT: e 104 LYS cc_start: 0.7064 (tttm) cc_final: 0.6539 (mmmt) REVERT: e 111 LYS cc_start: 0.7843 (tttt) cc_final: 0.7253 (mmmt) REVERT: e 119 GLU cc_start: 0.7865 (tt0) cc_final: 0.7083 (tp30) REVERT: e 126 LYS cc_start: 0.5975 (mtpt) cc_final: 0.5497 (ptmm) REVERT: f 6 LYS cc_start: 0.6938 (ptmt) cc_final: 0.6673 (mmtt) REVERT: f 48 LYS cc_start: 0.7372 (mtpp) cc_final: 0.7068 (mmmm) REVERT: f 59 GLU cc_start: 0.7146 (tt0) cc_final: 0.6428 (mp0) REVERT: f 81 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6700 (mt-10) REVERT: f 97 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.6995 (pp) REVERT: g 39 ARG cc_start: 0.8112 (mmm160) cc_final: 0.7565 (mtp180) REVERT: g 97 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.5957 (tm-30) REVERT: h 71 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6858 (pt0) REVERT: h 72 LYS cc_start: 0.7080 (ttpp) cc_final: 0.6689 (tttp) REVERT: h 73 TYR cc_start: 0.7564 (m-80) cc_final: 0.7194 (m-80) REVERT: j 50 GLU cc_start: 0.8572 (pt0) cc_final: 0.8022 (pt0) REVERT: j 63 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7473 (mm-30) REVERT: j 64 MET cc_start: 0.7826 (mtm) cc_final: 0.7478 (mtt) REVERT: k 62 GLU cc_start: 0.5476 (OUTLIER) cc_final: 0.5052 (mp0) REVERT: l 37 ARG cc_start: 0.8096 (mtp180) cc_final: 0.7510 (mmm-85) REVERT: o 21 CYS cc_start: 0.8296 (p) cc_final: 0.7712 (p) REVERT: p 6 LYS cc_start: 0.6565 (mtmt) cc_final: 0.6187 (mtmm) REVERT: p 13 LYS cc_start: 0.7860 (pttt) cc_final: 0.7374 (pttt) REVERT: p 30 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7539 (mm-30) outliers start: 197 outliers final: 148 residues processed: 1148 average time/residue: 1.0106 time to fit residues: 1934.0415 Evaluate side-chains 1190 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1013 time to evaluate : 5.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 211 TYR Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 187 CYS Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 64 ARG Chi-restraints excluded: chain H residue 129 HIS Chi-restraints excluded: chain I residue 21 ARG Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 130 ASN Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 138 LYS Chi-restraints excluded: chain L residue 6 ASN Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain O residue 38 GLU Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 126 SER Chi-restraints excluded: chain O residue 195 LEU Chi-restraints excluded: chain P residue 17 LYS Chi-restraints excluded: chain P residue 32 GLU Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 95 LYS Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 24 MET Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 141 HIS Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain S residue 2 SER Chi-restraints excluded: chain S residue 81 ARG Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 97 THR Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain V residue 14 PHE Chi-restraints excluded: chain V residue 96 ILE Chi-restraints excluded: chain V residue 112 MET Chi-restraints excluded: chain V residue 117 ILE Chi-restraints excluded: chain V residue 135 VAL Chi-restraints excluded: chain X residue 137 ILE Chi-restraints excluded: chain Y residue 2 VAL Chi-restraints excluded: chain Y residue 25 ASP Chi-restraints excluded: chain Y residue 97 PHE Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 104 LEU Chi-restraints excluded: chain Z residue 114 LEU Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 43 THR Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 77 VAL Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain a residue 105 ASP Chi-restraints excluded: chain b residue 10 HIS Chi-restraints excluded: chain b residue 11 ASN Chi-restraints excluded: chain c residue 44 LEU Chi-restraints excluded: chain c residue 101 SER Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 15 THR Chi-restraints excluded: chain e residue 20 ARG Chi-restraints excluded: chain e residue 27 ASN Chi-restraints excluded: chain e residue 65 ARG Chi-restraints excluded: chain e residue 70 ASN Chi-restraints excluded: chain e residue 83 LEU Chi-restraints excluded: chain f residue 12 THR Chi-restraints excluded: chain f residue 81 GLU Chi-restraints excluded: chain f residue 96 MET Chi-restraints excluded: chain f residue 97 LEU Chi-restraints excluded: chain g residue 60 THR Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 97 GLU Chi-restraints excluded: chain h residue 30 GLU Chi-restraints excluded: chain h residue 78 LEU Chi-restraints excluded: chain h residue 79 VAL Chi-restraints excluded: chain h residue 104 THR Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 62 LYS Chi-restraints excluded: chain j residue 22 CYS Chi-restraints excluded: chain j residue 37 CYS Chi-restraints excluded: chain k residue 62 GLU Chi-restraints excluded: chain m residue 84 SER Chi-restraints excluded: chain m residue 92 THR Chi-restraints excluded: chain m residue 122 LYS Chi-restraints excluded: chain o residue 62 THR Chi-restraints excluded: chain o residue 92 THR Chi-restraints excluded: chain p residue 32 SER Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 60 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 538 optimal weight: 0.8980 chunk 721 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 624 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 chunk 678 optimal weight: 0.5980 chunk 283 optimal weight: 10.0000 chunk 696 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 142 ASN A 147 GLN B 68 HIS B 377 ASN ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 GLN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 GLN ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 HIS ** N 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 HIS O 128 HIS ** S 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 135 HIS b 16 HIS ** g 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 32 ASN o 33 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.144054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.124398 restraints weight = 141564.354| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.25 r_work: 0.3099 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 115172 Z= 0.247 Angle : 0.589 12.657 169112 Z= 0.301 Chirality : 0.037 0.233 21128 Planarity : 0.004 0.065 11007 Dihedral : 22.417 179.842 49847 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.19 % Favored : 94.45 % Rotamer: Outliers : 4.26 % Allowed : 20.21 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.83 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.11), residues: 5785 helix: 0.65 (0.12), residues: 1909 sheet: -0.88 (0.18), residues: 819 loop : -1.20 (0.11), residues: 3057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP T 159 HIS 0.010 0.001 HIS H 126 PHE 0.024 0.002 PHE T 15 TYR 0.029 0.002 TYR F 186 ARG 0.009 0.001 ARG l 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28759.69 seconds wall clock time: 500 minutes 55.91 seconds (30055.91 seconds total)