Starting phenix.real_space_refine on Thu Dec 7 16:18:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xy3_6784/12_2023/5xy3_6784_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xy3_6784/12_2023/5xy3_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_6784/12_2023/5xy3_6784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xy3_6784/12_2023/5xy3_6784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xy3_6784/12_2023/5xy3_6784_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xy3_6784/12_2023/5xy3_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-1.21rc1-5172/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: 40.91, 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: 38.19 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: 35.76 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: 124.05 Time building geometry restraints manager: 41.85 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: 63935 35.99 - 71.99: 5176 71.99 - 107.98: 746 107.98 - 143.97: 23 143.97 - 179.96: 56 Dihedral angle restraints: 69936 sinusoidal: 52844 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 69933 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: 1.160 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: 10.280 Check model and map are aligned: 1.170 Set scattering table: 0.740 Process input model: 315.330 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 334.200 ------------------------------------------------------------------------------- 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 : 21.799 179.965 58831 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 : 5.527 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 outliers start: 170 outliers final: 57 residues processed: 1660 average time/residue: 1.1488 time to fit residues: 3113.1314 Evaluate side-chains 1088 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1031 time to evaluate : 5.402 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 3 residues processed: 57 average time/residue: 0.7673 time to fit residues: 89.5547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 721 optimal weight: 10.0000 chunk 647 optimal weight: 0.3980 chunk 359 optimal weight: 0.9990 chunk 221 optimal weight: 7.9990 chunk 436 optimal weight: 0.9980 chunk 345 optimal weight: 1.9990 chunk 669 optimal weight: 5.9990 chunk 259 optimal weight: 9.9990 chunk 407 optimal weight: 0.4980 chunk 498 optimal weight: 0.0370 chunk 775 optimal weight: 0.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- 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 136 ASN B 195 HIS B 211 ASN B 287 GLN B 292 HIS C 82 ASN C 135 GLN 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 111 GLN D 228 GLN D 276 HIS D 282 GLN E 70 GLN E 119 GLN F 37 ASN F 152 ASN F 205 HIS G 67 ASN G 71 HIS H 30 HIS H 129 HIS ** H 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 ASN I 57 HIS I 73 ASN I 90 ASN I 132 ASN I 185 GLN I 187 ASN J 6 ASN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 GLN M 83 GLN N 15 GLN N 32 GLN N 87 HIS O 12 HIS O 24 GLN O 44 GLN O 75 HIS O 199 GLN Q 28 HIS Q 126 GLN S 5 GLN S 62 HIS ** S 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 81 ASN T 95 HIS V 36 ASN V 45 HIS W 16 HIS Y 5 ASN Y 103 ASN Z 84 HIS b 11 ASN b 16 HIS b 36 ASN 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 h 106 GLN j 16 HIS j 24 ASN j 28 HIS o 18 HIS o 33 HIS Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 115172 Z= 0.164 Angle : 0.642 14.474 169112 Z= 0.339 Chirality : 0.040 0.323 21128 Planarity : 0.005 0.061 11007 Dihedral : 21.705 179.244 46928 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.20 % Favored : 95.33 % Rotamer: Outliers : 3.15 % Allowed : 14.39 % Favored : 82.47 % 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: -2.12 (0.10), residues: 5785 helix: -0.52 (0.11), residues: 1894 sheet: -2.03 (0.16), residues: 823 loop : -1.79 (0.10), residues: 3068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP T 159 HIS 0.015 0.001 HIS G 71 PHE 0.020 0.002 PHE O 198 TYR 0.026 0.001 TYR F 186 ARG 0.008 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 1268 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1113 time to evaluate : 5.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 155 outliers final: 92 residues processed: 1199 average time/residue: 1.0546 time to fit residues: 2102.1940 Evaluate side-chains 1031 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 939 time to evaluate : 5.517 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 92 outliers final: 1 residues processed: 92 average time/residue: 0.7897 time to fit residues: 142.7820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 431 optimal weight: 3.9990 chunk 240 optimal weight: 10.0000 chunk 645 optimal weight: 3.9990 chunk 528 optimal weight: 0.8980 chunk 213 optimal weight: 10.0000 chunk 776 optimal weight: 4.9990 chunk 839 optimal weight: 0.0870 chunk 691 optimal weight: 0.0270 chunk 770 optimal weight: 9.9990 chunk 264 optimal weight: 10.0000 chunk 623 optimal weight: 5.9990 overall best weight: 1.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 ASN A 147 GLN B 64 ASN B 117 ASN B 151 GLN B 164 GLN B 377 ASN C 47 GLN C 82 ASN C 84 ASN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 GLN E 99 GLN F 90 ASN F 163 ASN ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 GLN H 109 HIS H 189 GLN I 95 HIS I 169 ASN J 6 ASN J 141 GLN J 148 GLN L 6 ASN N 139 HIS N 156 HIS O 71 GLN P 70 HIS P 150 GLN S 73 ASN S 145 ASN T 112 ASN V 36 ASN Y 40 GLN b 22 HIS b 36 ASN d 15 HIS g 19 ASN g 70 GLN g 109 ASN o 33 HIS o 45 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 115172 Z= 0.214 Angle : 0.599 13.659 169112 Z= 0.313 Chirality : 0.038 0.273 21128 Planarity : 0.005 0.084 11007 Dihedral : 21.547 179.942 46928 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.84 % Favored : 94.75 % Rotamer: Outliers : 2.86 % Allowed : 17.39 % Favored : 79.75 % 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: -1.55 (0.10), residues: 5785 helix: 0.02 (0.11), residues: 1895 sheet: -1.66 (0.16), residues: 835 loop : -1.51 (0.10), residues: 3055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP T 159 HIS 0.011 0.001 HIS H 126 PHE 0.018 0.002 PHE C 267 TYR 0.050 0.002 TYR F 186 ARG 0.011 0.001 ARG R 62 *********************** 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 1180 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1039 time to evaluate : 5.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 141 outliers final: 78 residues processed: 1123 average time/residue: 1.0357 time to fit residues: 1936.7539 Evaluate side-chains 1018 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 940 time to evaluate : 5.426 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 78 outliers final: 1 residues processed: 78 average time/residue: 0.7562 time to fit residues: 118.4072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 767 optimal weight: 0.7980 chunk 584 optimal weight: 4.9990 chunk 403 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 370 optimal weight: 8.9990 chunk 521 optimal weight: 7.9990 chunk 779 optimal weight: 0.9990 chunk 825 optimal weight: 0.9980 chunk 407 optimal weight: 4.9990 chunk 738 optimal weight: 3.9990 chunk 222 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 106 GLN A 142 ASN B 64 ASN C 47 GLN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN D 111 GLN E 99 GLN ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN I 57 HIS ** I 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 ASN O 199 GLN Q 43 ASN Q 126 GLN V 36 ASN W 29 HIS Y 103 ASN ** b 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 93 HIS f 62 ASN g 103 GLN h 65 GLN ** k 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 33 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 115172 Z= 0.249 Angle : 0.612 12.980 169112 Z= 0.317 Chirality : 0.038 0.261 21128 Planarity : 0.005 0.079 11007 Dihedral : 21.532 179.897 46928 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.68 % Favored : 94.88 % Rotamer: Outliers : 3.10 % Allowed : 18.49 % Favored : 78.41 % 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: -1.36 (0.10), residues: 5785 helix: 0.14 (0.11), residues: 1911 sheet: -1.47 (0.17), residues: 812 loop : -1.40 (0.10), residues: 3062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP T 159 HIS 0.011 0.001 HIS H 126 PHE 0.016 0.002 PHE D 19 TYR 0.045 0.002 TYR F 186 ARG 0.010 0.001 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 1148 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 995 time to evaluate : 5.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 153 outliers final: 93 residues processed: 1084 average time/residue: 1.0297 time to fit residues: 1869.1044 Evaluate side-chains 1029 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 936 time to evaluate : 5.434 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 2 residues processed: 93 average time/residue: 0.7757 time to fit residues: 141.2801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 687 optimal weight: 3.9990 chunk 468 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 614 optimal weight: 1.9990 chunk 340 optimal weight: 2.9990 chunk 704 optimal weight: 0.6980 chunk 570 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 421 optimal weight: 2.9990 chunk 740 optimal weight: 3.9990 chunk 208 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 162 HIS B 377 ASN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 GLN F 109 HIS ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN H 126 HIS ** I 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 ASN ** N 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 36 ASN a 66 ASN b 16 HIS k 32 ASN o 33 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 115172 Z= 0.214 Angle : 0.583 12.373 169112 Z= 0.302 Chirality : 0.037 0.252 21128 Planarity : 0.005 0.070 11007 Dihedral : 21.490 179.741 46928 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.87 % Favored : 94.71 % Rotamer: Outliers : 2.29 % Allowed : 19.62 % Favored : 78.08 % 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: -1.15 (0.10), residues: 5785 helix: 0.36 (0.12), residues: 1899 sheet: -1.31 (0.17), residues: 814 loop : -1.32 (0.10), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP T 159 HIS 0.008 0.001 HIS H 126 PHE 0.014 0.002 PHE U 76 TYR 0.040 0.002 TYR F 186 ARG 0.009 0.001 ARG l 28 *********************** 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 1110 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 997 time to evaluate : 5.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 113 outliers final: 67 residues processed: 1063 average time/residue: 1.0797 time to fit residues: 1933.6792 Evaluate side-chains 1008 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 941 time to evaluate : 5.437 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 2 residues processed: 67 average time/residue: 0.8232 time to fit residues: 110.9837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 163 optimal weight: 10.0000 chunk 484 optimal weight: 1.9990 chunk 203 optimal weight: 7.9990 chunk 826 optimal weight: 3.9990 chunk 685 optimal weight: 9.9990 chunk 382 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 273 optimal weight: 10.0000 chunk 433 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN C 319 GLN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 GLN F 156 GLN ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN I 92 HIS J 6 ASN ** L 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 HIS O 128 HIS Q 13 GLN ** S 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 140 HIS V 36 ASN W 16 HIS W 61 HIS Z 138 GLN e 16 ASN h 65 GLN h 86 HIS i 58 GLN o 33 HIS o 45 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 115172 Z= 0.327 Angle : 0.660 12.381 169112 Z= 0.339 Chirality : 0.040 0.255 21128 Planarity : 0.005 0.067 11007 Dihedral : 21.513 179.962 46928 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.32 % Favored : 94.23 % Rotamer: Outliers : 2.74 % Allowed : 20.39 % Favored : 76.87 % 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: -1.30 (0.10), residues: 5785 helix: 0.20 (0.12), residues: 1895 sheet: -1.27 (0.17), residues: 804 loop : -1.43 (0.10), residues: 3086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP T 159 HIS 0.022 0.002 HIS T 140 PHE 0.018 0.002 PHE C 92 TYR 0.037 0.002 TYR F 186 ARG 0.009 0.001 ARG l 28 *********************** 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 1109 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 974 time to evaluate : 5.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 135 outliers final: 83 residues processed: 1048 average time/residue: 1.0313 time to fit residues: 1810.7901 Evaluate side-chains 1024 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 941 time to evaluate : 5.436 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 83 outliers final: 1 residues processed: 83 average time/residue: 0.7875 time to fit residues: 128.8680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 796 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 470 optimal weight: 2.9990 chunk 603 optimal weight: 0.9980 chunk 467 optimal weight: 0.4980 chunk 695 optimal weight: 0.9980 chunk 461 optimal weight: 9.9990 chunk 823 optimal weight: 9.9990 chunk 515 optimal weight: 1.9990 chunk 501 optimal weight: 0.9990 chunk 380 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 ASN C 47 GLN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 GLN G 67 ASN J 6 ASN L 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 140 HIS T 148 GLN V 36 ASN f 62 ASN i 75 ASN o 3 HIS o 33 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 115172 Z= 0.151 Angle : 0.584 12.631 169112 Z= 0.303 Chirality : 0.036 0.266 21128 Planarity : 0.005 0.209 11007 Dihedral : 21.524 179.901 46928 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.43 % Favored : 95.11 % Rotamer: Outliers : 1.52 % Allowed : 21.35 % Favored : 77.13 % 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: -1.07 (0.10), residues: 5785 helix: 0.43 (0.12), residues: 1890 sheet: -1.08 (0.18), residues: 800 loop : -1.34 (0.10), residues: 3095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP T 159 HIS 0.021 0.001 HIS T 140 PHE 0.023 0.001 PHE U 76 TYR 0.037 0.001 TYR F 186 ARG 0.022 0.000 ARG Y 79 *********************** 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 1050 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 975 time to evaluate : 5.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 44 residues processed: 1005 average time/residue: 1.0493 time to fit residues: 1772.4218 Evaluate side-chains 972 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 928 time to evaluate : 4.983 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 44 outliers final: 1 residues processed: 44 average time/residue: 0.7781 time to fit residues: 70.0725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 509 optimal weight: 0.8980 chunk 328 optimal weight: 5.9990 chunk 491 optimal weight: 5.9990 chunk 247 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 523 optimal weight: 7.9990 chunk 560 optimal weight: 0.0980 chunk 406 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 646 optimal weight: 6.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 106 GLN B 377 ASN C 47 GLN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN J 6 ASN J 141 GLN J 147 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 54 ASN T 140 HIS T 148 GLN V 36 ASN W 16 HIS ** b 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 62 ASN h 65 GLN o 33 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 115172 Z= 0.287 Angle : 0.632 13.140 169112 Z= 0.324 Chirality : 0.039 0.247 21128 Planarity : 0.005 0.068 11007 Dihedral : 21.477 179.856 46928 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.41 % Favored : 94.17 % Rotamer: Outliers : 1.72 % Allowed : 21.81 % Favored : 76.46 % 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: 0.31 (0.12), residues: 1896 sheet: -1.09 (0.17), residues: 811 loop : -1.40 (0.10), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP T 159 HIS 0.019 0.001 HIS T 140 PHE 0.028 0.002 PHE U 76 TYR 0.033 0.002 TYR F 186 ARG 0.009 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 1061 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 976 time to evaluate : 5.493 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 60 residues processed: 1013 average time/residue: 1.0632 time to fit residues: 1790.9621 Evaluate side-chains 1000 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 940 time to evaluate : 5.467 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 60 outliers final: 1 residues processed: 60 average time/residue: 0.8136 time to fit residues: 96.2393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 719 optimal weight: 3.9990 chunk 767 optimal weight: 1.9990 chunk 461 optimal weight: 5.9990 chunk 334 optimal weight: 0.6980 chunk 602 optimal weight: 1.9990 chunk 235 optimal weight: 8.9990 chunk 693 optimal weight: 0.9980 chunk 725 optimal weight: 9.9990 chunk 764 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 106 GLN A 142 ASN B 377 ASN C 47 GLN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 GLN J 6 ASN M 16 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 140 HIS T 148 GLN V 36 ASN b 11 ASN f 62 ASN k 32 ASN o 33 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3785 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= 0.159 Angle : 0.583 12.831 169112 Z= 0.303 Chirality : 0.036 0.242 21128 Planarity : 0.004 0.069 11007 Dihedral : 21.498 179.781 46928 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.84 % Favored : 94.76 % Rotamer: Outliers : 0.87 % Allowed : 22.24 % Favored : 76.89 % 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: -1.06 (0.11), residues: 5785 helix: 0.42 (0.12), residues: 1899 sheet: -1.00 (0.18), residues: 808 loop : -1.34 (0.10), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP T 159 HIS 0.019 0.001 HIS T 140 PHE 0.030 0.001 PHE J 163 TYR 0.041 0.001 TYR F 186 ARG 0.009 0.000 ARG l 28 *********************** 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 986 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 943 time to evaluate : 5.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 29 residues processed: 967 average time/residue: 1.0789 time to fit residues: 1751.8988 Evaluate side-chains 958 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 929 time to evaluate : 5.450 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 29 outliers final: 1 residues processed: 29 average time/residue: 0.8389 time to fit residues: 52.1575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 503 optimal weight: 3.9990 chunk 811 optimal weight: 5.9990 chunk 495 optimal weight: 1.9990 chunk 384 optimal weight: 9.9990 chunk 563 optimal weight: 3.9990 chunk 850 optimal weight: 10.0000 chunk 783 optimal weight: 2.9990 chunk 677 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 523 optimal weight: 0.8980 chunk 415 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN B 377 ASN C 47 GLN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 ASN M 103 ASN ** N 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 HIS O 199 GLN ** S 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 140 HIS T 148 GLN V 36 ASN Y 135 HIS ** b 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 62 ASN o 33 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 115172 Z= 0.286 Angle : 0.636 13.443 169112 Z= 0.326 Chirality : 0.039 0.243 21128 Planarity : 0.005 0.065 11007 Dihedral : 21.467 179.985 46928 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.77 % Favored : 93.85 % Rotamer: Outliers : 0.51 % Allowed : 22.89 % Favored : 76.60 % 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: -1.19 (0.10), residues: 5785 helix: 0.31 (0.12), residues: 1895 sheet: -1.04 (0.18), residues: 809 loop : -1.43 (0.10), residues: 3081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP T 159 HIS 0.018 0.001 HIS T 140 PHE 0.017 0.002 PHE H 123 TYR 0.038 0.002 TYR F 186 ARG 0.011 0.001 ARG J 48 ********************** 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 978 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 953 time to evaluate : 5.562 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 965 average time/residue: 1.0802 time to fit residues: 1741.5700 Evaluate side-chains 950 residues out of total 4959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 934 time to evaluate : 5.467 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.8608 time to fit residues: 32.0075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 538 optimal weight: 4.9990 chunk 721 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 624 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 chunk 188 optimal weight: 9.9990 chunk 678 optimal weight: 0.8980 chunk 283 optimal weight: 9.9990 chunk 696 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 106 GLN A 139 HIS A 142 ASN B 377 ASN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 ASN M 16 ASN ** N 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 99 GLN O 128 HIS ** S 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 54 HIS T 140 HIS T 148 GLN V 36 ASN b 11 ASN f 62 ASN ** k 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 33 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.142905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.123315 restraints weight = 141261.352| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.24 r_work: 0.3073 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 115172 Z= 0.220 Angle : 0.606 13.240 169112 Z= 0.314 Chirality : 0.037 0.241 21128 Planarity : 0.005 0.063 11007 Dihedral : 21.474 179.933 46928 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.34 % Favored : 94.28 % Rotamer: Outliers : 0.41 % Allowed : 23.50 % 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: -1.16 (0.10), residues: 5785 helix: 0.33 (0.12), residues: 1903 sheet: -1.02 (0.18), residues: 807 loop : -1.41 (0.10), residues: 3075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP T 159 HIS 0.018 0.001 HIS T 140 PHE 0.024 0.002 PHE J 100 TYR 0.040 0.002 TYR F 186 ARG 0.012 0.001 ARG J 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27925.42 seconds wall clock time: 486 minutes 42.87 seconds (29202.87 seconds total)