Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 03:24:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pwg_13681/04_2023/7pwg_13681_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pwg_13681/04_2023/7pwg_13681.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pwg_13681/04_2023/7pwg_13681_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pwg_13681/04_2023/7pwg_13681_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pwg_13681/04_2023/7pwg_13681_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pwg_13681/04_2023/7pwg_13681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pwg_13681/04_2023/7pwg_13681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pwg_13681/04_2023/7pwg_13681_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pwg_13681/04_2023/7pwg_13681_updated.pdb" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 181 8.98 5 P 2722 5.49 5 Mg 112 5.21 5 S 234 5.16 5 C 54936 2.51 5 N 19791 2.21 5 O 31175 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 23": "NH1" <-> "NH2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "B ARG 4": "NH1" <-> "NH2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B ARG 222": "NH1" <-> "NH2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 240": "NH1" <-> "NH2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C ARG 74": "NH1" <-> "NH2" Residue "C ARG 87": "NH1" <-> "NH2" Residue "C ARG 100": "NH1" <-> "NH2" Residue "C ARG 103": "NH1" <-> "NH2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C ARG 175": "NH1" <-> "NH2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "C ARG 209": "NH1" <-> "NH2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C ARG 271": "NH1" <-> "NH2" Residue "C ARG 306": "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 GLU 81": "OE1" <-> "OE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D ARG 201": "NH1" <-> "NH2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D GLU 221": "OE1" <-> "OE2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "F ARG 83": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "F GLU 137": "OE1" <-> "OE2" Residue "F ARG 140": "NH1" <-> "NH2" Residue "F GLU 182": "OE1" <-> "OE2" Residue "F GLU 192": "OE1" <-> "OE2" Residue "F PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 229": "OE1" <-> "OE2" Residue "G ARG 33": "NH1" <-> "NH2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G ARG 77": "NH1" <-> "NH2" Residue "G GLU 82": "OE1" <-> "OE2" Residue "G ARG 119": "NH1" <-> "NH2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "G ARG 128": "NH1" <-> "NH2" Residue "G GLU 142": "OE1" <-> "OE2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 217": "NH1" <-> "NH2" Residue "G ARG 218": "NH1" <-> "NH2" Residue "G GLU 219": "OE1" <-> "OE2" Residue "G GLU 221": "OE1" <-> "OE2" Residue "H ARG 22": "NH1" <-> "NH2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "H GLU 123": "OE1" <-> "OE2" Residue "H ARG 143": "NH1" <-> "NH2" Residue "H ARG 156": "NH1" <-> "NH2" Residue "H GLU 159": "OE1" <-> "OE2" Residue "H ARG 180": "NH1" <-> "NH2" Residue "I GLU 56": "OE1" <-> "OE2" Residue "I GLU 63": "OE1" <-> "OE2" Residue "I ARG 139": "NH1" <-> "NH2" Residue "I ARG 154": "NH1" <-> "NH2" Residue "I GLU 167": "OE1" <-> "OE2" Residue "I PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 189": "OE1" <-> "OE2" Residue "J GLU 44": "OE1" <-> "OE2" Residue "J GLU 166": "OE1" <-> "OE2" Residue "L GLU 108": "OE1" <-> "OE2" Residue "L ARG 130": "NH1" <-> "NH2" Residue "L GLU 136": "OE1" <-> "OE2" Residue "L GLU 191": "OE1" <-> "OE2" Residue "L GLU 224": "OE1" <-> "OE2" Residue "M GLU 66": "OE1" <-> "OE2" Residue "M GLU 71": "OE1" <-> "OE2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M GLU 78": "OE1" <-> "OE2" Residue "M GLU 118": "OE1" <-> "OE2" Residue "M ARG 119": "NH1" <-> "NH2" Residue "N GLU 17": "OE1" <-> "OE2" Residue "N GLU 29": "OE1" <-> "OE2" Residue "N GLU 103": "OE1" <-> "OE2" Residue "N TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 29": "OE1" <-> "OE2" Residue "O GLU 36": "OE1" <-> "OE2" Residue "O PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 141": "OE1" <-> "OE2" Residue "O GLU 154": "OE1" <-> "OE2" Residue "P ARG 17": "NH1" <-> "NH2" Residue "P ARG 42": "NH1" <-> "NH2" Residue "P ARG 81": "NH1" <-> "NH2" Residue "P GLU 109": "OE1" <-> "OE2" Residue "P ARG 125": "NH1" <-> "NH2" Residue "P ARG 127": "NH1" <-> "NH2" Residue "P ARG 131": "NH1" <-> "NH2" Residue "Q GLU 38": "OE1" <-> "OE2" Residue "Q ARG 51": "NH1" <-> "NH2" Residue "Q GLU 75": "OE1" <-> "OE2" Residue "Q GLU 89": "OE1" <-> "OE2" Residue "Q ARG 90": "NH1" <-> "NH2" Residue "Q ARG 176": "NH1" <-> "NH2" Residue "R GLU 29": "OE1" <-> "OE2" Residue "R GLU 39": "OE1" <-> "OE2" Residue "R GLU 113": "OE1" <-> "OE2" Residue "R ARG 117": "NH1" <-> "NH2" Residue "R GLU 121": "OE1" <-> "OE2" Residue "R GLU 140": "OE1" <-> "OE2" Residue "R GLU 148": "OE1" <-> "OE2" Residue "S ARG 10": "NH1" <-> "NH2" Residue "S ARG 11": "NH1" <-> "NH2" Residue "S TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 125": "OE1" <-> "OE2" Residue "T ARG 8": "NH1" <-> "NH2" Residue "T ARG 20": "NH1" <-> "NH2" Residue "T ARG 55": "NH1" <-> "NH2" Residue "T ARG 60": "NH1" <-> "NH2" Residue "T PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 79": "NH1" <-> "NH2" Residue "T ARG 81": "NH1" <-> "NH2" Residue "T ARG 102": "NH1" <-> "NH2" Residue "T ARG 131": "NH1" <-> "NH2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "V GLU 126": "OE1" <-> "OE2" Residue "X ARG 24": "NH1" <-> "NH2" Residue "X ARG 31": "NH1" <-> "NH2" Residue "X GLU 74": "OE1" <-> "OE2" Residue "X GLU 91": "OE1" <-> "OE2" Residue "X GLU 101": "OE1" <-> "OE2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Y ARG 72": "NH1" <-> "NH2" Residue "Z GLU 28": "OE1" <-> "OE2" Residue "Z GLU 121": "OE1" <-> "OE2" Residue "a GLU 98": "OE1" <-> "OE2" Residue "a GLU 135": "OE1" <-> "OE2" Residue "b ARG 14": "NH1" <-> "NH2" Residue "b ARG 47": "NH1" <-> "NH2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c ARG 36": "NH1" <-> "NH2" Residue "c ARG 72": "NH1" <-> "NH2" Residue "c PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 79": "NH1" <-> "NH2" Residue "c GLU 80": "OE1" <-> "OE2" Residue "d ARG 10": "NH1" <-> "NH2" Residue "d ARG 29": "NH1" <-> "NH2" Residue "d ARG 57": "NH1" <-> "NH2" Residue "d ARG 60": "NH1" <-> "NH2" Residue "d ARG 64": "NH1" <-> "NH2" Residue "d ARG 71": "NH1" <-> "NH2" Residue "f ARG 21": "NH1" <-> "NH2" Residue "f GLU 26": "OE1" <-> "OE2" Residue "g ARG 5": "NH1" <-> "NH2" Residue "h ARG 19": "NH1" <-> "NH2" Residue "h ARG 26": "NH1" <-> "NH2" Residue "h ARG 47": "NH1" <-> "NH2" Residue "h ARG 49": "NH1" <-> "NH2" Residue "h ARG 57": "NH1" <-> "NH2" Residue "h ARG 67": "NH1" <-> "NH2" Residue "h GLU 75": "OE1" <-> "OE2" Residue "h ARG 111": "NH1" <-> "NH2" Residue "i GLU 47": "OE1" <-> "OE2" Residue "i ARG 60": "NH1" <-> "NH2" Residue "i ARG 80": "NH1" <-> "NH2" Residue "l ARG 9": "NH1" <-> "NH2" Residue "l ARG 45": "NH1" <-> "NH2" Residue "m GLU 79": "OE1" <-> "OE2" Residue "m ARG 102": "NH1" <-> "NH2" Residue "o TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 48": "NH1" <-> "NH2" Residue "p ARG 85": "NH1" <-> "NH2" Residue "p ARG 90": "NH1" <-> "NH2" Residue "W ARG 57": "NH1" <-> "NH2" Residue "W ARG 58": "NH1" <-> "NH2" Residue "W ARG 60": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 109151 Number of models: 1 Model: "" Number of chains: 105 Chain: "1" Number of atoms: 52618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2450, 52618 Classifications: {'RNA': 2450} Modifications used: {'rna2p': 5, 'rna2p_pur': 247, 'rna2p_pyr': 135, 'rna3p': 15, 'rna3p_pur': 1057, 'rna3p_pyr': 987} Link IDs: {'rna2p': 386, 'rna3p': 2063} Chain breaks: 28 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2501 Classifications: {'RNA': 117} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 47} Link IDs: {'rna2p': 12, 'rna3p': 104} Chain: "4" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 2958 Classifications: {'RNA': 138} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 12, 'rna3p': 1, 'rna3p_pur': 56, 'rna3p_pyr': 54} Link IDs: {'rna2p': 27, 'rna3p': 110} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1865 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 235} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2987 Classifications: {'peptide': 378} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 356} Chain: "C" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2446 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 21, 'TRANS': 292} Chain: "D" Number of atoms: 2118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2118 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 256} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1730 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 6, 'TRANS': 207} Chain: "G" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1450 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 170} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1442 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 176} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1621 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1305 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 158} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1512 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 178} Chain breaks: 1 Chain: "M" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 990 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 123} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1712 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 193} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "O" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1587 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain: "P" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1235 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 148} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1402 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 9, 'TRANS': 168} Chain: "R" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1463 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 174} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "S" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 163} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "T" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1226 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "U" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 802 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 96} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1057 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 131} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "X" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 936 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 9, 'TRANS': 106} Chain: "Y" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1076 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 6, 'TRANS': 126} Chain: "Z" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 980 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "a" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1201 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 9, 'TRANS': 138} Chain: "b" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 463 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "c" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 756 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 97} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 748 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "e" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1039 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain: "f" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 974 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "g" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 798 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 6, 'TRANS': 92} Chain: "h" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 926 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "i" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 691 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "j" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 692 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "k" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 500 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "l" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 434 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 48} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "m" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 421 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "o" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 762 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "p" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "w" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 299 Classifications: {'RNA': 14} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 11} Chain breaks: 1 Chain: "W" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 540 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Chain: "1" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 272 Unusual residues: {' K': 163, ' MG': 99, 'PGE': 1} Classifications: {'undetermined': 263} Link IDs: {None: 262} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3220, 3220 Classifications: {'water': 3220} Link IDs: {None: 3219} Chain: "3" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "4" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 132 Classifications: {'water': 132} Link IDs: {None: 131} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "J" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "L" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "M" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "N" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "O" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "P" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "Q" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "R" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "S" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "T" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "U" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "V" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "X" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "Y" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "Z" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "a" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "b" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "c" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "f" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "g" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "h" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "i" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "k" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "l" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "m" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "o" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "p" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "w" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "W" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A01OD SG CYS o 12 168.300 67.278 165.339 1.00 38.92 S ATOM A0222 SG CYS o 72 167.330 63.348 165.750 1.00 40.52 S ATOM A022K SG CYS o 75 166.111 66.029 168.152 1.00 41.33 S Time building chain proxies: 41.33, per 1000 atoms: 0.38 Number of scatterers: 109151 At special positions: 0 Unit cell: (245.65, 197.2, 221.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 181 19.00 S 234 16.00 P 2722 15.00 Mg 112 11.99 O 31175 8.00 N 19791 7.00 C 54936 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS p 39 " - pdb=" SG CYS p 42 " distance=2.03 Simple disulfide: pdb=" SG CYS p 39 " - pdb=" SG CYS p 57 " distance=2.03 Simple disulfide: pdb=" SG CYS p 39 " - pdb=" SG CYS p 60 " distance=2.09 Simple disulfide: pdb=" SG CYS p 42 " - pdb=" SG CYS p 57 " distance=2.07 Simple disulfide: pdb=" SG CYS p 42 " - pdb=" SG CYS p 60 " distance=1.97 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: 37.76 Conformation dependent library (CDL) restraints added in 5.8 seconds 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10766 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Warning! O6 atom is missing from residue G 11827 Was trying to link: C 11526 N4 with G 11827 O6, Saenger class: 19 Warning! O6 atom is missing from residue G 11827 Was trying to link: C 11526 N4 with G 11827 O6, Saenger class: 19 Secondary structure from input PDB file: 205 helices and 55 sheets defined 41.3% alpha, 13.3% beta 809 base pairs and 1496 stacking pairs defined. Time for finding SS restraints: 44.35 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 4.250A pdb=" N GLY A 11 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ALA A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.796A pdb=" N ILE A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.618A pdb=" N ALA A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.880A pdb=" N MET A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 200 through 205' Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.619A pdb=" N LYS A 177 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'B' and resid 111 through 120 removed outlier: 3.869A pdb=" N ARG B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE B 118 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TYR B 119 " --> pdb=" O MET B 115 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ARG B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 138 removed outlier: 3.931A pdb=" N LYS B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 154 removed outlier: 3.665A pdb=" N ARG B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU B 150 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLN B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 removed outlier: 4.827A pdb=" N THR B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) Proline residue: B 169 - end of helix No H-bonds generated for 'chain 'B' and resid 164 through 169' Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.700A pdb=" N LYS B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 192 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 198 " --> pdb=" O TYR B 194 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 removed outlier: 4.001A pdb=" N VAL B 208 " --> pdb=" O SER B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 378 Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'C' and resid 29 through 45 removed outlier: 3.582A pdb=" N CYS C 43 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ARG C 45 " --> pdb=" O ARG C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 123 removed outlier: 3.646A pdb=" N SER C 121 " --> pdb=" O ALA C 117 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASN C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 131 removed outlier: 3.630A pdb=" N GLU C 128 " --> pdb=" O ALA C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 163 Processing helix chain 'C' and resid 164 through 175 removed outlier: 3.673A pdb=" N VAL C 168 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER C 174 " --> pdb=" O ARG C 170 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARG C 175 " --> pdb=" O CYS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 186 removed outlier: 3.960A pdb=" N ARG C 185 " --> pdb=" O ARG C 181 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 181 through 186' Processing helix chain 'C' and resid 204 through 209 Processing helix chain 'C' and resid 223 through 229 Proline residue: C 229 - end of helix Processing helix chain 'C' and resid 240 through 255 removed outlier: 3.660A pdb=" N LEU C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ASP C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASP C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS C 254 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLN C 255 " --> pdb=" O TYR C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 276 removed outlier: 3.516A pdb=" N LEU C 273 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER C 275 " --> pdb=" O ARG C 271 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASP C 276 " --> pdb=" O ILE C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 removed outlier: 4.650A pdb=" N THR C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE C 282 " --> pdb=" O VAL C 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 277 through 282' Processing helix chain 'C' and resid 296 through 301 removed outlier: 4.880A pdb=" N SER C 300 " --> pdb=" O ASP C 296 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LYS C 301 " --> pdb=" O PRO C 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 296 through 301' Processing helix chain 'C' and resid 302 through 308 removed outlier: 3.509A pdb=" N ARG C 306 " --> pdb=" O GLU C 302 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU C 307 " --> pdb=" O ALA C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 26 removed outlier: 3.501A pdb=" N PHE C 24 " --> pdb=" O PRO C 21 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL C 26 " --> pdb=" O VAL C 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 15 removed outlier: 3.518A pdb=" N PHE D 12 " --> pdb=" O THR D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 25 removed outlier: 3.684A pdb=" N GLY D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 37 removed outlier: 3.500A pdb=" N ILE D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 86 removed outlier: 4.406A pdb=" N LEU D 82 " --> pdb=" O TYR D 78 " (cutoff:3.500A) Proline residue: D 83 - end of helix Processing helix chain 'D' and resid 93 through 114 removed outlier: 3.972A pdb=" N VAL D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 126 removed outlier: 4.695A pdb=" N TYR D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Proline residue: D 126 - end of helix Processing helix chain 'D' and resid 137 through 142 removed outlier: 4.345A pdb=" N ASN D 141 " --> pdb=" O HIS D 137 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU D 142 " --> pdb=" O PRO D 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 137 through 142' Processing helix chain 'D' and resid 164 through 177 removed outlier: 3.585A pdb=" N ALA D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 176 " --> pdb=" O GLY D 172 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 206 removed outlier: 4.177A pdb=" N LEU D 200 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG D 203 " --> pdb=" O ALA D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 220 removed outlier: 3.544A pdb=" N ALA D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 228 removed outlier: 3.607A pdb=" N LYS D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 235 removed outlier: 3.544A pdb=" N LYS D 235 " --> pdb=" O TYR D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 256 removed outlier: 3.507A pdb=" N ALA D 250 " --> pdb=" O THR D 246 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) Proline residue: D 256 - end of helix Processing helix chain 'F' and resid 22 through 68 removed outlier: 3.624A pdb=" N ALA F 32 " --> pdb=" O LYS F 28 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA F 33 " --> pdb=" O GLU F 29 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN F 44 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL F 54 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU F 55 " --> pdb=" O ILE F 51 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS F 58 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS F 66 " --> pdb=" O GLU F 62 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN F 67 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASN F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 102 Processing helix chain 'F' and resid 115 through 126 removed outlier: 3.593A pdb=" N ALA F 121 " --> pdb=" O ALA F 117 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE F 124 " --> pdb=" O ASN F 120 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL F 125 " --> pdb=" O ALA F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 145 Processing helix chain 'F' and resid 160 through 168 removed outlier: 4.261A pdb=" N ILE F 164 " --> pdb=" O ASP F 160 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN F 167 " --> pdb=" O LEU F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 186 Processing helix chain 'F' and resid 189 through 197 removed outlier: 4.158A pdb=" N LEU F 197 " --> pdb=" O ALA F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 235 removed outlier: 3.631A pdb=" N PHE F 230 " --> pdb=" O TYR F 226 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG F 233 " --> pdb=" O GLU F 229 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N MET F 234 " --> pdb=" O PHE F 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 51 removed outlier: 3.504A pdb=" N GLN G 41 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 63 removed outlier: 4.814A pdb=" N PHE G 60 " --> pdb=" O THR G 56 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N MET G 61 " --> pdb=" O VAL G 57 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN G 62 " --> pdb=" O ASN G 58 " (cutoff:3.500A) Proline residue: G 63 - end of helix Processing helix chain 'G' and resid 65 through 80 removed outlier: 3.826A pdb=" N LEU G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS G 78 " --> pdb=" O ASN G 74 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR G 79 " --> pdb=" O LEU G 75 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 90 removed outlier: 4.477A pdb=" N LYS G 88 " --> pdb=" O LYS G 84 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG G 90 " --> pdb=" O GLU G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 127 removed outlier: 3.789A pdb=" N SER G 122 " --> pdb=" O ARG G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 155 Processing helix chain 'G' and resid 163 through 172 removed outlier: 3.632A pdb=" N LEU G 167 " --> pdb=" O THR G 163 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL G 171 " --> pdb=" O LEU G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 203 removed outlier: 3.991A pdb=" N LYS G 189 " --> pdb=" O ASN G 185 " (cutoff:3.500A) Proline residue: G 190 - end of helix removed outlier: 4.319A pdb=" N LYS G 194 " --> pdb=" O PRO G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 211 removed outlier: 3.614A pdb=" N LYS G 210 " --> pdb=" O ALA G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 222 Processing helix chain 'H' and resid 59 through 82 removed outlier: 6.002A pdb=" N ASN H 63 " --> pdb=" O ARG H 59 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ALA H 64 " --> pdb=" O GLY H 60 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU H 65 " --> pdb=" O LYS H 61 " (cutoff:3.500A) Proline residue: H 66 - end of helix removed outlier: 4.107A pdb=" N VAL H 80 " --> pdb=" O MET H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 162 removed outlier: 3.536A pdb=" N SER H 160 " --> pdb=" O ARG H 156 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU H 161 " --> pdb=" O ILE H 157 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LYS H 162 " --> pdb=" O HIS H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 172 removed outlier: 4.322A pdb=" N LEU H 172 " --> pdb=" O LEU H 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 47 removed outlier: 4.398A pdb=" N PHE I 46 " --> pdb=" O LYS I 42 " (cutoff:3.500A) Proline residue: I 47 - end of helix No H-bonds generated for 'chain 'I' and resid 42 through 47' Processing helix chain 'I' and resid 61 through 80 removed outlier: 3.517A pdb=" N LYS I 78 " --> pdb=" O LYS I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 160 removed outlier: 3.513A pdb=" N LYS I 145 " --> pdb=" O ARG I 141 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASP I 146 " --> pdb=" O ALA I 142 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N TYR I 147 " --> pdb=" O SER I 143 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL I 148 " --> pdb=" O ALA I 144 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N LYS I 149 " --> pdb=" O LYS I 145 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASP I 150 " --> pdb=" O ASP I 146 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS I 158 " --> pdb=" O ARG I 154 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE I 159 " --> pdb=" O ALA I 155 " (cutoff:3.500A) Proline residue: I 160 - end of helix Processing helix chain 'I' and resid 177 through 188 Processing helix chain 'J' and resid 28 through 42 Processing helix chain 'J' and resid 73 through 88 removed outlier: 3.522A pdb=" N ARG J 77 " --> pdb=" O GLY J 73 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU J 84 " --> pdb=" O ILE J 80 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS J 87 " --> pdb=" O GLY J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 114 removed outlier: 4.677A pdb=" N GLY J 113 " --> pdb=" O HIS J 109 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE J 114 " --> pdb=" O ILE J 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 109 through 114' Processing helix chain 'J' and resid 136 through 141 removed outlier: 4.061A pdb=" N LYS J 140 " --> pdb=" O PHE J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 167 removed outlier: 3.535A pdb=" N TRP J 162 " --> pdb=" O GLU J 158 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG J 165 " --> pdb=" O ALA J 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 76 removed outlier: 3.607A pdb=" N ILE L 62 " --> pdb=" O PRO L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 113 removed outlier: 3.848A pdb=" N VAL L 112 " --> pdb=" O GLU L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 123 removed outlier: 3.571A pdb=" N GLN L 121 " --> pdb=" O GLY L 117 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE L 122 " --> pdb=" O LYS L 118 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY L 123 " --> pdb=" O ALA L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 153 removed outlier: 3.971A pdb=" N VAL L 138 " --> pdb=" O SER L 134 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN L 141 " --> pdb=" O SER L 137 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER L 150 " --> pdb=" O LYS L 146 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS L 151 " --> pdb=" O GLU L 147 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N THR L 153 " --> pdb=" O LEU L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 197 removed outlier: 4.115A pdb=" N LYS L 194 " --> pdb=" O ALA L 190 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLU L 195 " --> pdb=" O GLU L 191 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL L 196 " --> pdb=" O ALA L 192 " (cutoff:3.500A) Proline residue: L 197 - end of helix Processing helix chain 'L' and resid 199 through 210 removed outlier: 3.528A pdb=" N ALA L 207 " --> pdb=" O TYR L 203 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 228 removed outlier: 3.755A pdb=" N GLU L 224 " --> pdb=" O ASP L 220 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA L 225 " --> pdb=" O ALA L 221 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA L 226 " --> pdb=" O GLU L 222 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA L 227 " --> pdb=" O ARG L 223 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 56 removed outlier: 3.831A pdb=" N ALA M 55 " --> pdb=" O SER M 51 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N MET M 56 " --> pdb=" O LEU M 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 51 through 56' Processing helix chain 'M' and resid 69 through 81 removed outlier: 3.537A pdb=" N SER M 80 " --> pdb=" O GLU M 76 " (cutoff:3.500A) Proline residue: M 81 - end of helix Processing helix chain 'M' and resid 82 through 90 removed outlier: 5.434A pdb=" N VAL M 90 " --> pdb=" O PHE M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 104 removed outlier: 3.623A pdb=" N LEU M 100 " --> pdb=" O GLN M 96 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA M 102 " --> pdb=" O GLN M 98 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LYS M 103 " --> pdb=" O ARG M 99 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ALA M 104 " --> pdb=" O LEU M 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 129 removed outlier: 3.587A pdb=" N LYS M 124 " --> pdb=" O LYS M 120 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET M 128 " --> pdb=" O LYS M 124 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N SER M 129 " --> pdb=" O ARG M 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 14 removed outlier: 4.851A pdb=" N TYR N 6 " --> pdb=" O GLY N 2 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG N 12 " --> pdb=" O GLN N 8 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LYS N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 34 removed outlier: 3.612A pdb=" N GLN N 32 " --> pdb=" O TRP N 28 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU N 33 " --> pdb=" O GLU N 29 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ASN N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 83 through 88 removed outlier: 4.063A pdb=" N ILE N 87 " --> pdb=" O LYS N 83 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLY N 88 " --> pdb=" O PRO N 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 83 through 88' Processing helix chain 'N' and resid 97 through 111 Proline residue: N 111 - end of helix Processing helix chain 'N' and resid 139 through 145 removed outlier: 3.865A pdb=" N ASP N 145 " --> pdb=" O TRP N 141 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 153 removed outlier: 4.480A pdb=" N CYS N 152 " --> pdb=" O ILE N 148 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASN N 153 " --> pdb=" O ASN N 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 148 through 153' Processing helix chain 'N' and resid 158 through 163 removed outlier: 3.716A pdb=" N ARG N 162 " --> pdb=" O ARG N 158 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 173 removed outlier: 3.559A pdb=" N ALA N 171 " --> pdb=" O ALA N 167 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG N 172 " --> pdb=" O GLY N 168 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 197 removed outlier: 3.649A pdb=" N THR N 197 " --> pdb=" O LYS N 193 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 27 removed outlier: 3.810A pdb=" N ILE O 19 " --> pdb=" O ARG O 15 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS O 26 " --> pdb=" O LYS O 22 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY O 27 " --> pdb=" O GLU O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 57 removed outlier: 3.651A pdb=" N MET O 55 " --> pdb=" O TYR O 51 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS O 56 " --> pdb=" O LEU O 52 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS O 57 " --> pdb=" O LYS O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 67 removed outlier: 3.956A pdb=" N GLY O 66 " --> pdb=" O ASN O 62 " (cutoff:3.500A) Proline residue: O 67 - end of helix No H-bonds generated for 'chain 'O' and resid 62 through 67' Processing helix chain 'O' and resid 72 through 86 removed outlier: 3.875A pdb=" N MET O 84 " --> pdb=" O THR O 80 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE O 85 " --> pdb=" O ILE O 81 " (cutoff:3.500A) Proline residue: O 86 - end of helix Processing helix chain 'O' and resid 89 through 100 removed outlier: 3.556A pdb=" N ALA O 95 " --> pdb=" O ARG O 91 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG O 98 " --> pdb=" O ASP O 94 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU O 99 " --> pdb=" O ALA O 95 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ARG O 100 " --> pdb=" O MET O 96 " (cutoff:3.500A) Processing helix chain 'O' and resid 117 through 122 removed outlier: 3.674A pdb=" N MET O 121 " --> pdb=" O CYS O 117 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ALA O 122 " --> pdb=" O PRO O 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 117 through 122' Processing helix chain 'O' and resid 134 through 143 Processing helix chain 'O' and resid 147 through 173 removed outlier: 3.571A pdb=" N GLU O 151 " --> pdb=" O ALA O 147 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN O 166 " --> pdb=" O ASP O 162 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP O 167 " --> pdb=" O LYS O 163 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN O 170 " --> pdb=" O GLN O 166 " (cutoff:3.500A) Processing helix chain 'O' and resid 181 through 195 removed outlier: 4.205A pdb=" N ARG O 187 " --> pdb=" O ALA O 183 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN O 189 " --> pdb=" O LEU O 185 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA O 190 " --> pdb=" O GLN O 186 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA O 193 " --> pdb=" O ASN O 189 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS O 194 " --> pdb=" O ALA O 190 " (cutoff:3.500A) Processing helix chain 'P' and resid 24 through 36 removed outlier: 3.507A pdb=" N SER P 30 " --> pdb=" O LYS P 26 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE P 35 " --> pdb=" O THR P 31 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS P 36 " --> pdb=" O CYS P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 53 Processing helix chain 'P' and resid 84 through 105 removed outlier: 3.776A pdb=" N ASP P 92 " --> pdb=" O VAL P 88 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN P 96 " --> pdb=" O ASP P 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 113 removed outlier: 3.800A pdb=" N LEU P 112 " --> pdb=" O GLU P 108 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR P 113 " --> pdb=" O GLU P 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 108 through 113' Processing helix chain 'Q' and resid 23 through 41 removed outlier: 3.533A pdb=" N ARG Q 27 " --> pdb=" O ASN Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 54 removed outlier: 4.001A pdb=" N CYS Q 53 " --> pdb=" O THR Q 49 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU Q 54 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 60 removed outlier: 5.743A pdb=" N ARG Q 59 " --> pdb=" O SER Q 55 " (cutoff:3.500A) Proline residue: Q 60 - end of helix No H-bonds generated for 'chain 'Q' and resid 55 through 60' Processing helix chain 'Q' and resid 63 through 72 removed outlier: 3.696A pdb=" N HIS Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 116 removed outlier: 3.730A pdb=" N GLY Q 116 " --> pdb=" O ILE Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 121 through 129 Processing helix chain 'Q' and resid 145 through 151 removed outlier: 3.846A pdb=" N LYS Q 149 " --> pdb=" O ARG Q 145 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS Q 150 " --> pdb=" O ALA Q 146 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE Q 151 " --> pdb=" O VAL Q 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 145 through 151' Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 28 through 36 removed outlier: 3.781A pdb=" N GLN R 34 " --> pdb=" O LYS R 30 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA R 35 " --> pdb=" O TYR R 31 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N SER R 36 " --> pdb=" O ILE R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 48 Processing helix chain 'R' and resid 60 through 73 removed outlier: 3.633A pdb=" N LEU R 72 " --> pdb=" O ALA R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 82 removed outlier: 3.732A pdb=" N ARG R 81 " --> pdb=" O GLY R 77 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ARG R 82 " --> pdb=" O HIS R 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 77 through 82' Processing helix chain 'R' and resid 84 through 113 Proline residue: R 90 - end of helix removed outlier: 6.440A pdb=" N THR R 93 " --> pdb=" O MET R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 130 removed outlier: 3.538A pdb=" N ASN R 130 " --> pdb=" O LYS R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 149 removed outlier: 3.795A pdb=" N LEU R 138 " --> pdb=" O ASN R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 178 removed outlier: 6.822A pdb=" N LYS R 155 " --> pdb=" O LEU R 151 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LYS R 156 " --> pdb=" O GLU R 152 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU R 159 " --> pdb=" O LYS R 155 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ALA R 178 " --> pdb=" O ALA R 174 " (cutoff:3.500A) Processing helix chain 'S' and resid 31 through 47 removed outlier: 3.769A pdb=" N SER S 45 " --> pdb=" O TYR S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 50 through 55 removed outlier: 3.684A pdb=" N GLY S 54 " --> pdb=" O LYS S 50 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLU S 55 " --> pdb=" O ARG S 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 50 through 55' Processing helix chain 'S' and resid 95 through 110 Processing helix chain 'S' and resid 114 through 119 removed outlier: 3.873A pdb=" N ILE S 118 " --> pdb=" O ARG S 114 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N GLN S 119 " --> pdb=" O TYR S 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 114 through 119' Processing helix chain 'S' and resid 133 through 141 removed outlier: 4.350A pdb=" N PHE S 139 " --> pdb=" O LYS S 135 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR S 140 " --> pdb=" O VAL S 136 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLN S 141 " --> pdb=" O ALA S 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 150 through 163 removed outlier: 4.593A pdb=" N HIS S 154 " --> pdb=" O CYS S 150 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL S 155 " --> pdb=" O PRO S 151 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG S 160 " --> pdb=" O LYS S 156 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR S 161 " --> pdb=" O ARG S 157 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ARG S 163 " --> pdb=" O ALA S 159 " (cutoff:3.500A) Processing helix chain 'T' and resid 27 through 32 Processing helix chain 'T' and resid 92 through 97 removed outlier: 4.199A pdb=" N VAL T 96 " --> pdb=" O ARG T 92 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N HIS T 97 " --> pdb=" O LEU T 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 92 through 97' Processing helix chain 'T' and resid 102 through 119 removed outlier: 3.545A pdb=" N ASP T 113 " --> pdb=" O VAL T 109 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA T 119 " --> pdb=" O ALA T 115 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 48 removed outlier: 3.774A pdb=" N PHE U 40 " --> pdb=" O ASN U 36 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 61 removed outlier: 4.795A pdb=" N LYS U 60 " --> pdb=" O GLY U 56 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 94 removed outlier: 4.084A pdb=" N VAL U 84 " --> pdb=" O ALA U 80 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR U 88 " --> pdb=" O VAL U 84 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLN U 94 " --> pdb=" O ARG U 90 " (cutoff:3.500A) Processing helix chain 'U' and resid 27 through 32 removed outlier: 3.946A pdb=" N LYS U 31 " --> pdb=" O SER U 28 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASP U 32 " --> pdb=" O ALA U 29 " (cutoff:3.500A) Processing helix chain 'V' and resid 71 through 76 removed outlier: 3.689A pdb=" N ARG V 75 " --> pdb=" O LYS V 71 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ARG V 76 " --> pdb=" O PRO V 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 71 through 76' Processing helix chain 'V' and resid 124 through 132 removed outlier: 3.677A pdb=" N ARG V 130 " --> pdb=" O GLU V 126 " (cutoff:3.500A) Proline residue: V 132 - end of helix Processing helix chain 'V' and resid 133 through 138 Processing helix chain 'X' and resid 56 through 61 removed outlier: 6.628A pdb=" N LEU X 60 " --> pdb=" O PRO X 56 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ARG X 61 " --> pdb=" O CYS X 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 56 through 61' Processing helix chain 'X' and resid 66 through 75 removed outlier: 3.753A pdb=" N ILE X 73 " --> pdb=" O ASN X 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 88 through 101 removed outlier: 3.507A pdb=" N LYS X 94 " --> pdb=" O PRO X 90 " (cutoff:3.500A) Processing helix chain 'X' and resid 128 through 137 removed outlier: 3.684A pdb=" N LYS X 135 " --> pdb=" O ASP X 131 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 21 removed outlier: 4.163A pdb=" N THR Y 20 " --> pdb=" O LYS Y 16 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA Y 21 " --> pdb=" O ALA Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 22 through 31 removed outlier: 3.531A pdb=" N LYS Y 28 " --> pdb=" O GLU Y 24 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER Y 31 " --> pdb=" O ALA Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 43 Processing helix chain 'Y' and resid 100 through 105 removed outlier: 4.159A pdb=" N CYS Y 104 " --> pdb=" O HIS Y 100 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE Y 105 " --> pdb=" O PRO Y 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 100 through 105' Processing helix chain 'Y' and resid 112 through 133 removed outlier: 3.515A pdb=" N ARG Y 125 " --> pdb=" O ARG Y 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 60 through 65 removed outlier: 4.429A pdb=" N ARG Z 65 " --> pdb=" O VAL Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 74 through 79 removed outlier: 3.989A pdb=" N LEU Z 78 " --> pdb=" O ASN Z 74 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N MET Z 79 " --> pdb=" O VAL Z 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 74 through 79' Processing helix chain 'Z' and resid 88 through 93 removed outlier: 4.596A pdb=" N PHE Z 92 " --> pdb=" O ASN Z 88 " (cutoff:3.500A) Processing helix chain 'Z' and resid 95 through 100 removed outlier: 5.028A pdb=" N ALA Z 99 " --> pdb=" O THR Z 95 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP Z 100 " --> pdb=" O GLN Z 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 95 through 100' Processing helix chain 'Z' and resid 101 through 122 removed outlier: 4.075A pdb=" N GLU Z 106 " --> pdb=" O THR Z 102 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE Z 108 " --> pdb=" O ARG Z 104 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP Z 114 " --> pdb=" O THR Z 110 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU Z 120 " --> pdb=" O GLN Z 116 " (cutoff:3.500A) Processing helix chain 'Z' and resid 124 through 129 Processing helix chain 'a' and resid 6 through 12 removed outlier: 4.135A pdb=" N LYS a 10 " --> pdb=" O ARG a 6 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG a 11 " --> pdb=" O LYS a 7 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ARG a 12 " --> pdb=" O SER a 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 6 through 12' Processing helix chain 'a' and resid 41 through 49 removed outlier: 3.608A pdb=" N LYS a 47 " --> pdb=" O THR a 43 " (cutoff:3.500A) Processing helix chain 'a' and resid 64 through 69 Processing helix chain 'a' and resid 74 through 83 removed outlier: 3.835A pdb=" N ILE a 78 " --> pdb=" O ASN a 74 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TRP a 79 " --> pdb=" O ILE a 75 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N SER a 80 " --> pdb=" O ASP a 76 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU a 81 " --> pdb=" O LYS a 77 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE a 82 " --> pdb=" O ILE a 78 " (cutoff:3.500A) Proline residue: a 83 - end of helix No H-bonds generated for 'chain 'a' and resid 74 through 83' Processing helix chain 'a' and resid 84 through 94 removed outlier: 4.324A pdb=" N ASP a 88 " --> pdb=" O GLU a 84 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLY a 89 " --> pdb=" O GLU a 85 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS a 94 " --> pdb=" O PHE a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 108 removed outlier: 4.168A pdb=" N PHE a 107 " --> pdb=" O ASP a 103 " (cutoff:3.500A) Processing helix chain 'a' and resid 131 through 142 removed outlier: 3.665A pdb=" N VAL a 141 " --> pdb=" O LYS a 137 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY a 142 " --> pdb=" O LEU a 138 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 19 removed outlier: 4.799A pdb=" N ASN b 19 " --> pdb=" O LYS b 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 25 through 31 removed outlier: 4.169A pdb=" N TYR b 29 " --> pdb=" O LYS b 25 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR b 30 " --> pdb=" O LYS b 26 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER b 31 " --> pdb=" O SER b 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 25 through 31' Processing helix chain 'b' and resid 36 through 51 removed outlier: 3.690A pdb=" N ASN b 42 " --> pdb=" O LYS b 38 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG b 47 " --> pdb=" O LEU b 43 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN b 49 " --> pdb=" O ARG b 45 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP b 50 " --> pdb=" O SER b 46 " (cutoff:3.500A) Proline residue: b 51 - end of helix Processing helix chain 'c' and resid 7 through 24 removed outlier: 3.532A pdb=" N ASP c 12 " --> pdb=" O LYS c 8 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER c 13 " --> pdb=" O LYS c 9 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL c 22 " --> pdb=" O LEU c 18 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 41 removed outlier: 3.534A pdb=" N ARG c 36 " --> pdb=" O ASP c 32 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP c 40 " --> pdb=" O ARG c 36 " (cutoff:3.500A) Processing helix chain 'c' and resid 53 through 68 Processing helix chain 'c' and resid 77 through 86 Processing helix chain 'd' and resid 10 through 16 removed outlier: 3.756A pdb=" N ALA d 14 " --> pdb=" O ARG d 10 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL d 15 " --> pdb=" O LEU d 11 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG d 16 " --> pdb=" O ASN d 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 10 through 16' Processing helix chain 'd' and resid 19 through 40 removed outlier: 3.821A pdb=" N ALA d 23 " --> pdb=" O PRO d 19 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ALA d 24 " --> pdb=" O SER d 20 " (cutoff:3.500A) Proline residue: d 25 - end of helix removed outlier: 3.551A pdb=" N ARG d 32 " --> pdb=" O ILE d 28 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA d 33 " --> pdb=" O ARG d 29 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS d 37 " --> pdb=" O ALA d 33 " (cutoff:3.500A) Processing helix chain 'd' and resid 47 through 56 Processing helix chain 'e' and resid 26 through 31 removed outlier: 3.870A pdb=" N PHE e 30 " --> pdb=" O GLN e 26 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N VAL e 31 " --> pdb=" O SER e 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 26 through 31' Processing helix chain 'e' and resid 45 through 50 Processing helix chain 'e' and resid 83 through 92 removed outlier: 3.641A pdb=" N PHE e 91 " --> pdb=" O LEU e 87 " (cutoff:3.500A) Processing helix chain 'e' and resid 106 through 121 removed outlier: 3.910A pdb=" N LYS e 111 " --> pdb=" O ALA e 107 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN e 112 " --> pdb=" O ARG e 108 " (cutoff:3.500A) Processing helix chain 'f' and resid 38 through 46 removed outlier: 3.819A pdb=" N THR f 42 " --> pdb=" O THR f 38 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASP f 43 " --> pdb=" O ARG f 39 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LYS f 44 " --> pdb=" O ALA f 40 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N VAL f 45 " --> pdb=" O GLU f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 107 through 113 removed outlier: 4.220A pdb=" N TYR f 113 " --> pdb=" O TYR f 109 " (cutoff:3.500A) Processing helix chain 'g' and resid 59 through 64 removed outlier: 4.008A pdb=" N LEU g 63 " --> pdb=" O ILE g 59 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N THR g 64 " --> pdb=" O PRO g 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 59 through 64' Processing helix chain 'g' and resid 65 through 70 removed outlier: 3.909A pdb=" N LYS g 69 " --> pdb=" O ARG g 65 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N VAL g 70 " --> pdb=" O GLN g 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 65 through 70' Processing helix chain 'g' and resid 79 through 98 removed outlier: 6.209A pdb=" N LEU g 83 " --> pdb=" O CYS g 79 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA g 98 " --> pdb=" O GLU g 94 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 11 removed outlier: 3.791A pdb=" N LEU h 9 " --> pdb=" O LYS h 5 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL h 10 " --> pdb=" O ALA h 6 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLY h 11 " --> pdb=" O LYS h 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 5 through 11' Processing helix chain 'h' and resid 13 through 37 removed outlier: 3.761A pdb=" N ASP h 23 " --> pdb=" O ARG h 19 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU h 24 " --> pdb=" O LYS h 20 " (cutoff:3.500A) Processing helix chain 'h' and resid 45 through 75 removed outlier: 4.098A pdb=" N ARG h 49 " --> pdb=" O ILE h 45 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL h 50 " --> pdb=" O ALA h 46 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS h 52 " --> pdb=" O PHE h 48 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS h 53 " --> pdb=" O ARG h 49 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA h 56 " --> pdb=" O LYS h 52 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP h 68 " --> pdb=" O GLN h 64 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA h 72 " --> pdb=" O ASP h 68 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU h 75 " --> pdb=" O ARG h 71 " (cutoff:3.500A) Processing helix chain 'h' and resid 81 through 86 removed outlier: 3.534A pdb=" N ARG h 85 " --> pdb=" O PRO h 81 " (cutoff:3.500A) Proline residue: h 86 - end of helix No H-bonds generated for 'chain 'h' and resid 81 through 86' Processing helix chain 'h' and resid 89 through 95 removed outlier: 3.708A pdb=" N CYS h 94 " --> pdb=" O HIS h 90 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN h 95 " --> pdb=" O ALA h 91 " (cutoff:3.500A) Processing helix chain 'h' and resid 97 through 103 Processing helix chain 'h' and resid 105 through 116 removed outlier: 3.500A pdb=" N ARG h 111 " --> pdb=" O LYS h 107 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS h 112 " --> pdb=" O LEU h 108 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN h 114 " --> pdb=" O LYS h 110 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE h 115 " --> pdb=" O ARG h 111 " (cutoff:3.500A) Proline residue: h 116 - end of helix Processing helix chain 'i' and resid 27 through 42 removed outlier: 3.687A pdb=" N GLU i 31 " --> pdb=" O LYS i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 44 through 57 Processing helix chain 'i' and resid 58 through 71 Processing helix chain 'i' and resid 72 through 88 removed outlier: 4.245A pdb=" N VAL i 85 " --> pdb=" O ASP i 81 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N TYR i 86 " --> pdb=" O GLN i 82 " (cutoff:3.500A) Processing helix chain 'j' and resid 4 through 11 removed outlier: 3.808A pdb=" N GLY j 9 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LYS j 10 " --> pdb=" O ALA j 6 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ARG j 11 " --> pdb=" O SER j 7 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 removed outlier: 3.963A pdb=" N ARG j 57 " --> pdb=" O SER j 53 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR j 58 " --> pdb=" O LEU j 54 " (cutoff:3.500A) Processing helix chain 'j' and resid 64 through 76 removed outlier: 3.811A pdb=" N LYS j 69 " --> pdb=" O SER j 65 " (cutoff:3.500A) Processing helix chain 'j' and resid 78 through 88 removed outlier: 3.745A pdb=" N ARG j 84 " --> pdb=" O LYS j 80 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA j 88 " --> pdb=" O ARG j 84 " (cutoff:3.500A) Processing helix chain 'k' and resid 6 through 17 removed outlier: 3.600A pdb=" N MET k 11 " --> pdb=" O GLU k 7 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS k 12 " --> pdb=" O GLU k 8 " (cutoff:3.500A) Processing helix chain 'k' and resid 52 through 63 removed outlier: 4.452A pdb=" N LYS k 58 " --> pdb=" O ALA k 54 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER k 59 " --> pdb=" O ASP k 55 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 20 removed outlier: 3.505A pdb=" N ARG l 12 " --> pdb=" O SER l 8 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN l 20 " --> pdb=" O LYS l 16 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 32 Processing helix chain 'm' and resid 79 through 90 removed outlier: 4.334A pdb=" N TYR m 89 " --> pdb=" O LEU m 85 " (cutoff:3.500A) Processing helix chain 'o' and resid 35 through 46 removed outlier: 3.694A pdb=" N ARG o 46 " --> pdb=" O ASP o 42 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 35 removed outlier: 3.510A pdb=" N ARG p 23 " --> pdb=" O GLY p 19 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS p 28 " --> pdb=" O LYS p 24 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA p 35 " --> pdb=" O THR p 31 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 92 removed outlier: 5.299A pdb=" N ASP p 92 " --> pdb=" O LEU p 88 " (cutoff:3.500A) Processing helix chain 'W' and resid 34 through 44 removed outlier: 3.508A pdb=" N LYS W 44 " --> pdb=" O HIS W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 46 through 51 removed outlier: 3.576A pdb=" N ILE W 50 " --> pdb=" O ASN W 46 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ARG W 51 " --> pdb=" O PRO W 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 46 through 51' Processing helix chain 'W' and resid 53 through 61 Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.506A pdb=" N ALA A 47 " --> pdb=" O ARG A 60 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG A 60 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLN A 86 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 111 through 114 removed outlier: 4.658A pdb=" N THR A 111 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ARG A 147 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 138 " --> pdb=" O ARG A 147 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 58 through 64 Processing sheet with id= 4, first strand: chain 'A' and resid 145 through 150 removed outlier: 4.343A pdb=" N GLN A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 44 through 50 removed outlier: 8.716A pdb=" N THR B 44 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ARG B 334 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ALA B 213 " --> pdb=" O VAL B 282 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.549A pdb=" N MET B 284 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 98 through 102 removed outlier: 7.164A pdb=" N GLY B 91 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL B 160 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS B 201 " --> pdb=" O CYS B 86 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 157 through 163 removed outlier: 4.960A pdb=" N ILE B 157 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASP B 176 " --> pdb=" O THR B 163 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 4 through 8 Processing sheet with id= 10, first strand: chain 'C' and resid 195 through 198 Processing sheet with id= 11, first strand: chain 'D' and resid 59 through 65 removed outlier: 3.531A pdb=" N PHE D 152 " --> pdb=" O TYR D 48 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'F' and resid 128 through 133 removed outlier: 7.264A pdb=" N TYR F 128 " --> pdb=" O ILE F 84 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LYS F 77 " --> pdb=" O CYS F 114 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASN F 108 " --> pdb=" O ARG F 83 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASN F 107 " --> pdb=" O LEU F 202 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU F 202 " --> pdb=" O ASN F 107 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'F' and resid 147 through 151 removed outlier: 5.775A pdb=" N GLY F 147 " --> pdb=" O ILE F 158 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 157 through 162 removed outlier: 3.857A pdb=" N LEU G 131 " --> pdb=" O PHE G 181 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'H' and resid 4 through 10 Processing sheet with id= 16, first strand: chain 'H' and resid 16 through 19 removed outlier: 6.390A pdb=" N ARG H 22 " --> pdb=" O PHE H 37 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'H' and resid 98 through 102 removed outlier: 7.323A pdb=" N LYS H 106 " --> pdb=" O CYS H 124 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'H' and resid 128 through 133 removed outlier: 6.412A pdb=" N GLU H 139 " --> pdb=" O SER H 133 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASP H 138 " --> pdb=" O LEU H 90 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU H 90 " --> pdb=" O ASP H 138 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'I' and resid 85 through 90 removed outlier: 7.209A pdb=" N LEU I 135 " --> pdb=" O ARG I 90 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU I 136 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N CYS I 49 " --> pdb=" O SER I 168 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL I 166 " --> pdb=" O HIS I 51 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ARG I 162 " --> pdb=" O GLY I 55 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'I' and resid 95 through 100 removed outlier: 6.458A pdb=" N HIS I 95 " --> pdb=" O THR I 125 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR I 125 " --> pdb=" O HIS I 95 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE I 97 " --> pdb=" O GLN I 123 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'I' and resid 189 through 192 removed outlier: 8.868A pdb=" N GLU I 189 " --> pdb=" O ILE I 200 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'J' and resid 45 through 49 removed outlier: 3.899A pdb=" N SER J 66 " --> pdb=" O SER J 48 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS J 16 " --> pdb=" O VAL J 130 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN J 20 " --> pdb=" O ASP J 126 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N CYS J 22 " --> pdb=" O GLY J 124 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY J 124 " --> pdb=" O CYS J 22 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET J 125 " --> pdb=" O ILE J 106 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'J' and resid 89 through 93 removed outlier: 3.550A pdb=" N VAL J 170 " --> pdb=" O PHE J 89 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU J 91 " --> pdb=" O VAL J 170 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR J 93 " --> pdb=" O THR J 172 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'L' and resid 84 through 88 No H-bonds generated for sheet with id= 24 Processing sheet with id= 25, first strand: chain 'M' and resid 11 through 15 removed outlier: 4.626A pdb=" N ARG M 11 " --> pdb=" O ILE M 27 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS M 23 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'M' and resid 28 through 31 removed outlier: 6.632A pdb=" N ALA M 35 " --> pdb=" O LEU M 31 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'N' and resid 35 through 39 removed outlier: 6.403A pdb=" N ALA N 35 " --> pdb=" O ARG N 65 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VAL N 61 " --> pdb=" O CYS N 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TRP N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN N 117 " --> pdb=" O ILE N 133 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'O' and resid 3 through 7 Processing sheet with id= 29, first strand: chain 'P' and resid 13 through 19 removed outlier: 3.592A pdb=" N SER P 116 " --> pdb=" O ILE P 149 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'P' and resid 56 through 59 removed outlier: 5.639A pdb=" N LYS P 79 " --> pdb=" O PHE P 59 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'Q' and resid 77 through 81 Processing sheet with id= 32, first strand: chain 'R' and resid 21 through 25 removed outlier: 6.591A pdb=" N ARG R 21 " --> pdb=" O LEU R 53 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE R 49 " --> pdb=" O ASN R 25 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'S' and resid 22 through 28 removed outlier: 4.430A pdb=" N LYS S 4 " --> pdb=" O ILE S 62 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP S 58 " --> pdb=" O TYR S 8 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'S' and resid 86 through 92 removed outlier: 4.369A pdb=" N ASN S 71 " --> pdb=" O VAL S 126 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'T' and resid 38 through 43 removed outlier: 4.667A pdb=" N GLN T 38 " --> pdb=" O ILE T 64 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG T 60 " --> pdb=" O ILE T 42 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'T' and resid 72 through 79 Processing sheet with id= 37, first strand: chain 'U' and resid 62 through 65 removed outlier: 5.516A pdb=" N GLU U 108 " --> pdb=" O ARG U 22 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'V' and resid 25 through 28 removed outlier: 4.394A pdb=" N ALA V 25 " --> pdb=" O MET V 40 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'V' and resid 62 through 65 Processing sheet with id= 40, first strand: chain 'V' and resid 87 through 91 removed outlier: 6.009A pdb=" N LYS V 88 " --> pdb=" O PHE V 100 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N PHE V 100 " --> pdb=" O LYS V 88 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'X' and resid 77 through 83 removed outlier: 6.768A pdb=" N ASN X 77 " --> pdb=" O LEU X 123 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS X 117 " --> pdb=" O VAL X 83 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'Y' and resid 70 through 73 Processing sheet with id= 43, first strand: chain 'Z' and resid 10 through 14 removed outlier: 4.745A pdb=" N LEU Z 10 " --> pdb=" O ILE Z 26 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS Z 22 " --> pdb=" O VAL Z 14 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE Z 40 " --> pdb=" O VAL Z 27 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'a' and resid 123 through 126 Processing sheet with id= 45, first strand: chain 'c' and resid 26 through 29 removed outlier: 6.259A pdb=" N LYS c 26 " --> pdb=" O LEU c 97 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU c 45 " --> pdb=" O ILE c 96 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET c 48 " --> pdb=" O ARG c 72 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'd' and resid 43 through 46 removed outlier: 4.425A pdb=" N ARG d 67 " --> pdb=" O LYS d 86 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS d 7 " --> pdb=" O LEU d 68 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE d 3 " --> pdb=" O LEU d 72 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'e' and resid 76 through 82 Processing sheet with id= 48, first strand: chain 'f' and resid 28 through 32 removed outlier: 7.206A pdb=" N MET f 74 " --> pdb=" O PRO f 68 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG f 76 " --> pdb=" O CYS f 66 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG f 48 " --> pdb=" O ILE f 65 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'g' and resid 20 through 25 removed outlier: 5.087A pdb=" N ILE g 20 " --> pdb=" O VAL g 36 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'k' and resid 2 through 5 removed outlier: 3.562A pdb=" N ILE k 5 " --> pdb=" O THR k 48 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N THR k 50 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS k 21 " --> pdb=" O ARG k 41 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'm' and resid 94 through 97 removed outlier: 8.443A pdb=" N ASN m 117 " --> pdb=" O ARG m 97 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'o' and resid 2 through 6 removed outlier: 4.416A pdb=" N ALA o 6 " --> pdb=" O SER o 92 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'o' and resid 7 through 10 removed outlier: 4.436A pdb=" N GLN o 66 " --> pdb=" O LEU o 83 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N CYS o 77 " --> pdb=" O CYS o 72 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'p' and resid 46 through 50 removed outlier: 8.020A pdb=" N LYS p 46 " --> pdb=" O ARG p 58 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE p 54 " --> pdb=" O THR p 50 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLY p 53 " --> pdb=" O GLY p 66 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS p 62 " --> pdb=" O CYS p 57 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'W' and resid 19 through 24 No H-bonds generated for sheet with id= 55 1590 hydrogen bonds defined for protein. 4695 hydrogen bond angles defined for protein. NA hbond rejected because one of the atoms is absent Restraints generated for nucleic acids: 2159 hydrogen bonds 3842 hydrogen bond angles 0 basepair planarities 809 basepair parallelities 1496 stacking parallelities Total time for adding SS restraints: 296.43 Time building geometry restraints manager: 40.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 18670 1.33 - 1.48: 55167 1.48 - 1.63: 38002 1.63 - 1.78: 66 1.78 - 1.93: 283 Bond restraints: 112188 Sorted by residual: bond pdb=" P OMU 11908 " pdb=" O5' OMU 11908 " ideal model delta sigma weight residual 1.593 1.859 -0.266 1.50e-02 4.44e+03 3.14e+02 bond pdb=" C2' A2M 1 396 " pdb=" C1' A2M 1 396 " ideal model delta sigma weight residual 1.305 1.569 -0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C2' A2M 11768 " pdb=" C1' A2M 11768 " ideal model delta sigma weight residual 1.305 1.564 -0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C2' A2M 1 523 " pdb=" C1' A2M 1 523 " ideal model delta sigma weight residual 1.305 1.561 -0.256 2.00e-02 2.50e+03 1.64e+02 bond pdb=" O4' A2M 1 396 " pdb=" C1' A2M 1 396 " ideal model delta sigma weight residual 1.615 1.373 0.242 2.00e-02 2.50e+03 1.47e+02 ... (remaining 112183 not shown) Histogram of bond angle deviations from ideal: 95.54 - 103.76: 7672 103.76 - 111.98: 62896 111.98 - 120.20: 50721 120.20 - 128.42: 39595 128.42 - 136.64: 3892 Bond angle restraints: 164776 Sorted by residual: angle pdb=" C1' A2M 1 396 " pdb=" N9 A2M 1 396 " pdb=" C8 A2M 1 396 " ideal model delta sigma weight residual 88.50 129.18 -40.68 3.00e+00 1.11e-01 1.84e+02 angle pdb=" C1' A2M 1 523 " pdb=" N9 A2M 1 523 " pdb=" C8 A2M 1 523 " ideal model delta sigma weight residual 88.50 127.58 -39.08 3.00e+00 1.11e-01 1.70e+02 angle pdb=" C1' A2M 11768 " pdb=" N9 A2M 11768 " pdb=" C8 A2M 11768 " ideal model delta sigma weight residual 88.50 127.34 -38.84 3.00e+00 1.11e-01 1.68e+02 angle pdb=" C1' A2M 1 393 " pdb=" N9 A2M 1 393 " pdb=" C8 A2M 1 393 " ideal model delta sigma weight residual 88.50 124.65 -36.15 3.00e+00 1.11e-01 1.45e+02 angle pdb=" P OMU 11908 " pdb=" O5' OMU 11908 " pdb=" C5' OMU 11908 " ideal model delta sigma weight residual 120.90 107.49 13.41 1.50e+00 4.44e-01 8.00e+01 ... (remaining 164771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 59176 35.98 - 71.96: 2097 71.96 - 107.94: 185 107.94 - 143.91: 14 143.91 - 179.89: 49 Dihedral angle restraints: 61521 sinusoidal: 44839 harmonic: 16682 Sorted by residual: dihedral pdb=" CA GLY A 13 " pdb=" C GLY A 13 " pdb=" N SER A 14 " pdb=" CA SER A 14 " ideal model delta harmonic sigma weight residual -180.00 -131.84 -48.16 0 5.00e+00 4.00e-02 9.28e+01 dihedral pdb=" O4' C 12268 " pdb=" C1' C 12268 " pdb=" N1 C 12268 " pdb=" C2 C 12268 " ideal model delta sinusoidal sigma weight residual 200.00 20.11 179.89 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 4 99 " pdb=" C1' C 4 99 " pdb=" N1 C 4 99 " pdb=" C2 C 4 99 " ideal model delta sinusoidal sigma weight residual 200.00 22.86 177.14 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 61518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 18358 0.086 - 0.172: 1799 0.172 - 0.258: 116 0.258 - 0.344: 18 0.344 - 0.431: 54 Chirality restraints: 20345 Sorted by residual: chirality pdb=" P G 11483 " pdb=" OP1 G 11483 " pdb=" OP2 G 11483 " pdb=" O5' G 11483 " both_signs ideal model delta sigma weight residual True 2.41 -2.84 -0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" P A 11885 " pdb=" OP1 A 11885 " pdb=" OP2 A 11885 " pdb=" O5' A 11885 " both_signs ideal model delta sigma weight residual True 2.41 -2.83 -0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" P C 12298 " pdb=" OP1 C 12298 " pdb=" OP2 C 12298 " pdb=" O5' C 12298 " both_signs ideal model delta sigma weight residual True 2.41 -2.83 -0.42 2.00e-01 2.50e+01 4.38e+00 ... (remaining 20342 not shown) Planarity restraints: 10814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG 11204 " -0.139 2.00e-02 2.50e+03 6.91e-01 1.08e+04 pdb=" C4' OMG 11204 " -0.464 2.00e-02 2.50e+03 pdb=" O4' OMG 11204 " -0.537 2.00e-02 2.50e+03 pdb=" C3' OMG 11204 " 0.542 2.00e-02 2.50e+03 pdb=" O3' OMG 11204 " 0.875 2.00e-02 2.50e+03 pdb=" C2' OMG 11204 " 0.036 2.00e-02 2.50e+03 pdb=" O2' OMG 11204 " -1.223 2.00e-02 2.50e+03 pdb=" C1' OMG 11204 " -0.180 2.00e-02 2.50e+03 pdb=" N9 OMG 11204 " 1.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG 1 624 " 0.913 2.00e-02 2.50e+03 6.15e-01 8.52e+03 pdb=" C4' OMG 1 624 " -0.190 2.00e-02 2.50e+03 pdb=" O4' OMG 1 624 " -0.617 2.00e-02 2.50e+03 pdb=" C3' OMG 1 624 " 0.163 2.00e-02 2.50e+03 pdb=" O3' OMG 1 624 " -1.024 2.00e-02 2.50e+03 pdb=" C2' OMG 1 624 " 0.583 2.00e-02 2.50e+03 pdb=" O2' OMG 1 624 " 0.716 2.00e-02 2.50e+03 pdb=" C1' OMG 1 624 " -0.472 2.00e-02 2.50e+03 pdb=" N9 OMG 1 624 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG 1 386 " 0.080 2.00e-02 2.50e+03 6.05e-01 8.24e+03 pdb=" C4' OMG 1 386 " 0.431 2.00e-02 2.50e+03 pdb=" O4' OMG 1 386 " 0.598 2.00e-02 2.50e+03 pdb=" C3' OMG 1 386 " -0.594 2.00e-02 2.50e+03 pdb=" O3' OMG 1 386 " -0.667 2.00e-02 2.50e+03 pdb=" C2' OMG 1 386 " -0.150 2.00e-02 2.50e+03 pdb=" O2' OMG 1 386 " 1.002 2.00e-02 2.50e+03 pdb=" C1' OMG 1 386 " 0.232 2.00e-02 2.50e+03 pdb=" N9 OMG 1 386 " -0.932 2.00e-02 2.50e+03 ... (remaining 10811 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.13: 185 2.13 - 2.88: 37772 2.88 - 3.63: 190108 3.63 - 4.39: 399490 4.39 - 5.14: 546531 Nonbonded interactions: 1174086 Sorted by model distance: nonbonded pdb="MG MG 12809 " pdb=" O HOH 13115 " model vdw 1.376 2.170 nonbonded pdb="MG MG 12826 " pdb=" O HOH 13114 " model vdw 1.694 2.170 nonbonded pdb="MG MG 12805 " pdb=" O HOH 13143 " model vdw 1.698 2.170 nonbonded pdb=" OP1 U 11628 " pdb="MG MG 12805 " model vdw 1.736 2.170 nonbonded pdb="MG MG 12892 " pdb=" O HOH 13583 " model vdw 1.751 2.170 ... (remaining 1174081 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: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 23.140 Check model and map are aligned: 1.200 Set scattering table: 0.730 Process input model: 493.650 Find NCS groups from input model: 2.400 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: 0.020 Load rotamer database and sin/cos tables:8.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 533.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 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 : 0.010 0.266 112188 Z= 0.627 Angle : 1.068 40.684 164776 Z= 0.527 Chirality : 0.056 0.431 20345 Planarity : 0.023 0.691 10814 Dihedral : 16.059 179.892 50740 Min Nonbonded Distance : 1.376 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.37 % Favored : 95.61 % Rotamer Outliers : 6.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.10), residues: 5669 helix: -1.95 (0.10), residues: 1803 sheet: -0.66 (0.17), residues: 826 loop : -1.29 (0.10), residues: 3040 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1206 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 912 time to evaluate : 5.937 Fit side-chains outliers start: 294 outliers final: 165 residues processed: 1139 average time/residue: 2.1331 time to fit residues: 3246.7769 Evaluate side-chains 1007 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 842 time to evaluate : 6.042 Switching outliers to nearest non-outliers outliers start: 165 outliers final: 136 residues processed: 29 average time/residue: 1.1739 time to fit residues: 62.0919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 827 random chunks: chunk 698 optimal weight: 4.9990 chunk 626 optimal weight: 5.9990 chunk 347 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 422 optimal weight: 6.9990 chunk 334 optimal weight: 6.9990 chunk 648 optimal weight: 1.9990 chunk 250 optimal weight: 9.9990 chunk 394 optimal weight: 1.9990 chunk 482 optimal weight: 0.0030 chunk 751 optimal weight: 4.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN B 352 GLN D 255 ASN F 44 GLN F 167 GLN H 94 HIS H 135 ASN I 170 ASN J 101 ASN M 60 GLN M 97 GLN M 98 GLN O 69 HIS O 189 ASN Q 39 ASN Q 87 ASN V 28 ASN V 39 ASN V 101 GLN X 77 ASN ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 88 GLN f 27 ASN o 21 HIS p 25 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 112188 Z= 0.214 Angle : 0.768 19.515 164776 Z= 0.414 Chirality : 0.041 0.319 20345 Planarity : 0.007 0.140 10814 Dihedral : 15.067 179.727 39066 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 5.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.10), residues: 5669 helix: -0.21 (0.11), residues: 1897 sheet: -0.30 (0.17), residues: 829 loop : -1.11 (0.10), residues: 2943 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1158 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 885 time to evaluate : 5.984 Fit side-chains outliers start: 273 outliers final: 152 residues processed: 1078 average time/residue: 2.0850 time to fit residues: 3043.9661 Evaluate side-chains 979 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 827 time to evaluate : 5.977 Switching outliers to nearest non-outliers outliers start: 152 outliers final: 128 residues processed: 25 average time/residue: 0.9048 time to fit residues: 47.9626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 827 random chunks: chunk 417 optimal weight: 0.0040 chunk 233 optimal weight: 10.0000 chunk 625 optimal weight: 0.9990 chunk 511 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 752 optimal weight: 5.9990 chunk 812 optimal weight: 9.9990 chunk 670 optimal weight: 7.9990 chunk 746 optimal weight: 0.3980 chunk 256 optimal weight: 10.0000 chunk 603 optimal weight: 0.8980 overall best weight: 1.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 HIS B 152 GLN D 255 ASN F 162 ASN F 167 GLN H 135 ASN I 170 ASN L 132 ASN M 60 GLN N 8 GLN P 103 HIS P 105 HIS Q 58 ASN Q 87 ASN S 3 GLN T 75 GLN V 28 ASN V 101 GLN ** Y 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 87 ASN c 88 GLN d 7 HIS f 27 ASN f 71 ASN i 61 HIS o 81 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.056 112188 Z= 0.124 Angle : 0.640 18.703 164776 Z= 0.355 Chirality : 0.035 0.296 20345 Planarity : 0.006 0.131 10814 Dihedral : 14.653 179.877 39066 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 4.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.11), residues: 5669 helix: 0.79 (0.12), residues: 1897 sheet: 0.01 (0.18), residues: 808 loop : -0.82 (0.10), residues: 2964 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 888 time to evaluate : 6.013 Fit side-chains outliers start: 227 outliers final: 131 residues processed: 1051 average time/residue: 2.0650 time to fit residues: 2968.8594 Evaluate side-chains 956 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 825 time to evaluate : 5.986 Switching outliers to nearest non-outliers outliers start: 131 outliers final: 106 residues processed: 26 average time/residue: 0.9910 time to fit residues: 52.3143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 827 random chunks: chunk 743 optimal weight: 0.0070 chunk 565 optimal weight: 7.9990 chunk 390 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 359 optimal weight: 0.0060 chunk 505 optimal weight: 0.9990 chunk 755 optimal weight: 5.9990 chunk 799 optimal weight: 5.9990 chunk 394 optimal weight: 6.9990 chunk 715 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 overall best weight: 2.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN C 108 ASN D 255 ASN F 162 ASN H 94 HIS H 135 ASN I 170 ASN I 196 ASN L 132 ASN M 60 GLN N 8 GLN P 100 ASN P 103 HIS U 47 HIS V 28 ASN c 88 GLN f 27 ASN i 61 HIS l 20 ASN l 22 ASN o 81 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 112188 Z= 0.197 Angle : 0.702 18.726 164776 Z= 0.381 Chirality : 0.038 0.332 20345 Planarity : 0.007 0.138 10814 Dihedral : 14.726 179.742 39066 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 5.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.11), residues: 5669 helix: 1.00 (0.12), residues: 1893 sheet: 0.08 (0.17), residues: 852 loop : -0.80 (0.11), residues: 2924 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1065 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 821 time to evaluate : 6.157 Fit side-chains outliers start: 244 outliers final: 156 residues processed: 982 average time/residue: 2.1581 time to fit residues: 2890.3827 Evaluate side-chains 959 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 803 time to evaluate : 6.026 Switching outliers to nearest non-outliers outliers start: 156 outliers final: 121 residues processed: 37 average time/residue: 1.1757 time to fit residues: 79.4274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 827 random chunks: chunk 665 optimal weight: 2.9990 chunk 453 optimal weight: 0.0970 chunk 11 optimal weight: 10.0000 chunk 595 optimal weight: 5.9990 chunk 329 optimal weight: 3.9990 chunk 682 optimal weight: 7.9990 chunk 552 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 408 optimal weight: 0.2980 chunk 717 optimal weight: 10.0000 chunk 201 optimal weight: 9.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 ASN D 255 ASN F 162 ASN H 135 ASN I 170 ASN I 196 ASN M 60 GLN N 8 GLN P 103 HIS Q 87 ASN V 28 ASN a 39 GLN c 88 GLN f 27 ASN f 71 ASN i 61 HIS l 22 ASN o 81 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 112188 Z= 0.178 Angle : 0.689 18.717 164776 Z= 0.376 Chirality : 0.038 0.326 20345 Planarity : 0.007 0.136 10814 Dihedral : 14.715 179.886 39066 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 4.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.11), residues: 5669 helix: 1.12 (0.12), residues: 1886 sheet: 0.09 (0.17), residues: 865 loop : -0.78 (0.11), residues: 2918 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1023 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 809 time to evaluate : 6.020 Fit side-chains outliers start: 214 outliers final: 151 residues processed: 962 average time/residue: 2.1214 time to fit residues: 2757.9939 Evaluate side-chains 946 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 795 time to evaluate : 6.045 Switching outliers to nearest non-outliers outliers start: 151 outliers final: 123 residues processed: 30 average time/residue: 1.1578 time to fit residues: 63.7708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 827 random chunks: chunk 268 optimal weight: 10.0000 chunk 719 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 469 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 chunk 800 optimal weight: 3.9990 chunk 664 optimal weight: 1.9990 chunk 370 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 420 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 GLN F 162 ASN F 167 GLN G 58 ASN H 94 HIS H 135 ASN I 170 ASN M 60 GLN N 8 GLN P 103 HIS V 28 ASN c 88 GLN f 27 ASN f 71 ASN i 61 HIS l 22 ASN o 81 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.128 112188 Z= 0.366 Angle : 0.867 20.908 164776 Z= 0.454 Chirality : 0.046 0.396 20345 Planarity : 0.008 0.149 10814 Dihedral : 15.081 179.971 39066 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 5.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.11), residues: 5669 helix: 0.75 (0.12), residues: 1884 sheet: -0.05 (0.17), residues: 859 loop : -0.96 (0.10), residues: 2926 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1078 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 823 time to evaluate : 5.997 Fit side-chains outliers start: 255 outliers final: 178 residues processed: 1005 average time/residue: 2.0795 time to fit residues: 2908.2140 Evaluate side-chains 984 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 806 time to evaluate : 6.015 Switching outliers to nearest non-outliers outliers start: 178 outliers final: 142 residues processed: 36 average time/residue: 1.1448 time to fit residues: 77.3477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 827 random chunks: chunk 771 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 455 optimal weight: 0.0470 chunk 584 optimal weight: 0.8980 chunk 452 optimal weight: 6.9990 chunk 673 optimal weight: 6.9990 chunk 446 optimal weight: 5.9990 chunk 797 optimal weight: 4.9990 chunk 498 optimal weight: 4.9990 chunk 485 optimal weight: 4.9990 chunk 368 optimal weight: 9.9990 overall best weight: 3.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 255 ASN F 44 GLN F 162 ASN F 167 GLN G 58 ASN H 135 ASN I 196 ASN J 101 ASN M 60 GLN N 8 GLN P 103 HIS Q 87 ASN V 28 ASN X 77 ASN Z 87 ASN c 50 ASN c 88 GLN f 27 ASN l 22 ASN o 81 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.096 112188 Z= 0.229 Angle : 0.749 18.837 164776 Z= 0.404 Chirality : 0.041 0.355 20345 Planarity : 0.007 0.140 10814 Dihedral : 14.932 179.925 39066 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 4.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.11), residues: 5669 helix: 0.93 (0.12), residues: 1886 sheet: -0.03 (0.17), residues: 862 loop : -0.90 (0.10), residues: 2921 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1033 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 819 time to evaluate : 5.725 Fit side-chains outliers start: 214 outliers final: 160 residues processed: 980 average time/residue: 2.0924 time to fit residues: 2816.7675 Evaluate side-chains 964 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 804 time to evaluate : 5.969 Switching outliers to nearest non-outliers outliers start: 160 outliers final: 135 residues processed: 27 average time/residue: 1.1471 time to fit residues: 59.7803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 827 random chunks: chunk 493 optimal weight: 5.9990 chunk 318 optimal weight: 4.9990 chunk 476 optimal weight: 6.9990 chunk 240 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 506 optimal weight: 0.9980 chunk 543 optimal weight: 7.9990 chunk 394 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 626 optimal weight: 7.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 255 ASN F 44 GLN F 162 ASN F 167 GLN G 58 ASN H 94 HIS H 135 ASN N 8 GLN P 103 HIS V 28 ASN Z 87 ASN c 88 GLN f 27 ASN l 22 ASN o 81 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.130 112188 Z= 0.352 Angle : 0.857 20.215 164776 Z= 0.450 Chirality : 0.046 0.400 20345 Planarity : 0.008 0.148 10814 Dihedral : 15.078 179.993 39066 Min Nonbonded Distance : 1.695 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 4.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.10), residues: 5669 helix: 0.70 (0.12), residues: 1889 sheet: -0.08 (0.17), residues: 861 loop : -1.00 (0.10), residues: 2919 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1018 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 799 time to evaluate : 5.784 Fit side-chains outliers start: 219 outliers final: 168 residues processed: 961 average time/residue: 2.0990 time to fit residues: 2730.6345 Evaluate side-chains 966 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 798 time to evaluate : 5.994 Switching outliers to nearest non-outliers outliers start: 168 outliers final: 136 residues processed: 33 average time/residue: 0.9414 time to fit residues: 59.7285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 827 random chunks: chunk 725 optimal weight: 7.9990 chunk 763 optimal weight: 3.9990 chunk 696 optimal weight: 0.0570 chunk 742 optimal weight: 3.9990 chunk 447 optimal weight: 5.9990 chunk 323 optimal weight: 1.9990 chunk 583 optimal weight: 4.9990 chunk 227 optimal weight: 8.9990 chunk 671 optimal weight: 5.9990 chunk 702 optimal weight: 7.9990 chunk 740 optimal weight: 6.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 255 ASN F 162 ASN F 167 GLN G 58 ASN H 94 HIS H 135 ASN N 8 GLN P 103 HIS Q 87 ASN V 28 ASN Z 87 ASN c 50 ASN c 88 GLN f 27 ASN l 22 ASN o 81 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.099 112188 Z= 0.233 Angle : 0.767 18.973 164776 Z= 0.412 Chirality : 0.041 0.357 20345 Planarity : 0.007 0.140 10814 Dihedral : 15.019 179.840 39066 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.21 % Favored : 96.77 % Rotamer Outliers : 3.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.11), residues: 5669 helix: 0.86 (0.12), residues: 1890 sheet: -0.08 (0.17), residues: 856 loop : -0.97 (0.10), residues: 2923 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 975 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 801 time to evaluate : 6.155 Fit side-chains outliers start: 174 outliers final: 146 residues processed: 949 average time/residue: 2.0796 time to fit residues: 2685.7025 Evaluate side-chains 934 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 788 time to evaluate : 6.012 Switching outliers to nearest non-outliers outliers start: 146 outliers final: 134 residues processed: 13 average time/residue: 1.0028 time to fit residues: 29.6537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 827 random chunks: chunk 487 optimal weight: 3.9990 chunk 785 optimal weight: 9.9990 chunk 479 optimal weight: 6.9990 chunk 372 optimal weight: 0.0270 chunk 546 optimal weight: 5.9990 chunk 823 optimal weight: 1.9990 chunk 758 optimal weight: 5.9990 chunk 656 optimal weight: 0.0980 chunk 68 optimal weight: 10.0000 chunk 506 optimal weight: 4.9990 chunk 402 optimal weight: 9.9990 overall best weight: 2.2244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 255 ASN F 44 GLN F 162 ASN F 167 GLN G 58 ASN H 94 HIS H 135 ASN N 8 GLN P 103 HIS V 28 ASN Z 87 ASN c 88 GLN f 27 ASN l 22 ASN o 81 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.084 112188 Z= 0.187 Angle : 0.727 18.713 164776 Z= 0.394 Chirality : 0.039 0.336 20345 Planarity : 0.007 0.138 10814 Dihedral : 14.916 179.652 39066 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 3.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.11), residues: 5669 helix: 1.01 (0.12), residues: 1891 sheet: 0.01 (0.17), residues: 856 loop : -0.89 (0.11), residues: 2922 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11338 Ramachandran restraints generated. 5669 Oldfield, 0 Emsley, 5669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 801 time to evaluate : 6.091 Fit side-chains outliers start: 149 outliers final: 137 residues processed: 935 average time/residue: 2.1140 time to fit residues: 2689.4512 Evaluate side-chains 932 residues out of total 4908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 795 time to evaluate : 5.960 Switching outliers to nearest non-outliers outliers start: 137 outliers final: 131 residues processed: 8 average time/residue: 1.0239 time to fit residues: 21.2193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 827 random chunks: chunk 521 optimal weight: 7.9990 chunk 698 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 chunk 604 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 657 optimal weight: 8.9990 chunk 275 optimal weight: 0.6980 chunk 674 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 overall best weight: 6.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 255 ASN F 44 GLN F 162 ASN F 167 GLN G 58 ASN H 94 HIS H 135 ASN N 8 GLN P 103 HIS V 28 ASN Z 87 ASN c 88 GLN f 27 ASN l 22 ASN o 81 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.118960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.102237 restraints weight = 111358.136| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 0.40 r_work: 0.2812 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.147 112188 Z= 0.419 Angle : 0.922 21.810 164776 Z= 0.478 Chirality : 0.048 0.421 20345 Planarity : 0.009 0.153 10814 Dihedral : 15.176 179.862 39066 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 3.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.10), residues: 5669 helix: 0.57 (0.12), residues: 1896 sheet: -0.10 (0.17), residues: 862 loop : -1.05 (0.10), residues: 2911 =============================================================================== Job complete usr+sys time: 36957.28 seconds wall clock time: 640 minutes 10.87 seconds (38410.87 seconds total)