Starting phenix.real_space_refine on Sun Mar 3 06:13:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q97_4476/03_2024/6q97_4476_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q97_4476/03_2024/6q97_4476.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q97_4476/03_2024/6q97_4476_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q97_4476/03_2024/6q97_4476_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q97_4476/03_2024/6q97_4476_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q97_4476/03_2024/6q97_4476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q97_4476/03_2024/6q97_4476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q97_4476/03_2024/6q97_4476_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q97_4476/03_2024/6q97_4476_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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 Zn 2 6.06 5 P 5051 5.49 5 Mg 439 5.21 5 S 160 5.16 5 C 78305 2.51 5 N 29030 2.21 5 O 43622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "5 GLU 31": "OE1" <-> "OE2" Residue "5 ARG 45": "NH1" <-> "NH2" Residue "5 ARG 59": "NH1" <-> "NH2" Residue "5 ARG 86": "NH1" <-> "NH2" Residue "5 ARG 88": "NH1" <-> "NH2" Residue "5 ARG 153": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D GLU 152": "OE1" <-> "OE2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E GLU 165": "OE1" <-> "OE2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F ARG 170": "NH1" <-> "NH2" Residue "G GLU 45": "OE1" <-> "OE2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "H GLU 17": "OE1" <-> "OE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 34": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K ARG 17": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K GLU 106": "OE1" <-> "OE2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L GLU 86": "OE1" <-> "OE2" Residue "L ARG 123": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N GLU 43": "OE1" <-> "OE2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O GLU 60": "OE1" <-> "OE2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "O GLU 112": "OE1" <-> "OE2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "P GLU 27": "OE1" <-> "OE2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P ARG 89": "NH1" <-> "NH2" Residue "P ARG 101": "NH1" <-> "NH2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "R TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R GLU 31": "OE1" <-> "OE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 92": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 3": "NH1" <-> "NH2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "T GLU 52": "OE1" <-> "OE2" Residue "T GLU 54": "OE1" <-> "OE2" Residue "T GLU 56": "OE1" <-> "OE2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U GLU 10": "OE1" <-> "OE2" Residue "U GLU 37": "OE1" <-> "OE2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U ARG 94": "NH1" <-> "NH2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V GLU 59": "OE1" <-> "OE2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ARG 18": "NH1" <-> "NH2" Residue "X PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "X ARG 45": "NH1" <-> "NH2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X GLU 70": "OE1" <-> "OE2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "Y GLU 17": "OE1" <-> "OE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 11": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z ARG 45": "NH1" <-> "NH2" Residue "a GLU 11": "OE1" <-> "OE2" Residue "a ARG 56": "NH1" <-> "NH2" Residue "a ARG 63": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c GLU 7": "OE1" <-> "OE2" Residue "c ARG 28": "NH1" <-> "NH2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 41": "NH1" <-> "NH2" Residue "e ARG 13": "NH1" <-> "NH2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ARG 42": "NH1" <-> "NH2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "g GLU 44": "OE1" <-> "OE2" Residue "g ARG 63": "NH1" <-> "NH2" Residue "g ARG 74": "NH1" <-> "NH2" Residue "g GLU 142": "OE1" <-> "OE2" Residue "g ARG 208": "NH1" <-> "NH2" Residue "g GLU 223": "OE1" <-> "OE2" Residue "g ARG 225": "NH1" <-> "NH2" Residue "h ARG 54": "NH1" <-> "NH2" Residue "h ARG 72": "NH1" <-> "NH2" Residue "h GLU 82": "OE1" <-> "OE2" Residue "h ARG 88": "NH1" <-> "NH2" Residue "h ARG 127": "NH1" <-> "NH2" Residue "h ARG 131": "NH1" <-> "NH2" Residue "h ARG 132": "NH1" <-> "NH2" Residue "h ARG 164": "NH1" <-> "NH2" Residue "h GLU 166": "OE1" <-> "OE2" Residue "h GLU 170": "OE1" <-> "OE2" Residue "i GLU 35": "OE1" <-> "OE2" Residue "i ARG 73": "NH1" <-> "NH2" Residue "i ARG 81": "NH1" <-> "NH2" Residue "j GLU 13": "OE1" <-> "OE2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j ARG 68": "NH1" <-> "NH2" Residue "j ARG 69": "NH1" <-> "NH2" Residue "j ARG 93": "NH1" <-> "NH2" Residue "j ARG 157": "NH1" <-> "NH2" Residue "j GLU 162": "OE1" <-> "OE2" Residue "k ARG 45": "NH1" <-> "NH2" Residue "k ARG 79": "NH1" <-> "NH2" Residue "l ARG 4": "NH1" <-> "NH2" Residue "l ARG 53": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ARG 79": "NH1" <-> "NH2" Residue "l ARG 92": "NH1" <-> "NH2" Residue "n ARG 11": "NH1" <-> "NH2" Residue "n ARG 41": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o ARG 45": "NH1" <-> "NH2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "p ARG 37": "NH1" <-> "NH2" Residue "p ARG 69": "NH1" <-> "NH2" Residue "p ARG 93": "NH1" <-> "NH2" Residue "p ARG 106": "NH1" <-> "NH2" Residue "q ARG 9": "NH1" <-> "NH2" Residue "q ARG 14": "NH1" <-> "NH2" Residue "q ARG 50": "NH1" <-> "NH2" Residue "q ARG 83": "NH1" <-> "NH2" Residue "r ARG 29": "NH1" <-> "NH2" Residue "r ARG 70": "NH1" <-> "NH2" Residue "r ARG 87": "NH1" <-> "NH2" Residue "r ARG 109": "NH1" <-> "NH2" Residue "s ARG 59": "NH1" <-> "NH2" Residue "s ARG 63": "NH1" <-> "NH2" Residue "s ARG 65": "NH1" <-> "NH2" Residue "s ARG 69": "NH1" <-> "NH2" Residue "s ARG 85": "NH1" <-> "NH2" Residue "t ARG 72": "NH1" <-> "NH2" Residue "t GLU 83": "OE1" <-> "OE2" Residue "t ARG 89": "NH1" <-> "NH2" Residue "u ARG 28": "NH1" <-> "NH2" Residue "u ARG 51": "NH1" <-> "NH2" Residue "v ARG 11": "NH1" <-> "NH2" Residue "v ARG 27": "NH1" <-> "NH2" Residue "v GLU 49": "OE1" <-> "OE2" Residue "v ARG 65": "NH1" <-> "NH2" Residue "v ARG 77": "NH1" <-> "NH2" Residue "w ARG 61": "NH1" <-> "NH2" Residue "w TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 32": "NH1" <-> "NH2" Residue "y ARG 60": "NH1" <-> "NH2" Residue "y ARG 74": "NH1" <-> "NH2" Residue "z GLU 24": "OE1" <-> "OE2" Residue "z ARG 33": "NH1" <-> "NH2" Residue "z ARG 45": "NH1" <-> "NH2" Residue "z ARG 55": "NH1" <-> "NH2" Residue "z ARG 62": "NH1" <-> "NH2" Residue "z ARG 67": "NH1" <-> "NH2" Residue "z ARG 69": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 156609 Number of models: 1 Model: "" Number of chains: 72 Chain: "1" Number of atoms: 62336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62336 Classifications: {'RNA': 2903} Modifications used: {'rna2p': 4, 'rna2p_pur': 288, 'rna2p_pyr': 165, 'rna3p': 18, 'rna3p_pur': 1378, 'rna3p_pyr': 1049} Link IDs: {'rna2p': 456, 'rna3p': 2446} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "2" Number of atoms: 32929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32929 Classifications: {'RNA': 1534} Modifications used: {'rna2p': 1, 'rna2p_pur': 118, 'rna2p_pyr': 90, 'rna3p': 10, 'rna3p_pur': 751, 'rna3p_pyr': 563} Link IDs: {'rna2p': 208, 'rna3p': 1325} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 105} Chain: "5" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1170 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "6" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 140 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "8" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1638 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 9, 'rna3p_pur': 31, 'rna3p_pyr': 29} Link IDs: {'rna2p': 16, 'rna3p': 60} Chain: "9" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 128 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 3} Link IDs: {'rna3p': 5} Chain: "B" Number of atoms: 2078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2078 Classifications: {'peptide': 270} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 252} Chain: "C" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Chain: "D" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "E" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "F" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1313 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "G" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 980 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "I" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 984 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 9, 'TRANS': 125} Chain: "J" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1121 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "K" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "O" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 884 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 840 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "T" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 746 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "U" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 788 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 582 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 477 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "Z" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 434 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "a" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "b" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 429 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "c" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "f" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "g" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "h" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1636 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "i" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "j" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "k" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "l" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "m" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "n" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1010 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "o" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 790 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "p" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "q" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'0TD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "s" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "t" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 708 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'TRANS': 86} Chain: "u" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "v" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "w" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "x" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "y" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 664 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "z" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4" Number of atoms: 7134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 7134 Classifications: {'RNA': 334} Modifications used: {'rna2p_pur': 22, 'rna2p_pyr': 17, 'rna3p_pur': 156, 'rna3p_pyr': 139} Link IDs: {'rna2p': 39, 'rna3p': 294} Chain breaks: 1 Chain: "7" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 32, 'rna3p_pyr': 30} Link IDs: {'rna2p': 14, 'rna3p': 62} Chain: "1" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 294 Unusual residues: {' MG': 294} Classifications: {'undetermined': 294} Link IDs: {None: 293} Chain: "2" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 128 Unusual residues: {' MG': 128} Classifications: {'undetermined': 128} Link IDs: {None: 127} Chain: "3" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "8" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0LUX SG CYS f 27 187.386 132.299 122.471 1.00 70.81 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MG MG 13144 " occ=0.50 Time building chain proxies: 60.85, per 1000 atoms: 0.39 Number of scatterers: 156609 At special positions: 0 Unit cell: (248.24, 310.3, 278.2, 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) Zn 2 29.99 S 160 16.00 P 5051 15.00 Mg 439 11.99 O 43622 8.00 N 29030 7.00 C 78305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS a 18 " - pdb=" SG CYS a 37 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 64.42 Conformation dependent library (CDL) restraints added in 8.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 33 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " 12030 Ramachandran restraints generated. 6015 Oldfield, 0 Emsley, 6015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11264 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 178 helices and 72 sheets defined 38.0% alpha, 17.6% beta 807 base pairs and 2097 stacking pairs defined. Time for finding SS restraints: 68.86 Creating SS restraints... Processing helix chain '5' and resid 17 through 24 removed outlier: 3.824A pdb=" N ARG 5 21 " --> pdb=" O ASN 5 17 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N HIS 5 22 " --> pdb=" O LYS 5 18 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLU 5 23 " --> pdb=" O ARG 5 19 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR 5 24 " --> pdb=" O ALA 5 20 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 17 through 24' Processing helix chain '5' and resid 37 through 45 removed outlier: 4.320A pdb=" N VAL 5 41 " --> pdb=" O GLN 5 37 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS 5 42 " --> pdb=" O GLY 5 38 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N SER 5 43 " --> pdb=" O TRP 5 39 " (cutoff:3.500A) Processing helix chain '5' and resid 93 through 107 removed outlier: 3.515A pdb=" N TYR 5 101 " --> pdb=" O LEU 5 97 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ARG 5 106 " --> pdb=" O GLY 5 102 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU 5 107 " --> pdb=" O ARG 5 103 " (cutoff:3.500A) Processing helix chain '5' and resid 138 through 157 removed outlier: 4.887A pdb=" N ILE 5 142 " --> pdb=" O LYS 5 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 removed outlier: 3.749A pdb=" N ARG B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N HIS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 10 through 15' Processing helix chain 'B' and resid 131 through 136 removed outlier: 3.712A pdb=" N ILE B 135 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Proline residue: B 136 - end of helix No H-bonds generated for 'chain 'B' and resid 131 through 136' Processing helix chain 'B' and resid 207 through 215 removed outlier: 4.484A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 268 removed outlier: 4.459A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 260 through 268' Processing helix chain 'C' and resid 61 through 72 removed outlier: 3.606A pdb=" N GLY C 66 " --> pdb=" O LYS C 62 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 20 removed outlier: 4.214A pdb=" N PHE D 19 " --> pdb=" O SER D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 40 removed outlier: 3.997A pdb=" N VAL D 31 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY D 38 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA D 39 " --> pdb=" O TYR D 35 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ARG D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 removed outlier: 4.239A pdb=" N SER D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU D 111 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 142 removed outlier: 4.054A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 162 removed outlier: 4.120A pdb=" N PHE D 158 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ARG D 162 " --> pdb=" O PHE D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 183 removed outlier: 4.671A pdb=" N ILE D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 201 removed outlier: 4.777A pdb=" N LYS D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN D 195 " --> pdb=" O ASP D 191 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N MET D 199 " --> pdb=" O GLN D 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 21 removed outlier: 3.603A pdb=" N LYS E 9 " --> pdb=" O HIS E 5 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASP E 10 " --> pdb=" O ASP E 6 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N VAL E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LYS E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LYS E 15 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N PHE E 20 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN E 21 " --> pdb=" O MET E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 62 removed outlier: 3.965A pdb=" N LEU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ALA E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE E 60 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER E 61 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 removed outlier: 3.708A pdb=" N TRP E 97 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE E 106 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL E 108 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Proline residue: E 109 - end of helix Processing helix chain 'E' and resid 162 through 172 removed outlier: 3.954A pdb=" N ARG E 167 " --> pdb=" O ASP E 163 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALA E 168 " --> pdb=" O GLU E 164 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LEU E 169 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU E 170 " --> pdb=" O GLY E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 29 removed outlier: 3.652A pdb=" N GLN E 27 " --> pdb=" O SER E 24 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL E 28 " --> pdb=" O VAL E 25 " (cutoff:3.500A) Proline residue: E 29 - end of helix No H-bonds generated for 'chain 'E' and resid 24 through 29' Processing helix chain 'E' and resid 134 through 139 removed outlier: 4.518A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Proline residue: E 139 - end of helix Processing helix chain 'F' and resid 2 through 8 Proline residue: F 8 - end of helix Processing helix chain 'F' and resid 60 through 81 removed outlier: 4.666A pdb=" N GLN F 64 " --> pdb=" O ASP F 60 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA F 65 " --> pdb=" O GLY F 61 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY F 66 " --> pdb=" O TRP F 62 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR F 67 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL F 76 " --> pdb=" O LEU F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 151 removed outlier: 3.634A pdb=" N GLN F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA F 145 " --> pdb=" O ILE F 141 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N TYR F 151 " --> pdb=" O ASP F 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 29 removed outlier: 4.138A pdb=" N ALA G 26 " --> pdb=" O LYS G 22 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG G 27 " --> pdb=" O ALA G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 51 removed outlier: 4.265A pdb=" N ALA G 49 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ARG G 50 " --> pdb=" O PHE G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 74 removed outlier: 5.461A pdb=" N LYS G 57 " --> pdb=" O GLU G 53 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU G 58 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ILE G 72 " --> pdb=" O ARG G 68 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ALA G 74 " --> pdb=" O GLU G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 removed outlier: 4.271A pdb=" N ALA G 102 " --> pdb=" O ASP G 98 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA G 105 " --> pdb=" O ASP G 101 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ALA G 106 " --> pdb=" O ALA G 102 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY G 107 " --> pdb=" O VAL G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 116 removed outlier: 3.737A pdb=" N VAL G 115 " --> pdb=" O ALA G 111 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG G 116 " --> pdb=" O LYS G 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 111 through 116' Processing helix chain 'H' and resid 3 through 21 removed outlier: 4.183A pdb=" N GLN H 9 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL H 18 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS H 20 " --> pdb=" O SER H 16 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY H 21 " --> pdb=" O GLU H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 49 removed outlier: 3.831A pdb=" N THR H 39 " --> pdb=" O VAL H 35 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU H 40 " --> pdb=" O ASP H 36 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS H 43 " --> pdb=" O THR H 39 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY H 49 " --> pdb=" O GLY H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 66 removed outlier: 4.407A pdb=" N ALA H 63 " --> pdb=" O LEU H 59 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL H 64 " --> pdb=" O LEU H 60 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLU H 65 " --> pdb=" O ARG H 61 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLY H 66 " --> pdb=" O ARG H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 59 through 66' Processing helix chain 'H' and resid 93 through 106 removed outlier: 4.672A pdb=" N LYS H 97 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU H 98 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ALA H 100 " --> pdb=" O PHE H 96 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 76 removed outlier: 3.761A pdb=" N ASP H 74 " --> pdb=" O CYS H 71 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA H 75 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE H 76 " --> pdb=" O LYS H 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 71 through 76' Processing helix chain 'I' and resid 33 through 49 removed outlier: 3.595A pdb=" N LYS I 39 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN I 42 " --> pdb=" O CYS I 38 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ALA I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR I 45 " --> pdb=" O PHE I 41 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP I 46 " --> pdb=" O ASN I 42 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N SER I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE I 48 " --> pdb=" O LYS I 44 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLU I 49 " --> pdb=" O THR I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 84 removed outlier: 4.642A pdb=" N LEU I 79 " --> pdb=" O ALA I 75 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LYS I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA I 83 " --> pdb=" O LEU I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 113 removed outlier: 4.742A pdb=" N ILE I 108 " --> pdb=" O GLN I 104 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN I 110 " --> pdb=" O GLN I 106 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.831A pdb=" N MET I 124 " --> pdb=" O ASP I 120 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG I 126 " --> pdb=" O GLU I 122 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER I 127 " --> pdb=" O ALA I 123 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE I 128 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR I 131 " --> pdb=" O SER I 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 12 removed outlier: 3.556A pdb=" N VAL J 11 " --> pdb=" O LYS J 7 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LYS J 12 " --> pdb=" O PRO J 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 7 through 12' Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.034A pdb=" N THR J 30 " --> pdb=" O GLY J 26 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU J 36 " --> pdb=" O LEU J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 3.782A pdb=" N LYS J 72 " --> pdb=" O LYS J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.767A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE J 103 " --> pdb=" O ARG J 99 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 4.163A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 119 removed outlier: 4.510A pdb=" N ILE K 116 " --> pdb=" O PHE K 112 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER K 117 " --> pdb=" O MET K 113 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA K 119 " --> pdb=" O ILE K 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 112 through 119' Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.775A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 74 removed outlier: 4.969A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 99 removed outlier: 4.067A pdb=" N LEU L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN L 99 " --> pdb=" O LEU L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 removed outlier: 3.658A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE L 135 " --> pdb=" O ALA L 131 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N GLU L 136 " --> pdb=" O ARG L 132 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ALA L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 84 removed outlier: 3.726A pdb=" N LEU L 82 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LYS L 84 " --> pdb=" O ASP L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 84' Processing helix chain 'M' and resid 42 through 58 removed outlier: 4.137A pdb=" N ILE M 46 " --> pdb=" O THR M 42 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU M 47 " --> pdb=" O ALA M 43 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 125 removed outlier: 4.357A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA M 120 " --> pdb=" O ALA M 116 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 removed outlier: 4.621A pdb=" N GLN N 18 " --> pdb=" O SER N 14 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA N 19 " --> pdb=" O SER N 15 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N PHE N 21 " --> pdb=" O ARG N 17 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL N 29 " --> pdb=" O ALA N 25 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG N 30 " --> pdb=" O GLY N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 57 removed outlier: 3.686A pdb=" N GLU N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU N 44 " --> pdb=" O LYS N 40 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 3.529A pdb=" N ALA N 55 " --> pdb=" O LEU N 51 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 removed outlier: 4.663A pdb=" N ARG N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE N 67 " --> pdb=" O ARG N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 88 removed outlier: 3.584A pdb=" N ALA N 77 " --> pdb=" O ASN N 73 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix removed outlier: 4.043A pdb=" N ALA N 88 " --> pdb=" O GLY N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 22 removed outlier: 4.572A pdb=" N ARG O 7 " --> pdb=" O LYS O 3 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE O 8 " --> pdb=" O LYS O 4 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG O 16 " --> pdb=" O THR O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 3.771A pdb=" N ALA O 59 " --> pdb=" O GLU O 55 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.823A pdb=" N ALA O 72 " --> pdb=" O LYS O 68 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG O 81 " --> pdb=" O ALA O 77 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLU O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 removed outlier: 4.191A pdb=" N ASP O 108 " --> pdb=" O GLN O 104 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA O 110 " --> pdb=" O LEU O 106 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ARG O 111 " --> pdb=" O ALA O 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 14 removed outlier: 3.844A pdb=" N GLN P 7 " --> pdb=" O ASN P 3 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU P 8 " --> pdb=" O ILE P 4 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLN P 10 " --> pdb=" O LYS P 6 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU P 11 " --> pdb=" O GLN P 7 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N MET P 13 " --> pdb=" O GLU P 9 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYS P 14 " --> pdb=" O GLN P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 5.458A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 104' Processing helix chain 'Q' and resid 6 through 22 removed outlier: 4.013A pdb=" N ALA Q 10 " --> pdb=" O ARG Q 6 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA Q 12 " --> pdb=" O VAL Q 8 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS Q 15 " --> pdb=" O ARG Q 11 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 5.028A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 72 removed outlier: 3.907A pdb=" N ARG Q 48 " --> pdb=" O GLN Q 44 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE Q 62 " --> pdb=" O ARG Q 58 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA Q 63 " --> pdb=" O GLN Q 59 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG Q 64 " --> pdb=" O LEU Q 60 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE Q 65 " --> pdb=" O TRP Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 removed outlier: 3.908A pdb=" N PHE Q 79 " --> pdb=" O SER Q 75 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 102 removed outlier: 3.745A pdb=" N ALA Q 99 " --> pdb=" O LEU Q 95 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE Q 101 " --> pdb=" O ASP Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 118 Processing helix chain 'S' and resid 13 through 25 removed outlier: 4.860A pdb=" N ARG S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA S 21 " --> pdb=" O VAL S 17 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP S 22 " --> pdb=" O ARG S 18 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 40 removed outlier: 4.142A pdb=" N LEU S 33 " --> pdb=" O VAL S 29 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU S 36 " --> pdb=" O ALA S 32 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN S 40 " --> pdb=" O LEU S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 4.710A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE S 55 " --> pdb=" O LEU S 51 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN S 57 " --> pdb=" O SER S 53 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N HIS S 60 " --> pdb=" O ALA S 56 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN S 61 " --> pdb=" O ASN S 57 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 11 removed outlier: 5.023A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 removed outlier: 3.903A pdb=" N THR T 22 " --> pdb=" O GLU T 18 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA T 23 " --> pdb=" O LYS T 19 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER T 27 " --> pdb=" O ALA T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 50 removed outlier: 3.717A pdb=" N LYS T 44 " --> pdb=" O LYS T 40 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.877A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ALA U 71 " --> pdb=" O VAL U 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 66 through 71' Processing helix chain 'V' and resid 14 through 24 removed outlier: 3.677A pdb=" N ARG V 19 " --> pdb=" O GLY V 15 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 52 removed outlier: 3.854A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N MET V 50 " --> pdb=" O LYS V 46 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 59 removed outlier: 4.417A pdb=" N TYR V 57 " --> pdb=" O LYS V 53 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 63 removed outlier: 3.828A pdb=" N MET X 56 " --> pdb=" O SER X 52 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG X 57 " --> pdb=" O ALA X 53 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP X 60 " --> pdb=" O MET X 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 75 removed outlier: 3.631A pdb=" N ALA X 73 " --> pdb=" O ALA X 69 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 9 removed outlier: 4.469A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 35 removed outlier: 4.027A pdb=" N THR Y 16 " --> pdb=" O GLU Y 12 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 41 through 60 removed outlier: 3.549A pdb=" N ARG Y 48 " --> pdb=" O LYS Y 44 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL Y 53 " --> pdb=" O ASP Y 49 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU Y 56 " --> pdb=" O ARG Y 52 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASN Y 58 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU Y 59 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 removed outlier: 4.148A pdb=" N ALA Z 22 " --> pdb=" O PRO Z 18 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR Z 23 " --> pdb=" O LYS Z 19 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU Z 24 " --> pdb=" O HIS Z 20 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU Z 25 " --> pdb=" O LYS Z 21 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY Z 26 " --> pdb=" O ALA Z 22 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 52 removed outlier: 3.587A pdb=" N ARG Z 45 " --> pdb=" O THR Z 41 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA Z 50 " --> pdb=" O GLY Z 46 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL Z 51 " --> pdb=" O MET Z 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 46 removed outlier: 4.359A pdb=" N THR a 45 " --> pdb=" O HIS a 41 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY a 46 " --> pdb=" O PRO a 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 41 through 46' Processing helix chain 'a' and resid 55 through 64 removed outlier: 4.274A pdb=" N ARG a 63 " --> pdb=" O ARG a 59 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE a 64 " --> pdb=" O PHE a 60 " (cutoff:3.500A) Processing helix chain 'a' and resid 47 through 52 removed outlier: 4.486A pdb=" N ASP a 50 " --> pdb=" O LYS a 47 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL a 51 " --> pdb=" O GLN a 48 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ALA a 52 " --> pdb=" O ARG a 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 47 through 52' Processing helix chain 'b' and resid 9 through 19 removed outlier: 5.120A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 removed outlier: 4.019A pdb=" N ARG d 14 " --> pdb=" O LEU d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 17 through 25 removed outlier: 4.341A pdb=" N ALA d 23 " --> pdb=" O ARG d 19 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LYS d 25 " --> pdb=" O ARG d 21 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 38 removed outlier: 4.000A pdb=" N VAL d 30 " --> pdb=" O ASN d 26 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA d 36 " --> pdb=" O ALA d 32 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS d 37 " --> pdb=" O ARG d 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.704A pdb=" N PHE e 14 " --> pdb=" O ALA e 10 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 46 removed outlier: 4.060A pdb=" N LYS e 41 " --> pdb=" O ALA e 37 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU e 44 " --> pdb=" O ARG e 40 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG e 45 " --> pdb=" O LYS e 41 " (cutoff:3.500A) Proline residue: e 46 - end of helix Processing helix chain 'e' and resid 54 through 63 removed outlier: 3.692A pdb=" N VAL e 58 " --> pdb=" O ASP e 54 " (cutoff:3.500A) Proline residue: e 63 - end of helix Processing helix chain 'g' and resid 5 through 13 removed outlier: 4.508A pdb=" N MET g 9 " --> pdb=" O SER g 5 " (cutoff:3.500A) Processing helix chain 'g' and resid 27 through 32 removed outlier: 3.822A pdb=" N ILE g 31 " --> pdb=" O MET g 27 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N PHE g 32 " --> pdb=" O LYS g 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 27 through 32' Processing helix chain 'g' and resid 42 through 64 Proline residue: g 48 - end of helix removed outlier: 4.518A pdb=" N LEU g 54 " --> pdb=" O PHE g 50 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS g 59 " --> pdb=" O ALA g 55 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ALA g 61 " --> pdb=" O LEU g 57 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N SER g 62 " --> pdb=" O ASN g 58 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG g 63 " --> pdb=" O LYS g 59 " (cutoff:3.500A) Processing helix chain 'g' and resid 73 through 88 removed outlier: 6.262A pdb=" N SER g 77 " --> pdb=" O LYS g 73 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLU g 78 " --> pdb=" O ARG g 74 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ALA g 79 " --> pdb=" O ALA g 75 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL g 80 " --> pdb=" O ALA g 76 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LYS g 81 " --> pdb=" O SER g 77 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA g 84 " --> pdb=" O VAL g 80 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU g 85 " --> pdb=" O LYS g 81 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER g 86 " --> pdb=" O ASP g 82 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N CYS g 87 " --> pdb=" O ALA g 83 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 123 removed outlier: 5.673A pdb=" N GLN g 109 " --> pdb=" O LYS g 105 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N SER g 110 " --> pdb=" O THR g 106 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU g 114 " --> pdb=" O SER g 110 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS g 115 " --> pdb=" O ILE g 111 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASP g 116 " --> pdb=" O LYS g 112 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER g 121 " --> pdb=" O LEU g 117 " (cutoff:3.500A) Processing helix chain 'g' and resid 130 through 148 removed outlier: 3.734A pdb=" N ALA g 134 " --> pdb=" O THR g 130 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU g 135 " --> pdb=" O LYS g 131 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN g 146 " --> pdb=" O GLU g 142 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER g 147 " --> pdb=" O LYS g 143 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU g 148 " --> pdb=" O LEU g 144 " (cutoff:3.500A) Processing helix chain 'g' and resid 149 through 155 removed outlier: 7.003A pdb=" N ASP g 153 " --> pdb=" O GLY g 149 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N MET g 154 " --> pdb=" O GLY g 150 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLY g 155 " --> pdb=" O ILE g 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 149 through 155' Processing helix chain 'g' and resid 169 through 180 removed outlier: 3.707A pdb=" N ILE g 173 " --> pdb=" O GLU g 169 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN g 177 " --> pdb=" O ILE g 173 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN g 178 " --> pdb=" O LYS g 174 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU g 179 " --> pdb=" O GLU g 175 " (cutoff:3.500A) Processing helix chain 'g' and resid 206 through 227 removed outlier: 3.660A pdb=" N LEU g 212 " --> pdb=" O ARG g 208 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR g 213 " --> pdb=" O ALA g 209 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA g 216 " --> pdb=" O LEU g 212 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N THR g 220 " --> pdb=" O ALA g 216 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 12 removed outlier: 3.637A pdb=" N ILE h 10 " --> pdb=" O HIS h 6 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARG h 11 " --> pdb=" O PRO h 7 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU h 12 " --> pdb=" O ASN h 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 6 through 12' Processing helix chain 'h' and resid 26 through 48 removed outlier: 4.125A pdb=" N ALA h 30 " --> pdb=" O THR h 26 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ASP h 31 " --> pdb=" O LYS h 27 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU h 33 " --> pdb=" O PHE h 29 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP h 34 " --> pdb=" O ALA h 30 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE h 37 " --> pdb=" O LEU h 33 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL h 39 " --> pdb=" O SER h 35 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR h 42 " --> pdb=" O LYS h 38 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU h 43 " --> pdb=" O VAL h 39 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA h 48 " --> pdb=" O THR h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 78 Processing helix chain 'h' and resid 82 through 96 removed outlier: 4.289A pdb=" N LYS h 89 " --> pdb=" O GLU h 85 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL h 90 " --> pdb=" O LYS h 86 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP h 93 " --> pdb=" O LYS h 89 " (cutoff:3.500A) Processing helix chain 'h' and resid 108 through 113 removed outlier: 4.207A pdb=" N ASP h 112 " --> pdb=" O LYS h 108 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ALA h 113 " --> pdb=" O PRO h 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 108 through 113' Processing helix chain 'h' and resid 114 through 127 removed outlier: 3.570A pdb=" N GLU h 125 " --> pdb=" O THR h 121 " (cutoff:3.500A) Processing helix chain 'h' and resid 129 through 145 removed outlier: 3.728A pdb=" N LYS h 135 " --> pdb=" O ARG h 131 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU h 144 " --> pdb=" O ASN h 140 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY h 145 " --> pdb=" O ALA h 141 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 16 removed outlier: 4.344A pdb=" N LEU i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU i 15 " --> pdb=" O LEU i 11 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 32 removed outlier: 4.142A pdb=" N LYS i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYS i 32 " --> pdb=" O ILE i 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 27 through 32' Processing helix chain 'i' and resid 49 through 66 removed outlier: 3.635A pdb=" N GLN i 54 " --> pdb=" O ASP i 50 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU i 57 " --> pdb=" O VAL i 53 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS i 60 " --> pdb=" O ARG i 56 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL i 61 " --> pdb=" O GLU i 57 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR i 65 " --> pdb=" O VAL i 61 " (cutoff:3.500A) Processing helix chain 'i' and resid 68 through 83 removed outlier: 3.574A pdb=" N ASN i 74 " --> pdb=" O ARG i 70 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA i 79 " --> pdb=" O TYR i 75 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS i 83 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 removed outlier: 4.217A pdb=" N ASN i 89 " --> pdb=" O ASN i 85 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ALA i 92 " --> pdb=" O GLU i 88 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU i 93 " --> pdb=" O ASN i 89 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU i 94 " --> pdb=" O LEU i 90 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU i 95 " --> pdb=" O LEU i 91 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG i 97 " --> pdb=" O LEU i 93 " (cutoff:3.500A) Processing helix chain 'i' and resid 98 through 106 removed outlier: 4.754A pdb=" N TYR i 103 " --> pdb=" O ASP i 99 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET i 105 " --> pdb=" O VAL i 101 " (cutoff:3.500A) Processing helix chain 'i' and resid 110 through 121 removed outlier: 3.753A pdb=" N ALA i 114 " --> pdb=" O THR i 110 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG i 115 " --> pdb=" O ARG i 111 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLN i 116 " --> pdb=" O ALA i 112 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS i 121 " --> pdb=" O LEU i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 146 through 151 removed outlier: 4.621A pdb=" N LYS i 151 " --> pdb=" O GLU i 147 " (cutoff:3.500A) Processing helix chain 'i' and resid 152 through 166 removed outlier: 3.958A pdb=" N LYS i 156 " --> pdb=" O GLN i 152 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA i 158 " --> pdb=" O ARG i 154 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU i 161 " --> pdb=" O ALA i 157 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLN i 164 " --> pdb=" O GLU i 160 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG i 165 " --> pdb=" O LEU i 161 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 4.329A pdb=" N LEU i 191 " --> pdb=" O GLU i 187 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N SER i 192 " --> pdb=" O ARG i 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 187 through 192' Processing helix chain 'i' and resid 197 through 206 removed outlier: 4.411A pdb=" N VAL i 201 " --> pdb=" O GLU i 197 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU i 202 " --> pdb=" O HIS i 198 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU i 203 " --> pdb=" O LEU i 199 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR i 204 " --> pdb=" O ILE i 200 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS i 206 " --> pdb=" O GLU i 202 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 71 removed outlier: 3.581A pdb=" N GLN j 61 " --> pdb=" O PRO j 57 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS j 62 " --> pdb=" O ALA j 58 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG j 69 " --> pdb=" O GLU j 65 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASN j 70 " --> pdb=" O LYS j 66 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N MET j 71 " --> pdb=" O ALA j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 109 through 119 removed outlier: 4.828A pdb=" N ALA j 113 " --> pdb=" O GLY j 109 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL j 114 " --> pdb=" O ALA j 110 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL j 117 " --> pdb=" O ALA j 113 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA j 118 " --> pdb=" O VAL j 114 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 148 removed outlier: 3.771A pdb=" N VAL j 136 " --> pdb=" O ASN j 132 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL j 137 " --> pdb=" O PRO j 133 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG j 138 " --> pdb=" O ILE j 134 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE j 141 " --> pdb=" O VAL j 137 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU j 144 " --> pdb=" O THR j 140 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN j 146 " --> pdb=" O ASP j 142 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET j 147 " --> pdb=" O GLY j 143 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ASN j 148 " --> pdb=" O LEU j 144 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 158 removed outlier: 4.257A pdb=" N ALA j 154 " --> pdb=" O PRO j 150 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA j 155 " --> pdb=" O GLU j 151 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG j 157 " --> pdb=" O VAL j 153 " (cutoff:3.500A) Processing helix chain 'j' and resid 160 through 165 Processing helix chain 'k' and resid 17 through 33 removed outlier: 4.682A pdb=" N ALA k 27 " --> pdb=" O GLU k 23 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA k 28 " --> pdb=" O ARG k 24 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE k 29 " --> pdb=" O TYR k 25 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA k 32 " --> pdb=" O ALA k 28 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 81 removed outlier: 4.001A pdb=" N ILE k 71 " --> pdb=" O PRO k 67 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP k 72 " --> pdb=" O GLN k 68 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU k 75 " --> pdb=" O ILE k 71 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N THR k 76 " --> pdb=" O ASP k 72 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR k 77 " --> pdb=" O GLU k 73 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE k 78 " --> pdb=" O LEU k 74 " (cutoff:3.500A) Processing helix chain 'l' and resid 20 through 32 removed outlier: 4.215A pdb=" N ALA l 24 " --> pdb=" O SER l 20 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LYS l 25 " --> pdb=" O GLU l 21 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE l 26 " --> pdb=" O LEU l 22 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN l 28 " --> pdb=" O ALA l 24 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU l 30 " --> pdb=" O PHE l 26 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N MET l 31 " --> pdb=" O VAL l 27 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL l 32 " --> pdb=" O ASN l 28 " (cutoff:3.500A) Processing helix chain 'l' and resid 35 through 55 removed outlier: 3.836A pdb=" N ALA l 39 " --> pdb=" O LYS l 35 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL l 43 " --> pdb=" O ALA l 39 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR l 44 " --> pdb=" O GLU l 40 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU l 48 " --> pdb=" O TYR l 44 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA l 51 " --> pdb=" O LEU l 47 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY l 55 " --> pdb=" O ALA l 51 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 70 removed outlier: 4.665A pdb=" N PHE l 62 " --> pdb=" O GLU l 58 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU l 63 " --> pdb=" O LEU l 59 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL l 64 " --> pdb=" O GLU l 60 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA l 65 " --> pdb=" O ALA l 61 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ASN l 68 " --> pdb=" O VAL l 64 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL l 69 " --> pdb=" O ALA l 65 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 111 removed outlier: 4.170A pdb=" N ASN l 97 " --> pdb=" O PRO l 93 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG l 102 " --> pdb=" O ALA l 98 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE l 104 " --> pdb=" O ALA l 100 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL l 105 " --> pdb=" O MET l 101 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG l 109 " --> pdb=" O VAL l 105 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LYS l 110 " --> pdb=" O GLU l 106 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG l 111 " --> pdb=" O ALA l 107 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 130 removed outlier: 3.615A pdb=" N GLU l 123 " --> pdb=" O ARG l 119 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA l 127 " --> pdb=" O GLU l 123 " (cutoff:3.500A) Processing helix chain 'l' and resid 132 through 149 removed outlier: 3.718A pdb=" N LYS l 137 " --> pdb=" O THR l 133 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA l 145 " --> pdb=" O VAL l 141 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU l 146 " --> pdb=" O HIS l 142 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN l 148 " --> pdb=" O MET l 144 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 21 removed outlier: 4.453A pdb=" N ASP m 9 " --> pdb=" O ASP m 5 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR m 12 " --> pdb=" O ALA m 8 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA m 20 " --> pdb=" O ASN m 16 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN m 21 " --> pdb=" O GLY m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 30 through 44 removed outlier: 4.275A pdb=" N VAL m 34 " --> pdb=" O SER m 30 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA m 35 " --> pdb=" O LYS m 31 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA m 37 " --> pdb=" O LYS m 33 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL m 39 " --> pdb=" O ALA m 35 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS m 41 " --> pdb=" O ALA m 37 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU m 42 " --> pdb=" O ASN m 38 " (cutoff:3.500A) Processing helix chain 'm' and resid 112 through 120 removed outlier: 4.524A pdb=" N GLN m 118 " --> pdb=" O ARG m 114 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY m 120 " --> pdb=" O ALA m 116 " (cutoff:3.500A) Processing helix chain 'n' and resid 34 through 40 removed outlier: 3.604A pdb=" N TYR n 38 " --> pdb=" O SER n 34 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE n 39 " --> pdb=" O LEU n 35 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N GLY n 40 " --> pdb=" O GLU n 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 34 through 40' Processing helix chain 'n' and resid 41 through 56 removed outlier: 3.730A pdb=" N ARG n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 51 - end of helix removed outlier: 3.673A pdb=" N VAL n 55 " --> pdb=" O PRO n 51 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASP n 56 " --> pdb=" O LEU n 52 " (cutoff:3.500A) Processing helix chain 'n' and resid 71 through 91 removed outlier: 3.913A pdb=" N ALA n 76 " --> pdb=" O ILE n 72 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE n 79 " --> pdb=" O GLN n 75 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N MET n 88 " --> pdb=" O THR n 84 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU n 89 " --> pdb=" O ARG n 85 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR n 90 " --> pdb=" O ALA n 86 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP n 91 " --> pdb=" O LEU n 87 " (cutoff:3.500A) Processing helix chain 'n' and resid 92 through 102 removed outlier: 5.019A pdb=" N SER n 96 " --> pdb=" O GLU n 92 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLU n 97 " --> pdb=" O SER n 93 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 33 removed outlier: 4.668A pdb=" N ASP o 19 " --> pdb=" O HIS o 15 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLN o 20 " --> pdb=" O ARG o 16 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA o 21 " --> pdb=" O LEU o 17 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE o 25 " --> pdb=" O ALA o 21 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR o 28 " --> pdb=" O GLU o 24 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ARG o 31 " --> pdb=" O GLU o 27 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 91 removed outlier: 3.624A pdb=" N VAL o 84 " --> pdb=" O THR o 80 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU o 87 " --> pdb=" O THR o 83 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET o 88 " --> pdb=" O VAL o 84 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU o 90 " --> pdb=" O ALA o 86 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ASP o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 3.981A pdb=" N SER p 50 " --> pdb=" O THR p 46 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY p 51 " --> pdb=" O ALA p 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 46 through 51' Processing helix chain 'p' and resid 59 through 75 removed outlier: 3.560A pdb=" N ALA p 63 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN p 64 " --> pdb=" O PRO p 60 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA p 66 " --> pdb=" O ALA p 62 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLU p 68 " --> pdb=" O GLN p 64 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG p 69 " --> pdb=" O VAL p 65 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA p 71 " --> pdb=" O ALA p 67 " (cutoff:3.500A) Processing helix chain 'p' and resid 92 through 104 removed outlier: 4.110A pdb=" N THR p 96 " --> pdb=" O GLY p 92 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ILE p 97 " --> pdb=" O ARG p 93 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN p 101 " --> pdb=" O ILE p 97 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLY p 104 " --> pdb=" O LEU p 100 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 11 Proline residue: q 11 - end of helix Processing helix chain 'q' and resid 113 through 118 removed outlier: 4.172A pdb=" N TYR q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 22 removed outlier: 3.923A pdb=" N THR r 20 " --> pdb=" O VAL r 16 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER r 21 " --> pdb=" O ILE r 17 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE r 22 " --> pdb=" O ALA r 18 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 38 removed outlier: 4.661A pdb=" N LYS r 31 " --> pdb=" O LYS r 27 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU r 34 " --> pdb=" O SER r 30 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLY r 38 " --> pdb=" O LEU r 34 " (cutoff:3.500A) Processing helix chain 'r' and resid 49 through 63 removed outlier: 4.162A pdb=" N ILE r 53 " --> pdb=" O SER r 49 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP r 58 " --> pdb=" O ASP r 54 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA r 61 " --> pdb=" O ARG r 57 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS r 62 " --> pdb=" O ASP r 58 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 84 removed outlier: 3.665A pdb=" N ARG r 70 " --> pdb=" O GLU r 66 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS r 78 " --> pdb=" O SER r 74 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU r 83 " --> pdb=" O ARG r 79 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLY r 84 " --> pdb=" O LEU r 80 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 94 removed outlier: 3.642A pdb=" N GLY r 94 " --> pdb=" O ARG r 90 " (cutoff:3.500A) Processing helix chain 'r' and resid 106 through 111 Processing helix chain 's' and resid 3 through 22 removed outlier: 4.288A pdb=" N LYS s 7 " --> pdb=" O LYS s 3 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA s 8 " --> pdb=" O GLN s 4 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA s 15 " --> pdb=" O VAL s 11 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU s 16 " --> pdb=" O LYS s 12 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE s 21 " --> pdb=" O ALA s 17 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA s 22 " --> pdb=" O ASP s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 23 through 33 removed outlier: 4.925A pdb=" N LYS s 28 " --> pdb=" O ARG s 24 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA s 29 " --> pdb=" O ALA s 25 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ILE s 30 " --> pdb=" O GLU s 26 " (cutoff:3.500A) Processing helix chain 's' and resid 37 through 52 removed outlier: 4.604A pdb=" N TRP s 42 " --> pdb=" O ASP s 38 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN s 43 " --> pdb=" O GLU s 39 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL s 45 " --> pdb=" O ARG s 41 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU s 46 " --> pdb=" O TRP s 42 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU s 48 " --> pdb=" O ALA s 44 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN s 49 " --> pdb=" O VAL s 45 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) Proline residue: s 52 - end of helix Processing helix chain 's' and resid 80 through 91 removed outlier: 3.641A pdb=" N VAL s 84 " --> pdb=" O SER s 80 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG s 85 " --> pdb=" O ARG s 81 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA s 87 " --> pdb=" O LYS s 83 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG s 90 " --> pdb=" O GLU s 86 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 16 removed outlier: 3.842A pdb=" N LYS t 10 " --> pdb=" O GLU t 6 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE t 11 " --> pdb=" O ALA t 7 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER t 13 " --> pdb=" O ALA t 9 " (cutoff:3.500A) Processing helix chain 't' and resid 24 through 44 removed outlier: 4.354A pdb=" N LEU t 32 " --> pdb=" O GLN t 28 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLN t 35 " --> pdb=" O LEU t 31 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N HIS t 38 " --> pdb=" O ALA t 34 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE t 43 " --> pdb=" O LEU t 39 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA t 44 " --> pdb=" O GLN t 40 " (cutoff:3.500A) Processing helix chain 't' and resid 50 through 74 removed outlier: 5.235A pdb=" N GLY t 55 " --> pdb=" O HIS t 51 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU t 56 " --> pdb=" O SER t 52 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS t 65 " --> pdb=" O SER t 61 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU t 70 " --> pdb=" O LEU t 66 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG t 72 " --> pdb=" O ASP t 68 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 86 removed outlier: 3.919A pdb=" N THR t 79 " --> pdb=" O VAL t 75 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN t 80 " --> pdb=" O ALA t 76 " (cutoff:3.500A) Processing helix chain 'u' and resid 53 through 64 removed outlier: 4.101A pdb=" N ALA u 58 " --> pdb=" O LEU u 54 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL u 61 " --> pdb=" O ILE u 57 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN u 63 " --> pdb=" O HIS u 59 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY u 64 " --> pdb=" O TRP u 60 " (cutoff:3.500A) Processing helix chain 'u' and resid 68 through 81 removed outlier: 3.920A pdb=" N LYS u 80 " --> pdb=" O LYS u 76 " (cutoff:3.500A) Processing helix chain 'w' and resid 11 through 17 removed outlier: 4.941A pdb=" N ALA w 15 " --> pdb=" O CYS w 11 " (cutoff:3.500A) Processing helix chain 'w' and resid 25 through 34 removed outlier: 4.550A pdb=" N LEU w 29 " --> pdb=" O ASP w 25 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASN w 31 " --> pdb=" O ALA w 27 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR w 32 " --> pdb=" O THR w 28 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE w 33 " --> pdb=" O LEU w 29 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N THR w 34 " --> pdb=" O LYS w 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 41 through 46 Processing helix chain 'w' and resid 48 through 66 removed outlier: 5.154A pdb=" N ARG w 53 " --> pdb=" O ALA w 49 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN w 54 " --> pdb=" O LYS w 50 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS w 60 " --> pdb=" O ALA w 56 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA w 62 " --> pdb=" O ALA w 58 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR w 64 " --> pdb=" O LYS w 60 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 26 removed outlier: 4.124A pdb=" N LYS x 18 " --> pdb=" O HIS x 14 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU x 24 " --> pdb=" O GLU x 20 " (cutoff:3.500A) Processing helix chain 'x' and resid 71 through 76 removed outlier: 4.520A pdb=" N ALA x 75 " --> pdb=" O LEU x 71 " (cutoff:3.500A) Proline residue: x 76 - end of helix No H-bonds generated for 'chain 'x' and resid 71 through 76' Processing helix chain 'y' and resid 4 through 42 removed outlier: 4.060A pdb=" N ARG y 10 " --> pdb=" O SER y 6 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER y 14 " --> pdb=" O ARG y 10 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU y 15 " --> pdb=" O ALA y 11 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS y 16 " --> pdb=" O ILE y 12 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ALA y 17 " --> pdb=" O GLN y 13 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N HIS y 20 " --> pdb=" O LYS y 16 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG y 25 " --> pdb=" O ASN y 21 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET y 28 " --> pdb=" O ARG y 24 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL y 35 " --> pdb=" O PHE y 31 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE y 39 " --> pdb=" O VAL y 35 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLU y 40 " --> pdb=" O TYR y 36 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA y 41 " --> pdb=" O ALA y 37 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLY y 42 " --> pdb=" O ALA y 38 " (cutoff:3.500A) Processing helix chain 'y' and resid 44 through 65 removed outlier: 3.881A pdb=" N GLN y 48 " --> pdb=" O LYS y 44 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS y 49 " --> pdb=" O ALA y 45 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA y 50 " --> pdb=" O ALA y 46 " (cutoff:3.500A) Proline residue: y 56 - end of helix removed outlier: 4.748A pdb=" N GLN y 61 " --> pdb=" O ILE y 57 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA y 63 " --> pdb=" O ASP y 59 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY y 65 " --> pdb=" O GLN y 61 " (cutoff:3.500A) Processing helix chain 'y' and resid 68 through 86 removed outlier: 3.821A pdb=" N HIS y 75 " --> pdb=" O LYS y 71 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS y 76 " --> pdb=" O ALA y 72 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA y 77 " --> pdb=" O ALA y 73 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N THR y 80 " --> pdb=" O LYS y 76 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA y 81 " --> pdb=" O ALA y 77 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU y 86 " --> pdb=" O GLN y 82 " (cutoff:3.500A) Processing helix chain 'z' and resid 11 through 27 removed outlier: 4.360A pdb=" N PHE z 19 " --> pdb=" O ALA z 15 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA z 26 " --> pdb=" O SER z 22 " (cutoff:3.500A) Processing helix chain 'z' and resid 28 through 37 removed outlier: 4.017A pdb=" N ARG z 33 " --> pdb=" O LEU z 29 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU z 36 " --> pdb=" O VAL z 32 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE z 37 " --> pdb=" O ARG z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 69 removed outlier: 3.800A pdb=" N ARG z 45 " --> pdb=" O PRO z 41 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ALA z 52 " --> pdb=" O ALA z 48 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS z 54 " --> pdb=" O ALA z 50 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG z 55 " --> pdb=" O SER z 51 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS z 58 " --> pdb=" O LYS z 54 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ARG z 62 " --> pdb=" O LYS z 58 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLU z 63 " --> pdb=" O LYS z 59 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN z 64 " --> pdb=" O LEU z 60 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ARG z 67 " --> pdb=" O GLU z 63 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR z 68 " --> pdb=" O ASN z 64 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG z 69 " --> pdb=" O ALA z 65 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '5' and resid 27 through 33 removed outlier: 3.881A pdb=" N GLU 5 28 " --> pdb=" O VAL 5 129 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE 5 127 " --> pdb=" O PHE 5 30 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '5' and resid 63 through 66 removed outlier: 6.184A pdb=" N ALA 5 63 " --> pdb=" O LEU 5 90 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG 5 88 " --> pdb=" O LEU 5 65 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '5' and resid 115 through 119 removed outlier: 4.323A pdb=" N SER 5 115 " --> pdb=" O LYS 5 126 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS 5 126 " --> pdb=" O SER 5 115 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 33 through 36 removed outlier: 7.030A pdb=" N LEU B 33 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 35 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR B 62 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.789A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU B 93 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ILE B 74 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER B 118 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASP B 114 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 138 through 142 removed outlier: 4.724A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE B 164 " --> pdb=" O SER B 139 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 171 through 176 removed outlier: 3.797A pdb=" N ARG B 182 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 3 through 7 removed outlier: 7.948A pdb=" N ASP C 200 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N THR C 112 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N GLU C 168 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 11 through 16 removed outlier: 3.570A pdb=" N THR C 16 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 186 " --> pdb=" O ASP C 181 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG C 179 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 36 through 39 removed outlier: 3.871A pdb=" N LYS C 38 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA C 47 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N THR C 52 " --> pdb=" O GLY C 78 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY C 78 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ALA C 54 " --> pdb=" O GLY C 76 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLY C 76 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 118 through 121 removed outlier: 4.328A pdb=" N GLY C 163 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N THR C 121 " --> pdb=" O MET C 161 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N MET C 161 " --> pdb=" O THR C 121 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 2 through 6 removed outlier: 4.617A pdb=" N SER D 10 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'D' and resid 117 through 120 removed outlier: 5.812A pdb=" N ARG D 117 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE D 149 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP D 168 " --> pdb=" O VAL D 146 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 86 through 92 removed outlier: 3.755A pdb=" N CYS E 87 " --> pdb=" O MET E 38 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN E 37 " --> pdb=" O ASP E 153 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLY E 39 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLY E 151 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU E 152 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL E 132 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE E 156 " --> pdb=" O TYR E 128 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'F' and resid 16 through 19 Processing sheet with id= 16, first strand: chain 'F' and resid 41 through 45 removed outlier: 3.532A pdb=" N GLY F 53 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS F 44 " --> pdb=" O THR F 51 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 95 through 98 removed outlier: 4.337A pdb=" N ARG F 95 " --> pdb=" O SER F 106 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'F' and resid 121 through 125 removed outlier: 4.070A pdb=" N THR F 122 " --> pdb=" O LYS F 134 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 2 through 5 removed outlier: 5.177A pdb=" N GLN G 2 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA G 39 " --> pdb=" O GLN G 2 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 76 through 82 removed outlier: 5.866A pdb=" N GLU G 76 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL G 147 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL G 142 " --> pdb=" O VAL G 130 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'H' and resid 23 through 26 removed outlier: 7.471A pdb=" N LEU H 23 " --> pdb=" O MET H 86 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N MET H 86 " --> pdb=" O LEU H 23 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ALA H 25 " --> pdb=" O TYR H 84 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'J' and resid 52 through 57 removed outlier: 4.051A pdb=" N TYR J 53 " --> pdb=" O ASP J 14 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'J' and resid 74 through 77 removed outlier: 3.550A pdb=" N ALA J 87 " --> pdb=" O TYR J 74 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS J 76 " --> pdb=" O LYS J 85 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'K' and resid 17 through 21 removed outlier: 5.946A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'K' and resid 68 through 71 removed outlier: 4.875A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'L' and resid 75 through 78 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 75 through 78 current: chain 'L' and resid 108 through 111 No H-bonds generated for sheet with id= 26 Processing sheet with id= 27, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.766A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'M' and resid 62 through 65 removed outlier: 4.277A pdb=" N LYS M 62 " --> pdb=" O ASP M 106 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'N' and resid 33 through 36 removed outlier: 4.171A pdb=" N ALA N 108 " --> pdb=" O ARG N 103 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET N 110 " --> pdb=" O GLY N 101 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLY N 101 " --> pdb=" O MET N 110 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'O' and resid 49 through 52 removed outlier: 4.539A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL O 39 " --> pdb=" O VAL O 49 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N HIS O 34 " --> pdb=" O THR O 31 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR O 31 " --> pdb=" O HIS O 34 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR O 36 " --> pdb=" O HIS O 29 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'P' and resid 38 through 45 removed outlier: 6.691A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER P 83 " --> pdb=" O LYS P 29 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'P' and resid 49 through 53 removed outlier: 4.153A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ARG P 53 " --> pdb=" O HIS P 56 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE P 59 " --> pdb=" O PHE P 74 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'R' and resid 11 through 15 Processing sheet with id= 34, first strand: chain 'R' and resid 19 through 23 removed outlier: 6.521A pdb=" N HIS R 89 " --> pdb=" O LYS R 71 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS R 71 " --> pdb=" O HIS R 89 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N GLN R 91 " --> pdb=" O GLY R 69 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS R 97 " --> pdb=" O VAL R 63 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL R 63 " --> pdb=" O LYS R 97 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR R 99 " --> pdb=" O ALA R 61 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA R 61 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE R 59 " --> pdb=" O PHE R 35 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'R' and resid 57 through 60 removed outlier: 6.426A pdb=" N ALA R 103 " --> pdb=" O GLY R 57 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE R 59 " --> pdb=" O ILE R 101 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE R 101 " --> pdb=" O ILE R 59 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'S' and resid 3 through 8 removed outlier: 3.748A pdb=" N VAL S 107 " --> pdb=" O THR S 3 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'S' and resid 74 through 85 No H-bonds generated for sheet with id= 37 Processing sheet with id= 38, first strand: chain 'T' and resid 28 through 33 removed outlier: 5.812A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'U' and resid 10 through 13 removed outlier: 4.334A pdb=" N LYS U 21 " --> pdb=" O VAL U 13 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'U' and resid 40 through 45 removed outlier: 5.149A pdb=" N ASN U 40 " --> pdb=" O ALA U 63 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'U' and resid 83 through 87 Processing sheet with id= 42, first strand: chain 'V' and resid 2 through 5 removed outlier: 5.084A pdb=" N PHE V 2 " --> pdb=" O VAL V 60 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR V 62 " --> pdb=" O PHE V 2 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'V' and resid 37 through 43 removed outlier: 3.886A pdb=" N ILE V 40 " --> pdb=" O ALA V 28 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE V 26 " --> pdb=" O LEU V 42 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS V 88 " --> pdb=" O GLN V 78 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP V 76 " --> pdb=" O ASP V 90 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'W' and resid 50 through 54 removed outlier: 8.962A pdb=" N ASN W 50 " --> pdb=" O LYS W 62 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'X' and resid 12 through 19 removed outlier: 3.689A pdb=" N VAL X 13 " --> pdb=" O PHE X 29 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY X 15 " --> pdb=" O ARG X 27 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG X 27 " --> pdb=" O GLY X 15 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Z' and resid 6 through 10 removed outlier: 3.913A pdb=" N LYS Z 6 " --> pdb=" O GLU Z 58 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'a' and resid 11 through 15 removed outlier: 3.649A pdb=" N MET a 22 " --> pdb=" O ALA a 14 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'c' and resid 19 through 24 removed outlier: 5.891A pdb=" N HIS c 19 " --> pdb=" O SER c 13 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU c 36 " --> pdb=" O TYR c 49 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'f' and resid 14 through 19 removed outlier: 3.522A pdb=" N ILE f 26 " --> pdb=" O LYS f 15 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ILE f 23 " --> pdb=" O GLN f 37 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN f 37 " --> pdb=" O ILE f 23 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL f 25 " --> pdb=" O GLN f 35 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'g' and resid 15 through 18 removed outlier: 5.844A pdb=" N HIS g 15 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N HIS g 39 " --> pdb=" O GLY g 17 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'g' and resid 89 through 92 Processing sheet with id= 52, first strand: chain 'h' and resid 53 through 59 removed outlier: 3.595A pdb=" N ARG h 54 " --> pdb=" O HIS h 69 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU h 58 " --> pdb=" O ARG h 65 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE h 64 " --> pdb=" O PRO h 98 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN h 100 " --> pdb=" O ILE h 64 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE h 68 " --> pdb=" O ASN h 102 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'h' and resid 164 through 169 removed outlier: 5.934A pdb=" N ARG h 164 " --> pdb=" O GLY h 155 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY h 148 " --> pdb=" O PHE h 203 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY h 194 " --> pdb=" O THR h 191 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA h 189 " --> pdb=" O ILE h 196 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN h 185 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS h 204 " --> pdb=" O ASP h 181 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASP h 181 " --> pdb=" O LYS h 204 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'i' and resid 171 through 175 removed outlier: 3.651A pdb=" N GLU i 179 " --> pdb=" O ASP i 174 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'j' and resid 11 through 16 removed outlier: 6.759A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'j' and resid 84 through 88 removed outlier: 3.674A pdb=" N ARG j 93 " --> pdb=" O TYR j 128 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'j' and resid 32 through 40 removed outlier: 3.721A pdb=" N ALA j 35 " --> pdb=" O GLY j 51 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY j 51 " --> pdb=" O ALA j 35 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'k' and resid 38 through 43 removed outlier: 5.636A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR k 92 " --> pdb=" O HIS k 3 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG k 86 " --> pdb=" O MET k 9 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'k' and resid 44 through 47 removed outlier: 7.808A pdb=" N HIS k 55 " --> pdb=" O LEU k 47 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'l' and resid 73 through 79 removed outlier: 5.894A pdb=" N TYR l 85 " --> pdb=" O ARG l 78 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'm' and resid 23 through 29 removed outlier: 6.429A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL m 25 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU m 60 " --> pdb=" O LYS m 50 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR m 62 " --> pdb=" O ASP m 48 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'm' and resid 74 through 77 removed outlier: 4.668A pdb=" N SER m 74 " --> pdb=" O ALA m 130 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR m 128 " --> pdb=" O GLN m 76 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS m 127 " --> pdb=" O VAL m 103 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'n' and resid 5 through 11 removed outlier: 3.645A pdb=" N VAL n 19 " --> pdb=" O GLY n 8 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY n 10 " --> pdb=" O ALA n 17 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA n 16 " --> pdb=" O LYS n 68 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS n 68 " --> pdb=" O ALA n 16 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'o' and resid 35 through 38 removed outlier: 8.164A pdb=" N GLN o 35 " --> pdb=" O VAL o 77 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ASP o 75 " --> pdb=" O ARG o 37 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ARG o 5 " --> pdb=" O GLY o 103 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG o 9 " --> pdb=" O GLN o 99 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN o 99 " --> pdb=" O ARG o 9 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'o' and resid 42 through 52 removed outlier: 4.346A pdb=" N LEU o 71 " --> pdb=" O PRO o 43 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG o 45 " --> pdb=" O THR o 69 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'p' and resid 29 through 36 removed outlier: 3.577A pdb=" N ASN p 29 " --> pdb=" O SER p 26 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER p 26 " --> pdb=" O ASN p 29 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE p 23 " --> pdb=" O MET p 85 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS p 87 " --> pdb=" O ILE p 23 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN p 109 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLY p 88 " --> pdb=" O VAL p 113 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'q' and resid 29 through 33 removed outlier: 5.397A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N HIS q 96 " --> pdb=" O ARG q 83 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'q' and resid 36 through 41 removed outlier: 3.682A pdb=" N ARG q 36 " --> pdb=" O ARG q 54 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE q 67 " --> pdb=" O LYS q 51 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'u' and resid 4 through 10 removed outlier: 4.364A pdb=" N GLY u 37 " --> pdb=" O VAL u 19 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'v' and resid 7 through 11 removed outlier: 6.984A pdb=" N GLU v 60 " --> pdb=" O VAL v 76 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'v' and resid 20 through 31 No H-bonds generated for sheet with id= 71 Processing sheet with id= 72, first strand: chain 'x' and resid 30 through 33 removed outlier: 3.708A pdb=" N LEU x 47 " --> pdb=" O VAL x 62 " (cutoff:3.500A) 1422 hydrogen bonds defined for protein. 4227 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2057 hydrogen bonds 3332 hydrogen bond angles 0 basepair planarities 807 basepair parallelities 2097 stacking parallelities Total time for adding SS restraints: 222.33 Time building geometry restraints manager: 70.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.65: 169505 1.65 - 2.15: 291 2.15 - 2.65: 0 2.65 - 3.15: 0 3.15 - 3.64: 1 Bond restraints: 169797 Sorted by residual: bond pdb=" P G 1 388 " pdb=" O5' G 1 388 " ideal model delta sigma weight residual 1.593 3.645 -2.052 2.00e-02 2.50e+03 1.05e+04 bond pdb=" N9 A 8 77 " pdb=" C4 A 8 77 " ideal model delta sigma weight residual 1.374 2.058 -0.684 2.00e-02 2.50e+03 1.17e+03 bond pdb=" N9 A 8 77 " pdb=" C8 A 8 77 " ideal model delta sigma weight residual 1.373 2.054 -0.681 2.00e-02 2.50e+03 1.16e+03 bond pdb=" C8 A 8 77 " pdb=" N7 A 8 77 " ideal model delta sigma weight residual 1.311 1.961 -0.650 2.00e-02 2.50e+03 1.06e+03 bond pdb=" N7 A 8 77 " pdb=" C5 A 8 77 " ideal model delta sigma weight residual 1.388 2.025 -0.637 2.00e-02 2.50e+03 1.01e+03 ... (remaining 169792 not shown) Histogram of bond angle deviations from ideal: 62.15 - 81.08: 1 81.08 - 100.01: 95 100.01 - 118.94: 169995 118.94 - 137.87: 84165 137.87 - 156.80: 5 Bond angle restraints: 254261 Sorted by residual: angle pdb=" O3' G 7 72 " pdb=" P C 7 73 " pdb=" OP1 C 7 73 " ideal model delta sigma weight residual 108.00 62.15 45.85 3.00e+00 1.11e-01 2.34e+02 angle pdb=" P G 1 388 " pdb=" O5' G 1 388 " pdb=" C5' G 1 388 " ideal model delta sigma weight residual 120.90 156.80 -35.90 3.00e+00 1.11e-01 1.43e+02 angle pdb=" C1' G7M 12069 " pdb=" N9 G7M 12069 " pdb=" C8 G7M 12069 " ideal model delta sigma weight residual 94.96 128.87 -33.91 3.00e+00 1.11e-01 1.28e+02 angle pdb=" O4' 1MG 1 745 " pdb=" C1' 1MG 1 745 " pdb=" N9 1MG 1 745 " ideal model delta sigma weight residual 108.50 124.55 -16.05 1.50e+00 4.44e-01 1.15e+02 angle pdb=" O3' C 4 48 " pdb=" P C 4 49 " pdb=" O5' C 4 49 " ideal model delta sigma weight residual 104.00 119.23 -15.23 1.50e+00 4.44e-01 1.03e+02 ... (remaining 254256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 94425 35.92 - 71.84: 12781 71.84 - 107.76: 1396 107.76 - 143.69: 52 143.69 - 179.61: 76 Dihedral angle restraints: 108730 sinusoidal: 91276 harmonic: 17454 Sorted by residual: dihedral pdb=" C5* PSU 2 516 " pdb=" C4* PSU 2 516 " pdb=" C3* PSU 2 516 " pdb=" O3* PSU 2 516 " ideal model delta sinusoidal sigma weight residual 82.00 -88.63 170.63 1 8.00e+00 1.56e-02 2.98e+02 dihedral pdb=" C5* PSU 12605 " pdb=" C4* PSU 12605 " pdb=" C3* PSU 12605 " pdb=" O3* PSU 12605 " ideal model delta sinusoidal sigma weight residual 82.00 -86.13 168.13 1 8.00e+00 1.56e-02 2.97e+02 dihedral pdb=" C5* PSU 12504 " pdb=" C4* PSU 12504 " pdb=" C3* PSU 12504 " pdb=" O3* PSU 12504 " ideal model delta sinusoidal sigma weight residual 82.00 -79.84 161.84 1 8.00e+00 1.56e-02 2.93e+02 ... (remaining 108727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.096: 32436 1.096 - 2.193: 3 2.193 - 3.289: 1 3.289 - 4.385: 1 4.385 - 5.481: 30 Chirality restraints: 32471 Sorted by residual: chirality pdb=" C2' 6MZ 12030 " pdb=" C3' 6MZ 12030 " pdb=" O2' 6MZ 12030 " pdb=" C1' 6MZ 12030 " both_signs ideal model delta sigma weight residual False -2.75 2.73 -5.48 2.00e-01 2.50e+01 7.51e+02 chirality pdb=" C2' G7M 12069 " pdb=" C3' G7M 12069 " pdb=" O2' G7M 12069 " pdb=" C1' G7M 12069 " both_signs ideal model delta sigma weight residual False -2.75 2.73 -5.48 2.00e-01 2.50e+01 7.50e+02 chirality pdb=" C3' 6MZ 11618 " pdb=" C4' 6MZ 11618 " pdb=" O3' 6MZ 11618 " pdb=" C2' 6MZ 11618 " both_signs ideal model delta sigma weight residual False -2.74 2.67 -5.42 2.00e-01 2.50e+01 7.33e+02 ... (remaining 32468 not shown) Planarity restraints: 13456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC 12498 " -0.458 2.00e-02 2.50e+03 6.03e-01 8.17e+03 pdb=" C4' OMC 12498 " 0.228 2.00e-02 2.50e+03 pdb=" O4' OMC 12498 " -0.622 2.00e-02 2.50e+03 pdb=" C3' OMC 12498 " 0.775 2.00e-02 2.50e+03 pdb=" O3' OMC 12498 " 0.582 2.00e-02 2.50e+03 pdb=" C2' OMC 12498 " 0.119 2.00e-02 2.50e+03 pdb=" O2' OMC 12498 " -1.029 2.00e-02 2.50e+03 pdb=" C1' OMC 12498 " -0.311 2.00e-02 2.50e+03 pdb=" N1 OMC 12498 " 0.715 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21207 " -0.047 2.00e-02 2.50e+03 6.00e-01 8.09e+03 pdb=" C4' 2MG 21207 " -0.435 2.00e-02 2.50e+03 pdb=" O4' 2MG 21207 " -0.670 2.00e-02 2.50e+03 pdb=" C3' 2MG 21207 " 0.600 2.00e-02 2.50e+03 pdb=" O3' 2MG 21207 " 0.617 2.00e-02 2.50e+03 pdb=" C2' 2MG 21207 " 0.190 2.00e-02 2.50e+03 pdb=" O2' 2MG 21207 " -0.962 2.00e-02 2.50e+03 pdb=" C1' 2MG 21207 " -0.213 2.00e-02 2.50e+03 pdb=" N9 2MG 21207 " 0.921 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 12445 " 0.007 2.00e-02 2.50e+03 5.88e-01 7.78e+03 pdb=" C4' 2MG 12445 " -0.458 2.00e-02 2.50e+03 pdb=" O4' 2MG 12445 " -0.838 2.00e-02 2.50e+03 pdb=" C3' 2MG 12445 " 0.581 2.00e-02 2.50e+03 pdb=" O3' 2MG 12445 " 0.503 2.00e-02 2.50e+03 pdb=" C2' 2MG 12445 " 0.276 2.00e-02 2.50e+03 pdb=" O2' 2MG 12445 " -0.798 2.00e-02 2.50e+03 pdb=" C1' 2MG 12445 " -0.198 2.00e-02 2.50e+03 pdb=" N9 2MG 12445 " 0.925 2.00e-02 2.50e+03 ... (remaining 13453 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 20 2.04 - 2.75: 28112 2.75 - 3.47: 197857 3.47 - 4.18: 457251 4.18 - 4.90: 643614 Nonbonded interactions: 1326854 Sorted by model distance: nonbonded pdb="MG MG 13235 " pdb="MG MG 13252 " model vdw 1.320 1.300 nonbonded pdb="MG MG 13285 " pdb="MG MG 13286 " model vdw 1.956 1.300 nonbonded pdb=" OP1 A 2 174 " pdb="MG MG 21650 " model vdw 1.998 2.170 nonbonded pdb=" O5' U 2 531 " pdb="MG MG 21613 " model vdw 2.005 2.170 nonbonded pdb=" OP2 G 2 588 " pdb="MG MG 21695 " model vdw 2.008 2.170 ... (remaining 1326849 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.510 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: 0.110 Extract box with map and model: 17.830 Check model and map are aligned: 1.720 Set scattering table: 1.180 Process input model: 551.060 Find NCS groups from input model: 3.660 Set up NCS constraints: 0.450 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: 0.040 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 582.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0117 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 : 0.011 2.052 169797 Z= 0.715 Angle : 1.204 45.853 254261 Z= 0.593 Chirality : 0.164 5.481 32471 Planarity : 0.018 0.603 13456 Dihedral : 24.866 179.608 97463 Min Nonbonded Distance : 1.320 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.09 % Favored : 89.79 % Rotamer: Outliers : 0.38 % Allowed : 9.36 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.34 (0.08), residues: 6015 helix: -4.01 (0.07), residues: 1761 sheet: -3.01 (0.14), residues: 1056 loop : -3.51 (0.08), residues: 3198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP h 201 HIS 0.022 0.002 HIS B 53 PHE 0.038 0.003 PHE C 118 TYR 0.040 0.003 TYR k 49 ARG 0.015 0.001 ARG W 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12030 Ramachandran restraints generated. 6015 Oldfield, 0 Emsley, 6015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12030 Ramachandran restraints generated. 6015 Oldfield, 0 Emsley, 6015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 443 time to evaluate : 6.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 134 LYS cc_start: 0.0140 (OUTLIER) cc_final: -0.0683 (pptt) REVERT: 5 143 LYS cc_start: 0.4118 (mttp) cc_final: 0.2445 (tptt) REVERT: B 218 PRO cc_start: 0.2639 (Cg_exo) cc_final: 0.2192 (Cg_endo) REVERT: D 1 MET cc_start: 0.1741 (tpt) cc_final: 0.1392 (tmm) REVERT: D 132 LYS cc_start: -0.1485 (ptpt) cc_final: -0.1982 (ptpp) REVERT: D 170 ARG cc_start: 0.0616 (tpp80) cc_final: 0.0340 (ttm170) REVERT: K 18 ARG cc_start: 0.0243 (tpp80) cc_final: -0.2641 (mtt90) REVERT: L 14 LYS cc_start: -0.1881 (tttt) cc_final: -0.2369 (tttt) REVERT: M 6 ARG cc_start: 0.0734 (ttt-90) cc_final: -0.0119 (mmt180) REVERT: R 92 TRP cc_start: 0.2336 (m-10) cc_final: 0.0663 (m100) REVERT: W 21 LEU cc_start: 0.0182 (mt) cc_final: -0.0830 (mm) REVERT: Y 26 PHE cc_start: 0.5279 (t80) cc_final: 0.4928 (t80) REVERT: d 39 ARG cc_start: 0.1776 (mtt180) cc_final: 0.1155 (mtt180) REVERT: i 70 ARG cc_start: 0.0752 (tpp-160) cc_final: -0.0093 (ttm170) REVERT: k 86 ARG cc_start: 0.4327 (mtt180) cc_final: 0.3955 (mtm-85) REVERT: l 144 MET cc_start: -0.2040 (mmp) cc_final: -0.2590 (ttt) REVERT: m 10 MET cc_start: -0.0025 (ttt) cc_final: -0.0632 (ttt) REVERT: n 88 MET cc_start: 0.0481 (mtm) cc_final: 0.0209 (mtm) REVERT: v 43 LYS cc_start: -0.0863 (mttm) cc_final: -0.1809 (ttpp) outliers start: 19 outliers final: 4 residues processed: 461 average time/residue: 1.6177 time to fit residues: 1245.2918 Evaluate side-chains 277 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 272 time to evaluate : 6.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 134 LYS Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain p residue 113 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1089 random chunks: chunk 919 optimal weight: 5.9990 chunk 825 optimal weight: 20.0000 chunk 458 optimal weight: 9.9990 chunk 281 optimal weight: 30.0000 chunk 556 optimal weight: 10.0000 chunk 440 optimal weight: 0.9980 chunk 853 optimal weight: 5.9990 chunk 330 optimal weight: 20.0000 chunk 519 optimal weight: 0.4980 chunk 635 optimal weight: 6.9990 chunk 988 optimal weight: 5.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 50 ASN B 45 ASN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN B 90 ASN ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 GLN ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN C 150 GLN C 164 GLN F 48 ASN F 104 ASN G 43 ASN G 119 ASN ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN I 30 GLN I 104 GLN I 110 GLN ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN ** L 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 HIS N 81 ASN O 29 HIS O 104 GLN P 10 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN S 60 HIS S 61 ASN T 28 ASN T 91 GLN U 45 HIS ** U 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 5 ASN V 44 HIS V 75 GLN X 20 HIS ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN Y 36 GLN Y 41 HIS a 20 ASN c 46 HIS d 16 HIS ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 28 ASN f 33 HIS ** f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 ASN g 39 HIS g 109 GLN h 140 ASN i 126 ASN i 198 HIS k 14 GLN k 63 ASN l 97 ASN m 21 ASN n 31 ASN n 75 GLN ** n 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 126 GLN o 64 GLN p 15 GLN ** p 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 20 ASN q 112 GLN ** r 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 28 GLN t 40 GLN t 46 HIS ** t 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 HIS ** y 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 70 ASN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1008 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.880 169797 Z= 0.333 Angle : 0.976 42.027 254261 Z= 0.491 Chirality : 0.047 2.049 32471 Planarity : 0.008 0.128 13456 Dihedral : 25.190 179.822 85504 Min Nonbonded Distance : 1.104 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.40 % Favored : 91.52 % Rotamer: Outliers : 2.47 % Allowed : 15.62 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.05 % 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: -4.36 (0.09), residues: 6015 helix: -2.91 (0.10), residues: 1782 sheet: -2.40 (0.15), residues: 1046 loop : -3.10 (0.09), residues: 3187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP h 201 HIS 0.020 0.002 HIS B 15 PHE 0.036 0.002 PHE l 62 TYR 0.031 0.002 TYR i 204 ARG 0.016 0.001 ARG t 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12030 Ramachandran restraints generated. 6015 Oldfield, 0 Emsley, 6015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12030 Ramachandran restraints generated. 6015 Oldfield, 0 Emsley, 6015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 272 time to evaluate : 6.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 155 MET cc_start: -0.0361 (tpt) cc_final: -0.0955 (tpt) REVERT: B 199 GLU cc_start: 0.2742 (OUTLIER) cc_final: 0.1321 (mt-10) REVERT: D 1 MET cc_start: 0.1987 (tpt) cc_final: 0.1553 (tmm) REVERT: D 132 LYS cc_start: -0.1172 (ptpt) cc_final: -0.1818 (ptpp) REVERT: D 170 ARG cc_start: 0.0348 (tpp80) cc_final: -0.3138 (tpm170) REVERT: G 83 LYS cc_start: 0.1253 (OUTLIER) cc_final: 0.0864 (mmmm) REVERT: J 92 MET cc_start: 0.1469 (tpp) cc_final: 0.0765 (tpp) REVERT: M 82 MET cc_start: 0.1026 (mtp) cc_final: 0.0572 (mtp) REVERT: N 4 ARG cc_start: 0.4760 (mmm160) cc_final: 0.4558 (ttm110) REVERT: d 39 ARG cc_start: 0.3004 (mtt180) cc_final: 0.1221 (mtt180) REVERT: k 14 GLN cc_start: 0.2596 (OUTLIER) cc_final: 0.1495 (mp10) REVERT: k 79 ARG cc_start: 0.2234 (OUTLIER) cc_final: -0.1945 (mtp-110) REVERT: l 44 TYR cc_start: -0.0048 (m-80) cc_final: -0.0266 (m-80) REVERT: l 90 GLU cc_start: 0.1595 (OUTLIER) cc_final: 0.1334 (mp0) REVERT: l 102 ARG cc_start: 0.0828 (ttm170) cc_final: 0.0117 (tpt90) REVERT: m 10 MET cc_start: -0.0667 (ttt) cc_final: -0.0927 (ttt) REVERT: n 57 MET cc_start: 0.2257 (ppp) cc_final: 0.1570 (ppp) REVERT: n 59 GLU cc_start: -0.1202 (OUTLIER) cc_final: -0.1829 (mm-30) REVERT: n 61 LEU cc_start: 0.1480 (OUTLIER) cc_final: 0.1252 (pp) REVERT: r 75 MET cc_start: 0.0354 (tpp) cc_final: 0.0141 (tpt) REVERT: r 101 ARG cc_start: 0.1977 (ttp80) cc_final: 0.1358 (tpp80) outliers start: 123 outliers final: 60 residues processed: 381 average time/residue: 1.3659 time to fit residues: 910.4473 Evaluate side-chains 281 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 214 time to evaluate : 5.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 24 TYR Chi-restraints excluded: chain 5 residue 135 GLN Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain G residue 35 LYS Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 21 ARG Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain X residue 78 TYR Chi-restraints excluded: chain Z residue 14 ILE Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain g residue 136 MET Chi-restraints excluded: chain h residue 68 ILE Chi-restraints excluded: chain h residue 77 ILE Chi-restraints excluded: chain h residue 149 ILE Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain k residue 14 GLN Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 63 ASN Chi-restraints excluded: chain k residue 74 LEU Chi-restraints excluded: chain k residue 79 ARG Chi-restraints excluded: chain k residue 88 MET Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 58 GLU Chi-restraints excluded: chain l residue 90 GLU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 59 GLU Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 118 LEU Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 83 ARG Chi-restraints excluded: chain q residue 93 VAL Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 17 ILE Chi-restraints excluded: chain t residue 51 HIS Chi-restraints excluded: chain v residue 83 VAL Chi-restraints excluded: chain x residue 40 ILE Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain z residue 42 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1089 random chunks: chunk 549 optimal weight: 1.9990 chunk 306 optimal weight: 20.0000 chunk 823 optimal weight: 9.9990 chunk 673 optimal weight: 1.9990 chunk 272 optimal weight: 30.0000 chunk 990 optimal weight: 30.0000 chunk 1070 optimal weight: 100.0000 chunk 882 optimal weight: 50.0000 chunk 982 optimal weight: 0.7980 chunk 337 optimal weight: 50.0000 chunk 794 optimal weight: 10.0000 overall best weight: 4.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 22 HIS ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN C 49 GLN C 67 HIS ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 ASN ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 ASN L 35 HIS M 22 GLN N 13 ASN ** O 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 HIS R 87 GLN S 9 HIS ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 66 GLN U 74 ASN W 46 HIS ** X 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 36 HIS ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 HIS c 19 HIS g 18 HIS h 69 HIS h 140 ASN h 185 ASN i 59 GLN ** j 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 68 ASN ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 18 GLN n 5 GLN n 126 GLN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 24 HIS ** p 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 20 ASN q 96 HIS q 112 GLN ** r 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 62 ASN ** t 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 46 HIS t 50 HIS x 57 HIS y 3 ASN y 13 GLN ** y 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1527 moved from start: 0.6989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.919 169797 Z= 0.385 Angle : 1.028 38.803 254261 Z= 0.521 Chirality : 0.050 1.994 32471 Planarity : 0.009 0.129 13456 Dihedral : 25.524 177.889 85499 Min Nonbonded Distance : 0.779 Molprobity Statistics. All-atom Clashscore : 22.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.28 % Favored : 90.66 % Rotamer: Outliers : 4.94 % Allowed : 18.63 % Favored : 76.43 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.09), residues: 6015 helix: -2.62 (0.10), residues: 1777 sheet: -2.14 (0.16), residues: 937 loop : -3.03 (0.09), residues: 3301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.002 TRP B 213 HIS 0.020 0.002 HIS f 33 PHE 0.051 0.003 PHE B 266 TYR 0.044 0.003 TYR y 36 ARG 0.042 0.001 ARG s 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12030 Ramachandran restraints generated. 6015 Oldfield, 0 Emsley, 6015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12030 Ramachandran restraints generated. 6015 Oldfield, 0 Emsley, 6015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 278 time to evaluate : 6.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 21 ARG cc_start: -0.0777 (OUTLIER) cc_final: -0.4764 (ptt90) REVERT: 5 22 HIS cc_start: 0.1039 (OUTLIER) cc_final: -0.0735 (t-170) REVERT: 5 133 LYS cc_start: 0.2224 (OUTLIER) cc_final: 0.1232 (pttp) REVERT: 5 144 GLU cc_start: 0.0521 (OUTLIER) cc_final: -0.0062 (pp20) REVERT: 5 148 GLN cc_start: -0.1524 (OUTLIER) cc_final: -0.3506 (mt0) REVERT: B 46 ASN cc_start: 0.1723 (OUTLIER) cc_final: -0.1903 (t0) REVERT: B 53 HIS cc_start: 0.3012 (OUTLIER) cc_final: 0.0583 (m-70) REVERT: B 194 GLU cc_start: 0.3673 (OUTLIER) cc_final: -0.0551 (tt0) REVERT: B 199 GLU cc_start: 0.3167 (OUTLIER) cc_final: 0.0486 (mp0) REVERT: E 77 PHE cc_start: 0.0933 (OUTLIER) cc_final: 0.0456 (m-80) REVERT: G 83 LYS cc_start: 0.1560 (OUTLIER) cc_final: 0.0808 (mmmt) REVERT: G 93 SER cc_start: 0.8114 (m) cc_final: 0.7774 (t) REVERT: H 84 TYR cc_start: 0.0501 (OUTLIER) cc_final: 0.0180 (m-80) REVERT: J 108 MET cc_start: -0.0511 (OUTLIER) cc_final: -0.1731 (tpt) REVERT: J 114 LEU cc_start: -0.3302 (OUTLIER) cc_final: -0.3551 (tp) REVERT: J 118 MET cc_start: 0.0545 (OUTLIER) cc_final: 0.0072 (mtt) REVERT: K 1 MET cc_start: 0.3747 (tmm) cc_final: 0.2688 (ptm) REVERT: K 20 MET cc_start: 0.3221 (mmt) cc_final: 0.2094 (mmt) REVERT: K 53 LYS cc_start: -0.1067 (OUTLIER) cc_final: -0.2035 (tptp) REVERT: M 82 MET cc_start: 0.1003 (mtp) cc_final: 0.0681 (mtp) REVERT: N 5 LYS cc_start: 0.5774 (OUTLIER) cc_final: 0.5427 (tttt) REVERT: N 110 MET cc_start: 0.1178 (ptp) cc_final: 0.0494 (ptp) REVERT: P 26 VAL cc_start: -0.1507 (OUTLIER) cc_final: -0.1860 (p) REVERT: P 64 ILE cc_start: -0.1029 (OUTLIER) cc_final: -0.1284 (tt) REVERT: P 92 VAL cc_start: -0.1974 (OUTLIER) cc_final: -0.3591 (p) REVERT: R 78 ARG cc_start: 0.1913 (OUTLIER) cc_final: 0.0414 (ttm-80) REVERT: S 82 MET cc_start: -0.1958 (pmm) cc_final: -0.3381 (ptt) REVERT: U 14 LEU cc_start: 0.3961 (OUTLIER) cc_final: 0.3675 (mm) REVERT: X 41 GLU cc_start: -0.0370 (OUTLIER) cc_final: -0.1544 (mp0) REVERT: d 10 LEU cc_start: 0.3072 (OUTLIER) cc_final: 0.2492 (mt) REVERT: d 39 ARG cc_start: 0.3556 (mtt180) cc_final: 0.2287 (mtt180) REVERT: e 5 LYS cc_start: 0.0661 (OUTLIER) cc_final: -0.0030 (mtmm) REVERT: g 18 HIS cc_start: 0.1977 (OUTLIER) cc_final: -0.0058 (m170) REVERT: i 70 ARG cc_start: 0.3669 (tpp-160) cc_final: -0.0154 (mmm-85) REVERT: k 21 MET cc_start: 0.4737 (mmt) cc_final: 0.4006 (tpt) REVERT: k 29 ILE cc_start: -0.0645 (OUTLIER) cc_final: -0.2786 (tp) REVERT: k 49 TYR cc_start: 0.5267 (OUTLIER) cc_final: 0.4923 (p90) REVERT: k 63 ASN cc_start: -0.0395 (OUTLIER) cc_final: -0.2819 (m-40) REVERT: k 69 GLU cc_start: 0.0233 (OUTLIER) cc_final: -0.3869 (pt0) REVERT: k 82 ASP cc_start: -0.0838 (OUTLIER) cc_final: -0.1994 (p0) REVERT: k 102 MET cc_start: 0.1516 (mmm) cc_final: -0.1104 (mtm) REVERT: l 66 LEU cc_start: -0.0602 (OUTLIER) cc_final: -0.0830 (mp) REVERT: l 135 VAL cc_start: 0.1664 (OUTLIER) cc_final: 0.0715 (t) REVERT: l 143 ARG cc_start: 0.3167 (OUTLIER) cc_final: 0.2419 (mtm180) REVERT: n 49 ARG cc_start: 0.2863 (mtp180) cc_final: 0.2513 (tmm160) REVERT: n 57 MET cc_start: 0.2149 (ppp) cc_final: 0.1440 (ppp) REVERT: p 125 LYS cc_start: 0.1780 (OUTLIER) cc_final: 0.0416 (pttt) REVERT: q 82 ILE cc_start: -0.2297 (OUTLIER) cc_final: -0.2962 (tt) REVERT: q 83 ARG cc_start: 0.0044 (OUTLIER) cc_final: -0.1652 (ptt180) REVERT: r 75 MET cc_start: 0.0922 (tpp) cc_final: 0.0562 (tpp) REVERT: r 105 ASN cc_start: 0.0624 (OUTLIER) cc_final: -0.0312 (m-40) REVERT: r 113 ARG cc_start: 0.3021 (tpp-160) cc_final: 0.2652 (ppt170) REVERT: s 74 LEU cc_start: 0.2090 (OUTLIER) cc_final: 0.1679 (mp) REVERT: t 53 ARG cc_start: 0.1603 (OUTLIER) cc_final: -0.3646 (ttm110) REVERT: t 54 ARG cc_start: 0.2409 (OUTLIER) cc_final: -0.1054 (ttp-110) REVERT: t 63 ARG cc_start: 0.0480 (ttp-170) cc_final: 0.0264 (ptt180) REVERT: v 40 ARG cc_start: -0.0488 (mmt180) cc_final: -0.1358 (mtt90) REVERT: w 61 ARG cc_start: 0.3973 (mtt180) cc_final: 0.1790 (mtt90) REVERT: y 29 ARG cc_start: 0.0326 (OUTLIER) cc_final: -0.4255 (mmm-85) REVERT: y 33 LYS cc_start: -0.0006 (OUTLIER) cc_final: -0.1212 (ptmm) REVERT: y 75 HIS cc_start: -0.0968 (OUTLIER) cc_final: -0.5221 (m170) outliers start: 246 outliers final: 111 residues processed: 501 average time/residue: 1.3397 time to fit residues: 1175.1913 Evaluate side-chains 395 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 240 time to evaluate : 6.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 21 ARG Chi-restraints excluded: chain 5 residue 22 HIS Chi-restraints excluded: chain 5 residue 24 TYR Chi-restraints excluded: chain 5 residue 133 LYS Chi-restraints excluded: chain 5 residue 144 GLU Chi-restraints excluded: chain 5 residue 148 GLN Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 84 TYR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain K residue 49 ARG Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 98 TYR Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain X residue 41 GLU Chi-restraints excluded: chain X residue 60 ASP Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Z residue 23 THR Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain c residue 20 PHE Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 10 LEU Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 5 LYS Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain g residue 18 HIS Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 88 ASP Chi-restraints excluded: chain h residue 129 MET Chi-restraints excluded: chain h residue 144 LEU Chi-restraints excluded: chain h residue 149 ILE Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain k residue 29 ILE Chi-restraints excluded: chain k residue 49 TYR Chi-restraints excluded: chain k residue 63 ASN Chi-restraints excluded: chain k residue 69 GLU Chi-restraints excluded: chain k residue 82 ASP Chi-restraints excluded: chain l residue 21 GLU Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 58 GLU Chi-restraints excluded: chain l residue 66 LEU Chi-restraints excluded: chain l residue 83 SER Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain l residue 143 ARG Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain o residue 58 ASN Chi-restraints excluded: chain o residue 60 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain p residue 96 THR Chi-restraints excluded: chain p residue 113 VAL Chi-restraints excluded: chain p residue 125 LYS Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 82 ILE Chi-restraints excluded: chain q residue 83 ARG Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain q residue 90 LEU Chi-restraints excluded: chain q residue 93 VAL Chi-restraints excluded: chain q residue 95 TYR Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 89 LEU Chi-restraints excluded: chain r residue 105 ASN Chi-restraints excluded: chain s residue 74 LEU Chi-restraints excluded: chain t residue 38 HIS Chi-restraints excluded: chain t residue 51 HIS Chi-restraints excluded: chain t residue 53 ARG Chi-restraints excluded: chain t residue 54 ARG Chi-restraints excluded: chain t residue 58 ARG Chi-restraints excluded: chain t residue 65 LYS Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain v residue 21 ILE Chi-restraints excluded: chain v residue 34 TYR Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain x residue 41 PHE Chi-restraints excluded: chain x residue 52 HIS Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain y residue 14 SER Chi-restraints excluded: chain y residue 29 ARG Chi-restraints excluded: chain y residue 33 LYS Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain y residue 75 HIS Chi-restraints excluded: chain z residue 42 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1089 random chunks: chunk 978 optimal weight: 0.0970 chunk 744 optimal weight: 9.9990 chunk 514 optimal weight: 50.0000 chunk 109 optimal weight: 40.0000 chunk 472 optimal weight: 30.0000 chunk 665 optimal weight: 8.9990 chunk 994 optimal weight: 8.9990 chunk 1052 optimal weight: 20.0000 chunk 519 optimal weight: 0.4980 chunk 942 optimal weight: 0.9980 chunk 283 optimal weight: 50.0000 overall best weight: 3.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 94 GLN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 HIS ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 ASN ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS L 104 GLN ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 ASN O 98 GLN P 41 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 HIS R 87 GLN T 28 ASN ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 99 ASN ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 26 HIS j 132 ASN k 63 ASN l 148 ASN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 64 GLN ** p 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 20 ASN r 105 ASN ** t 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 61 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1619 moved from start: 0.8182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.899 169797 Z= 0.319 Angle : 0.844 39.490 254261 Z= 0.435 Chirality : 0.043 1.972 32471 Planarity : 0.007 0.126 13456 Dihedral : 25.389 179.587 85498 Min Nonbonded Distance : 0.839 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.23 % Favored : 91.74 % Rotamer: Outliers : 4.58 % Allowed : 21.42 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.09), residues: 6015 helix: -2.21 (0.11), residues: 1770 sheet: -2.05 (0.16), residues: 977 loop : -2.94 (0.09), residues: 3268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 213 HIS 0.024 0.002 HIS 5 22 PHE 0.034 0.002 PHE x 74 TYR 0.049 0.002 TYR Q 32 ARG 0.019 0.001 ARG 5 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12030 Ramachandran restraints generated. 6015 Oldfield, 0 Emsley, 6015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12030 Ramachandran restraints generated. 6015 Oldfield, 0 Emsley, 6015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 263 time to evaluate : 6.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 22 HIS cc_start: 0.0365 (OUTLIER) cc_final: -0.2028 (t-170) REVERT: 5 133 LYS cc_start: 0.1862 (OUTLIER) cc_final: 0.0860 (pttp) REVERT: 5 144 GLU cc_start: 0.0606 (OUTLIER) cc_final: 0.0304 (pp20) REVERT: 5 155 MET cc_start: -0.1301 (tpt) cc_final: -0.1544 (tpt) REVERT: B 110 LEU cc_start: 0.4703 (tp) cc_final: 0.4443 (tp) REVERT: B 180 GLU cc_start: 0.4282 (OUTLIER) cc_final: 0.3193 (tt0) REVERT: B 194 GLU cc_start: 0.3924 (OUTLIER) cc_final: -0.0172 (tt0) REVERT: B 195 VAL cc_start: 0.5919 (OUTLIER) cc_final: 0.5668 (m) REVERT: B 199 GLU cc_start: 0.3484 (OUTLIER) cc_final: 0.0921 (mp0) REVERT: C 139 SER cc_start: 0.3908 (OUTLIER) cc_final: 0.3465 (m) REVERT: D 121 VAL cc_start: 0.0842 (p) cc_final: 0.0582 (p) REVERT: E 52 ASN cc_start: 0.1578 (m-40) cc_final: 0.1361 (m-40) REVERT: G 57 LYS cc_start: 0.2373 (tmmt) cc_final: 0.1330 (ptpp) REVERT: G 83 LYS cc_start: 0.2168 (OUTLIER) cc_final: 0.1425 (mmmt) REVERT: H 84 TYR cc_start: 0.0635 (OUTLIER) cc_final: -0.0728 (m-80) REVERT: J 118 MET cc_start: 0.0615 (OUTLIER) cc_final: 0.0328 (mtt) REVERT: L 47 ARG cc_start: 0.1001 (OUTLIER) cc_final: -0.1165 (pmt-80) REVERT: L 109 LYS cc_start: 0.3151 (mtmt) cc_final: 0.0426 (mttt) REVERT: M 82 MET cc_start: 0.1014 (mtp) cc_final: 0.0438 (mtp) REVERT: R 40 MET cc_start: 0.1040 (ppp) cc_final: 0.0651 (ppp) REVERT: R 78 ARG cc_start: 0.1446 (OUTLIER) cc_final: 0.0357 (ttm-80) REVERT: S 82 MET cc_start: -0.2299 (pmm) cc_final: -0.4613 (ptt) REVERT: S 99 ARG cc_start: 0.2761 (OUTLIER) cc_final: 0.2450 (mtt180) REVERT: T 27 SER cc_start: 0.2392 (OUTLIER) cc_final: 0.2076 (t) REVERT: a 30 HIS cc_start: -0.0338 (OUTLIER) cc_final: -0.2150 (p-80) REVERT: c 46 HIS cc_start: -0.2090 (OUTLIER) cc_final: -0.2812 (p-80) REVERT: d 1 MET cc_start: 0.1553 (ptp) cc_final: 0.0546 (ptp) REVERT: d 39 ARG cc_start: 0.3519 (mtt180) cc_final: 0.2568 (mtt180) REVERT: e 41 LYS cc_start: -0.2994 (OUTLIER) cc_final: -0.3380 (ttpp) REVERT: g 18 HIS cc_start: 0.2496 (OUTLIER) cc_final: 0.0943 (m170) REVERT: h 184 TYR cc_start: 0.3513 (OUTLIER) cc_final: 0.2953 (t80) REVERT: k 21 MET cc_start: 0.4754 (mmt) cc_final: 0.4409 (tpt) REVERT: k 29 ILE cc_start: -0.0941 (OUTLIER) cc_final: -0.2804 (tp) REVERT: k 75 GLU cc_start: -0.0916 (OUTLIER) cc_final: -0.5215 (tp30) REVERT: k 79 ARG cc_start: 0.1108 (OUTLIER) cc_final: -0.2735 (mmm160) REVERT: k 102 MET cc_start: 0.1892 (mmm) cc_final: 0.1116 (mmp) REVERT: l 66 LEU cc_start: -0.0593 (OUTLIER) cc_final: -0.0841 (mp) REVERT: l 148 ASN cc_start: 0.3285 (OUTLIER) cc_final: 0.0913 (t0) REVERT: n 45 ARG cc_start: -0.0296 (OUTLIER) cc_final: -0.2838 (mmm-85) REVERT: n 57 MET cc_start: 0.1880 (ppp) cc_final: 0.1215 (ppp) REVERT: n 59 GLU cc_start: -0.0913 (OUTLIER) cc_final: -0.1376 (mm-30) REVERT: p 125 LYS cc_start: 0.1576 (OUTLIER) cc_final: 0.0568 (pttt) REVERT: q 15 LYS cc_start: -0.1330 (OUTLIER) cc_final: -0.2969 (mtpt) REVERT: q 83 ARG cc_start: 0.0141 (OUTLIER) cc_final: -0.0743 (ptt180) REVERT: r 93 ARG cc_start: 0.3291 (mmp-170) cc_final: 0.0961 (tpt90) REVERT: r 113 ARG cc_start: 0.3760 (tpp-160) cc_final: 0.2815 (ppt170) REVERT: s 81 ARG cc_start: 0.3388 (OUTLIER) cc_final: 0.1807 (ttm-80) REVERT: t 61 SER cc_start: 0.6321 (t) cc_final: 0.5957 (p) REVERT: v 38 ILE cc_start: -0.2585 (OUTLIER) cc_final: -0.3931 (tp) REVERT: v 40 ARG cc_start: 0.0693 (mmt180) cc_final: -0.0473 (tpp80) REVERT: w 18 VAL cc_start: -0.3732 (OUTLIER) cc_final: -0.4403 (m) REVERT: w 67 LEU cc_start: 0.4238 (mt) cc_final: 0.3983 (mp) REVERT: y 33 LYS cc_start: -0.0140 (OUTLIER) cc_final: -0.1574 (ptmm) REVERT: y 34 LYS cc_start: 0.1271 (mttt) cc_final: 0.0950 (ttpp) REVERT: y 55 GLN cc_start: 0.2011 (OUTLIER) cc_final: 0.1750 (mt0) REVERT: y 75 HIS cc_start: -0.1023 (OUTLIER) cc_final: -0.4798 (m-70) outliers start: 228 outliers final: 107 residues processed: 463 average time/residue: 1.3899 time to fit residues: 1108.4647 Evaluate side-chains 381 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 238 time to evaluate : 6.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 22 HIS Chi-restraints excluded: chain 5 residue 24 TYR Chi-restraints excluded: chain 5 residue 26 ILE Chi-restraints excluded: chain 5 residue 78 THR Chi-restraints excluded: chain 5 residue 133 LYS Chi-restraints excluded: chain 5 residue 135 GLN Chi-restraints excluded: chain 5 residue 144 GLU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 84 TYR Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 49 ARG Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain P residue 98 TYR Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain R residue 5 PHE Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 99 ARG Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 25 VAL Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain a residue 30 HIS Chi-restraints excluded: chain a residue 44 PHE Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain c residue 46 HIS Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 41 LYS Chi-restraints excluded: chain g residue 18 HIS Chi-restraints excluded: chain g residue 88 ASP Chi-restraints excluded: chain h residue 144 LEU Chi-restraints excluded: chain h residue 149 ILE Chi-restraints excluded: chain h residue 184 TYR Chi-restraints excluded: chain i residue 200 ILE Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain k residue 29 ILE Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 63 ASN Chi-restraints excluded: chain k residue 75 GLU Chi-restraints excluded: chain k residue 79 ARG Chi-restraints excluded: chain k residue 92 THR Chi-restraints excluded: chain l residue 4 ARG Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain l residue 58 GLU Chi-restraints excluded: chain l residue 66 LEU Chi-restraints excluded: chain l residue 120 LEU Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain l residue 148 ASN Chi-restraints excluded: chain n residue 13 LYS Chi-restraints excluded: chain n residue 39 PHE Chi-restraints excluded: chain n residue 45 ARG Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 59 GLU Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 72 ILE Chi-restraints excluded: chain n residue 123 ARG Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain p residue 27 PHE Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 125 LYS Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain q residue 15 LYS Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 83 ARG Chi-restraints excluded: chain q residue 90 LEU Chi-restraints excluded: chain q residue 93 VAL Chi-restraints excluded: chain q residue 95 TYR Chi-restraints excluded: chain r residue 17 ILE Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 110 LYS Chi-restraints excluded: chain s residue 81 ARG Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 27 VAL Chi-restraints excluded: chain t residue 38 HIS Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain t residue 49 ASP Chi-restraints excluded: chain t residue 51 HIS Chi-restraints excluded: chain t residue 65 LYS Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 68 SER Chi-restraints excluded: chain w residue 18 VAL Chi-restraints excluded: chain x residue 20 GLU Chi-restraints excluded: chain x residue 52 HIS Chi-restraints excluded: chain y residue 14 SER Chi-restraints excluded: chain y residue 33 LYS Chi-restraints excluded: chain y residue 55 GLN Chi-restraints excluded: chain y residue 75 HIS Chi-restraints excluded: chain z residue 42 THR Chi-restraints excluded: chain z residue 63 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1089 random chunks: chunk 876 optimal weight: 40.0000 chunk 597 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 chunk 783 optimal weight: 30.0000 chunk 434 optimal weight: 8.9990 chunk 898 optimal weight: 10.0000 chunk 727 optimal weight: 0.7980 chunk 1 optimal weight: 20.0000 chunk 537 optimal weight: 4.9990 chunk 944 optimal weight: 8.9990 chunk 265 optimal weight: 90.0000 overall best weight: 6.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 22 HIS B 15 HIS ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN H 88 HIS I 29 GLN ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 HIS ** O 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 75 GLN Q 37 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN T 15 HIS T 28 ASN ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 75 GLN X 20 HIS ** X 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN ** d 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 140 ASN ** i 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 16 ASN n 5 GLN n 126 GLN o 58 ASN o 64 GLN p 24 HIS ** p 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 56 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2056 moved from start: 1.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.903 169797 Z= 0.425 Angle : 1.199 38.937 254261 Z= 0.602 Chirality : 0.057 1.918 32471 Planarity : 0.009 0.125 13456 Dihedral : 26.255 179.223 85497 Min Nonbonded Distance : 0.628 Molprobity Statistics. All-atom Clashscore : 29.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.69 % Favored : 88.18 % Rotamer: Outliers : 6.93 % Allowed : 21.44 % Favored : 71.63 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.09), residues: 6015 helix: -2.32 (0.11), residues: 1736 sheet: -1.83 (0.16), residues: 896 loop : -3.12 (0.09), residues: 3383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 60 HIS 0.022 0.003 HIS 5 22 PHE 0.044 0.003 PHE B 266 TYR 0.058 0.004 TYR y 36 ARG 0.028 0.001 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12030 Ramachandran restraints generated. 6015 Oldfield, 0 Emsley, 6015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12030 Ramachandran restraints generated. 6015 Oldfield, 0 Emsley, 6015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 345 poor density : 262 time to evaluate : 6.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 22 HIS cc_start: 0.0379 (OUTLIER) cc_final: 0.0070 (t-170) REVERT: 5 28 GLU cc_start: 0.0018 (OUTLIER) cc_final: -0.2234 (mm-30) REVERT: 5 144 GLU cc_start: 0.0713 (OUTLIER) cc_final: 0.0302 (pp20) REVERT: 5 148 GLN cc_start: -0.0718 (OUTLIER) cc_final: -0.2488 (mm110) REVERT: B 7 LYS cc_start: 0.1593 (tptm) cc_final: -0.0323 (mmtt) REVERT: B 46 ASN cc_start: 0.2301 (OUTLIER) cc_final: -0.1428 (t0) REVERT: B 128 ASN cc_start: 0.2700 (OUTLIER) cc_final: 0.2062 (m-40) REVERT: B 171 TYR cc_start: -0.1693 (OUTLIER) cc_final: -0.3413 (m-80) REVERT: B 194 GLU cc_start: 0.3689 (OUTLIER) cc_final: -0.0473 (tt0) REVERT: B 199 GLU cc_start: 0.2800 (OUTLIER) cc_final: 0.1374 (pm20) REVERT: B 201 MET cc_start: 0.0204 (mtm) cc_final: -0.1296 (mmp) REVERT: B 268 VAL cc_start: -0.0713 (OUTLIER) cc_final: -0.1863 (m) REVERT: E 77 PHE cc_start: 0.1233 (OUTLIER) cc_final: 0.0636 (m-80) REVERT: E 94 GLU cc_start: 0.2698 (OUTLIER) cc_final: 0.2428 (pm20) REVERT: E 115 ARG cc_start: 0.3737 (OUTLIER) cc_final: 0.3254 (mtm180) REVERT: E 130 MET cc_start: 0.0185 (OUTLIER) cc_final: -0.0971 (mmm) REVERT: E 141 ILE cc_start: 0.2348 (OUTLIER) cc_final: 0.2072 (tt) REVERT: G 98 ASP cc_start: 0.1429 (OUTLIER) cc_final: 0.0906 (t0) REVERT: G 143 ILE cc_start: 0.1364 (OUTLIER) cc_final: 0.0856 (tp) REVERT: H 117 LEU cc_start: 0.3134 (OUTLIER) cc_final: 0.2910 (mp) REVERT: K 1 MET cc_start: 0.4030 (tmm) cc_final: 0.2769 (ptp) REVERT: K 53 LYS cc_start: -0.1301 (OUTLIER) cc_final: -0.1555 (tptp) REVERT: L 21 ARG cc_start: 0.4670 (OUTLIER) cc_final: 0.3321 (ttm-80) REVERT: L 47 ARG cc_start: 0.1743 (OUTLIER) cc_final: 0.1196 (ptm-80) REVERT: L 109 LYS cc_start: 0.3286 (mtmt) cc_final: 0.1129 (mtmm) REVERT: M 82 MET cc_start: 0.1017 (mtp) cc_final: 0.0452 (mtp) REVERT: N 11 ASN cc_start: 0.1426 (OUTLIER) cc_final: 0.1163 (m-40) REVERT: N 20 MET cc_start: 0.2728 (ttp) cc_final: 0.0937 (mmp) REVERT: P 92 VAL cc_start: -0.1225 (OUTLIER) cc_final: -0.2614 (p) REVERT: Q 22 LYS cc_start: 0.3708 (OUTLIER) cc_final: 0.3120 (pttt) REVERT: R 40 MET cc_start: 0.1458 (ppp) cc_final: 0.0941 (pmm) REVERT: R 78 ARG cc_start: 0.2716 (OUTLIER) cc_final: -0.0260 (mtm180) REVERT: S 99 ARG cc_start: 0.3431 (OUTLIER) cc_final: 0.3114 (mtt180) REVERT: U 14 LEU cc_start: 0.5041 (OUTLIER) cc_final: 0.4734 (mm) REVERT: U 41 LEU cc_start: 0.5066 (OUTLIER) cc_final: 0.4784 (pp) REVERT: U 45 HIS cc_start: 0.0967 (OUTLIER) cc_final: -0.0114 (m-70) REVERT: U 82 ARG cc_start: -0.0093 (OUTLIER) cc_final: -0.2534 (mmt180) REVERT: W 17 GLU cc_start: 0.0689 (OUTLIER) cc_final: -0.0022 (pm20) REVERT: W 83 GLU cc_start: 0.1374 (OUTLIER) cc_final: 0.0734 (pm20) REVERT: Z 47 MET cc_start: 0.0996 (tpt) cc_final: 0.0542 (ttt) REVERT: a 30 HIS cc_start: 0.0140 (OUTLIER) cc_final: -0.1426 (p90) REVERT: b 19 HIS cc_start: 0.2534 (OUTLIER) cc_final: 0.1567 (t-90) REVERT: d 3 ARG cc_start: 0.5150 (OUTLIER) cc_final: 0.4081 (tpp-160) REVERT: e 19 LYS cc_start: 0.5065 (mtpt) cc_final: 0.3703 (pttm) REVERT: g 18 HIS cc_start: 0.2671 (OUTLIER) cc_final: 0.2081 (m-70) REVERT: h 110 GLU cc_start: 0.3173 (OUTLIER) cc_final: 0.0790 (mp0) REVERT: h 144 LEU cc_start: 0.1893 (OUTLIER) cc_final: 0.1148 (mm) REVERT: h 166 GLU cc_start: 0.5764 (OUTLIER) cc_final: 0.3199 (mm-30) REVERT: h 184 TYR cc_start: 0.4215 (OUTLIER) cc_final: 0.3200 (t80) REVERT: k 49 TYR cc_start: 0.5265 (OUTLIER) cc_final: 0.4903 (p90) REVERT: k 75 GLU cc_start: -0.1359 (OUTLIER) cc_final: -0.6279 (tm-30) REVERT: k 82 ASP cc_start: -0.0102 (OUTLIER) cc_final: -0.1238 (p0) REVERT: l 85 TYR cc_start: 0.1245 (OUTLIER) cc_final: -0.2263 (m-10) REVERT: l 94 VAL cc_start: 0.1537 (t) cc_final: 0.0637 (m) REVERT: l 140 ASP cc_start: -0.0119 (OUTLIER) cc_final: -0.0737 (m-30) REVERT: l 144 MET cc_start: -0.0966 (mmp) cc_final: -0.4542 (mmm) REVERT: n 39 PHE cc_start: 0.1418 (OUTLIER) cc_final: -0.2574 (p90) REVERT: n 57 MET cc_start: 0.1605 (ppp) cc_final: 0.1136 (ppp) REVERT: n 123 ARG cc_start: 0.0928 (OUTLIER) cc_final: 0.0256 (tmt-80) REVERT: o 60 ASP cc_start: 0.6593 (OUTLIER) cc_final: 0.4868 (t0) REVERT: o 88 MET cc_start: 0.0169 (tpt) cc_final: -0.0230 (mmm) REVERT: p 125 LYS cc_start: 0.2079 (OUTLIER) cc_final: 0.0986 (pttt) REVERT: q 83 ARG cc_start: -0.0669 (OUTLIER) cc_final: -0.1969 (ttt90) REVERT: r 93 ARG cc_start: 0.4031 (mmp-170) cc_final: 0.1685 (tpt90) REVERT: r 113 ARG cc_start: 0.4141 (tpp-160) cc_final: 0.3398 (ppt170) REVERT: s 81 ARG cc_start: 0.3731 (OUTLIER) cc_final: 0.2718 (ttm-80) REVERT: s 89 MET cc_start: 0.3070 (OUTLIER) cc_final: 0.1763 (ttp) REVERT: s 98 LYS cc_start: -0.0274 (tttt) cc_final: -0.0532 (mmtm) REVERT: t 53 ARG cc_start: 0.1354 (OUTLIER) cc_final: -0.2542 (ttt180) REVERT: t 54 ARG cc_start: 0.3144 (OUTLIER) cc_final: 0.0036 (ttp-170) REVERT: v 39 LYS cc_start: 0.0159 (OUTLIER) cc_final: -0.0958 (mtpt) REVERT: v 40 ARG cc_start: 0.1615 (mmt180) cc_final: 0.0403 (tpp80) REVERT: v 83 VAL cc_start: 0.3837 (OUTLIER) cc_final: 0.2384 (p) REVERT: w 35 GLU cc_start: 0.0618 (OUTLIER) cc_final: -0.0467 (mt-10) REVERT: w 48 ARG cc_start: 0.2025 (ttt-90) cc_final: 0.1644 (ttm170) REVERT: w 67 LEU cc_start: 0.4557 (mt) cc_final: 0.4338 (mp) REVERT: x 20 GLU cc_start: 0.1834 (OUTLIER) cc_final: 0.1414 (pp20) REVERT: x 40 ILE cc_start: 0.2467 (OUTLIER) cc_final: 0.2231 (mp) REVERT: y 31 PHE cc_start: 0.4390 (OUTLIER) cc_final: 0.3376 (t80) REVERT: y 33 LYS cc_start: 0.0003 (OUTLIER) cc_final: -0.1682 (ttpt) REVERT: y 75 HIS cc_start: -0.0583 (OUTLIER) cc_final: -0.3898 (m170) REVERT: y 83 ILE cc_start: 0.1911 (OUTLIER) cc_final: 0.1590 (mt) REVERT: z 5 LYS cc_start: 0.3228 (mtmm) cc_final: 0.1656 (ttpt) outliers start: 345 outliers final: 175 residues processed: 574 average time/residue: 1.4995 time to fit residues: 1496.4865 Evaluate side-chains 472 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 234 time to evaluate : 6.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 22 HIS Chi-restraints excluded: chain 5 residue 26 ILE Chi-restraints excluded: chain 5 residue 28 GLU Chi-restraints excluded: chain 5 residue 144 GLU Chi-restraints excluded: chain 5 residue 148 GLN Chi-restraints excluded: chain B residue 15 HIS Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain D residue 60 TRP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain G residue 35 LYS Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 123 ARG Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 49 ARG Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 21 ARG Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 88 ARG Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 22 LYS Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 99 ARG Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 15 HIS Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 25 VAL Chi-restraints excluded: chain U residue 41 LEU Chi-restraints excluded: chain U residue 45 HIS Chi-restraints excluded: chain U residue 82 ARG Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 83 GLU Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 60 ASP Chi-restraints excluded: chain X residue 78 TYR Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain a residue 30 HIS Chi-restraints excluded: chain a residue 32 LEU Chi-restraints excluded: chain a residue 53 THR Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 19 HIS Chi-restraints excluded: chain b residue 42 HIS Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 20 PHE Chi-restraints excluded: chain c residue 46 HIS Chi-restraints excluded: chain c residue 49 TYR Chi-restraints excluded: chain d residue 3 ARG Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain e residue 28 ASN Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain g residue 18 HIS Chi-restraints excluded: chain h residue 110 GLU Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 132 ARG Chi-restraints excluded: chain h residue 144 LEU Chi-restraints excluded: chain h residue 149 ILE Chi-restraints excluded: chain h residue 166 GLU Chi-restraints excluded: chain h residue 172 ARG Chi-restraints excluded: chain h residue 184 TYR Chi-restraints excluded: chain i residue 200 ILE Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 29 ILE Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 49 TYR Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 74 LEU Chi-restraints excluded: chain k residue 75 GLU Chi-restraints excluded: chain k residue 82 ASP Chi-restraints excluded: chain k residue 88 MET Chi-restraints excluded: chain k residue 92 THR Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain l residue 21 GLU Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain l residue 30 LEU Chi-restraints excluded: chain l residue 41 SER Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 56 LYS Chi-restraints excluded: chain l residue 58 GLU Chi-restraints excluded: chain l residue 85 TYR Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain l residue 120 LEU Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain l residue 140 ASP Chi-restraints excluded: chain m residue 27 MET Chi-restraints excluded: chain n residue 39 PHE Chi-restraints excluded: chain n residue 45 ARG Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 59 GLU Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 68 LYS Chi-restraints excluded: chain n residue 72 ILE Chi-restraints excluded: chain n residue 123 ARG Chi-restraints excluded: chain o residue 5 ARG Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain o residue 59 LYS Chi-restraints excluded: chain o residue 60 ASP Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain p residue 13 ARG Chi-restraints excluded: chain p residue 74 VAL Chi-restraints excluded: chain p residue 83 GLU Chi-restraints excluded: chain p residue 125 LYS Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 27 CYS Chi-restraints excluded: chain q residue 29 GLN Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 81 LEU Chi-restraints excluded: chain q residue 83 ARG Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain q residue 93 VAL Chi-restraints excluded: chain q residue 95 TYR Chi-restraints excluded: chain q residue 97 THR Chi-restraints excluded: chain r residue 17 ILE Chi-restraints excluded: chain r residue 33 ILE Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain r residue 110 LYS Chi-restraints excluded: chain s residue 81 ARG Chi-restraints excluded: chain s residue 89 MET Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 17 ARG Chi-restraints excluded: chain t residue 27 VAL Chi-restraints excluded: chain t residue 29 VAL Chi-restraints excluded: chain t residue 31 LEU Chi-restraints excluded: chain t residue 38 HIS Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain t residue 53 ARG Chi-restraints excluded: chain t residue 54 ARG Chi-restraints excluded: chain t residue 65 LYS Chi-restraints excluded: chain t residue 67 LEU Chi-restraints excluded: chain t residue 87 LEU Chi-restraints excluded: chain t residue 89 ARG Chi-restraints excluded: chain v residue 21 ILE Chi-restraints excluded: chain v residue 29 VAL Chi-restraints excluded: chain v residue 34 TYR Chi-restraints excluded: chain v residue 39 LYS Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 68 SER Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain v residue 83 VAL Chi-restraints excluded: chain w residue 35 GLU Chi-restraints excluded: chain w residue 68 LEU Chi-restraints excluded: chain x residue 20 GLU Chi-restraints excluded: chain x residue 40 ILE Chi-restraints excluded: chain x residue 52 HIS Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain y residue 14 SER Chi-restraints excluded: chain y residue 31 PHE Chi-restraints excluded: chain y residue 33 LYS Chi-restraints excluded: chain y residue 36 TYR Chi-restraints excluded: chain y residue 55 GLN Chi-restraints excluded: chain y residue 75 HIS Chi-restraints excluded: chain y residue 83 ILE Chi-restraints excluded: chain z residue 42 THR Chi-restraints excluded: chain z residue 63 GLU Chi-restraints excluded: chain z residue 67 ARG Chi-restraints excluded: chain z residue 69 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1089 random chunks: chunk 354 optimal weight: 60.0000 chunk 947 optimal weight: 8.9990 chunk 208 optimal weight: 9.9990 chunk 618 optimal weight: 7.9990 chunk 259 optimal weight: 8.9990 chunk 1053 optimal weight: 50.0000 chunk 874 optimal weight: 10.0000 chunk 487 optimal weight: 50.0000 chunk 87 optimal weight: 50.0000 chunk 348 optimal weight: 9.9990 chunk 553 optimal weight: 20.0000 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 148 GLN ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN B 90 ASN ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 ASN ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 69 ASN ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 30 HIS ** a 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 26 HIS ** e 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 122 ASN l 68 ASN ** p 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 26 ASN ** y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2298 moved from start: 1.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.896 169797 Z= 0.503 Angle : 1.349 40.347 254261 Z= 0.665 Chirality : 0.063 1.902 32471 Planarity : 0.010 0.139 13456 Dihedral : 26.741 179.826 85496 Min Nonbonded Distance : 0.862 Molprobity Statistics. All-atom Clashscore : 32.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.47 % Favored : 87.41 % Rotamer: Outliers : 7.27 % Allowed : 22.55 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 2.49 % Twisted General : 0.70 % 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: -4.09 (0.09), residues: 6015 helix: -2.42 (0.11), residues: 1677 sheet: -1.91 (0.17), residues: 855 loop : -3.21 (0.09), residues: 3483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP D 60 HIS 0.069 0.004 HIS B 15 PHE 0.047 0.003 PHE R 35 TYR 0.070 0.004 TYR w 64 ARG 0.029 0.002 ARG l 138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12030 Ramachandran restraints generated. 6015 Oldfield, 0 Emsley, 6015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12030 Ramachandran restraints generated. 6015 Oldfield, 0 Emsley, 6015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 362 poor density : 261 time to evaluate : 6.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 28 GLU cc_start: 0.0723 (OUTLIER) cc_final: -0.1449 (mm-30) REVERT: 5 144 GLU cc_start: 0.0724 (OUTLIER) cc_final: 0.0263 (pp20) REVERT: B 7 LYS cc_start: 0.1583 (tptm) cc_final: -0.0713 (mmtt) REVERT: B 36 LYS cc_start: 0.3792 (OUTLIER) cc_final: 0.3506 (ptpp) REVERT: B 46 ASN cc_start: 0.2566 (OUTLIER) cc_final: -0.1032 (t0) REVERT: B 128 ASN cc_start: 0.2984 (OUTLIER) cc_final: 0.2509 (m-40) REVERT: B 171 TYR cc_start: -0.1798 (OUTLIER) cc_final: -0.3309 (m-80) REVERT: B 182 ARG cc_start: 0.5874 (OUTLIER) cc_final: 0.5510 (ttt180) REVERT: B 199 GLU cc_start: 0.3450 (OUTLIER) cc_final: 0.2477 (pm20) REVERT: B 201 MET cc_start: -0.0221 (mtm) cc_final: -0.0470 (mmt) REVERT: B 205 LEU cc_start: 0.3803 (OUTLIER) cc_final: 0.3514 (tp) REVERT: B 239 ASN cc_start: 0.3736 (OUTLIER) cc_final: 0.1920 (t0) REVERT: D 88 ARG cc_start: 0.3841 (OUTLIER) cc_final: 0.3119 (ttm110) REVERT: E 77 PHE cc_start: 0.1280 (OUTLIER) cc_final: 0.0545 (m-10) REVERT: E 130 MET cc_start: 0.0200 (OUTLIER) cc_final: -0.1828 (mmm) REVERT: G 1 MET cc_start: -0.0422 (tpt) cc_final: -0.1729 (tpp) REVERT: G 101 ASP cc_start: 0.7401 (m-30) cc_final: 0.7127 (m-30) REVERT: G 143 ILE cc_start: 0.0550 (OUTLIER) cc_final: -0.0326 (tp) REVERT: J 118 MET cc_start: 0.2222 (mmt) cc_final: 0.1322 (mmt) REVERT: K 1 MET cc_start: 0.4816 (tmm) cc_final: 0.3970 (ptp) REVERT: K 49 ARG cc_start: 0.5123 (OUTLIER) cc_final: 0.2067 (mtm110) REVERT: K 53 LYS cc_start: -0.0869 (OUTLIER) cc_final: -0.2924 (tppt) REVERT: K 78 ARG cc_start: 0.6193 (mtm-85) cc_final: 0.4978 (mtm-85) REVERT: L 21 ARG cc_start: 0.4579 (OUTLIER) cc_final: 0.3239 (ttm-80) REVERT: L 47 ARG cc_start: 0.1933 (OUTLIER) cc_final: -0.0924 (pmt-80) REVERT: L 78 ARG cc_start: 0.4276 (ttp-110) cc_final: 0.3927 (ptt-90) REVERT: L 109 LYS cc_start: 0.3932 (mtmt) cc_final: 0.1198 (tptp) REVERT: L 143 GLU cc_start: 0.0927 (OUTLIER) cc_final: 0.0660 (pm20) REVERT: M 82 MET cc_start: 0.0758 (mtp) cc_final: 0.0272 (mtp) REVERT: M 112 LEU cc_start: -0.2107 (OUTLIER) cc_final: -0.2473 (mt) REVERT: N 11 ASN cc_start: 0.1847 (OUTLIER) cc_final: 0.1170 (m-40) REVERT: N 20 MET cc_start: 0.2496 (ttp) cc_final: 0.0672 (mmp) REVERT: P 92 VAL cc_start: 0.0009 (OUTLIER) cc_final: -0.0259 (t) REVERT: Q 22 LYS cc_start: 0.4075 (OUTLIER) cc_final: 0.3208 (pttt) REVERT: Q 48 ARG cc_start: 0.0903 (OUTLIER) cc_final: 0.0061 (ttp-110) REVERT: R 40 MET cc_start: 0.1611 (ppp) cc_final: 0.0831 (ppp) REVERT: R 78 ARG cc_start: 0.3150 (OUTLIER) cc_final: -0.0620 (mtm-85) REVERT: R 92 TRP cc_start: 0.3240 (OUTLIER) cc_final: 0.2177 (m-10) REVERT: S 95 ARG cc_start: 0.3179 (OUTLIER) cc_final: 0.2838 (ttm170) REVERT: S 99 ARG cc_start: 0.3887 (OUTLIER) cc_final: 0.3048 (mtt180) REVERT: U 14 LEU cc_start: 0.5120 (OUTLIER) cc_final: 0.4555 (mm) REVERT: W 17 GLU cc_start: 0.1867 (OUTLIER) cc_final: -0.0921 (mm-30) REVERT: X 78 TYR cc_start: 0.1852 (OUTLIER) cc_final: -0.0089 (t80) REVERT: Y 5 GLU cc_start: 0.4337 (OUTLIER) cc_final: 0.4031 (mt-10) REVERT: a 30 HIS cc_start: 0.1327 (OUTLIER) cc_final: -0.2020 (m90) REVERT: b 19 HIS cc_start: 0.2325 (OUTLIER) cc_final: 0.1725 (t-90) REVERT: c 49 TYR cc_start: 0.0051 (OUTLIER) cc_final: -0.0510 (t80) REVERT: d 22 MET cc_start: -0.3335 (ttp) cc_final: -0.3683 (tmm) REVERT: d 39 ARG cc_start: 0.3802 (mtt180) cc_final: 0.0806 (tmt-80) REVERT: e 19 LYS cc_start: 0.5425 (mtpt) cc_final: 0.3919 (pttp) REVERT: g 16 PHE cc_start: -0.1695 (OUTLIER) cc_final: -0.3401 (m-80) REVERT: g 23 TRP cc_start: 0.0572 (OUTLIER) cc_final: 0.0336 (p-90) REVERT: g 188 ASP cc_start: 0.3441 (OUTLIER) cc_final: 0.3137 (t70) REVERT: h 144 LEU cc_start: 0.2542 (OUTLIER) cc_final: 0.2246 (mm) REVERT: h 166 GLU cc_start: 0.5902 (OUTLIER) cc_final: 0.3591 (mm-30) REVERT: i 206 LYS cc_start: 0.5922 (mttt) cc_final: 0.5220 (mttt) REVERT: j 96 MET cc_start: 0.0432 (tpp) cc_final: -0.0276 (mpp) REVERT: k 49 TYR cc_start: 0.4865 (OUTLIER) cc_final: 0.4192 (p90) REVERT: k 69 GLU cc_start: -0.0444 (OUTLIER) cc_final: -0.3748 (tp30) REVERT: k 75 GLU cc_start: -0.0778 (OUTLIER) cc_final: -0.6158 (tm-30) REVERT: k 82 ASP cc_start: 0.0704 (OUTLIER) cc_final: -0.1441 (t0) REVERT: l 4 ARG cc_start: 0.4010 (OUTLIER) cc_final: 0.3788 (ptm160) REVERT: l 47 LEU cc_start: 0.1502 (OUTLIER) cc_final: -0.1010 (mp) REVERT: l 62 PHE cc_start: 0.3627 (OUTLIER) cc_final: 0.2410 (t80) REVERT: l 78 ARG cc_start: 0.6235 (mmt90) cc_final: 0.5977 (ttt90) REVERT: l 85 TYR cc_start: 0.3076 (OUTLIER) cc_final: -0.0119 (m-10) REVERT: l 140 ASP cc_start: -0.1522 (OUTLIER) cc_final: -0.2639 (m-30) REVERT: l 143 ARG cc_start: 0.1654 (OUTLIER) cc_final: 0.0002 (ttt90) REVERT: n 39 PHE cc_start: 0.1310 (OUTLIER) cc_final: -0.2678 (p90) REVERT: n 45 ARG cc_start: 0.0105 (OUTLIER) cc_final: -0.3848 (tmt170) REVERT: n 57 MET cc_start: 0.1140 (ppp) cc_final: 0.0831 (ppp) REVERT: n 59 GLU cc_start: 0.1603 (OUTLIER) cc_final: 0.0660 (mm-30) REVERT: n 119 ARG cc_start: 0.6959 (ttp-170) cc_final: 0.5849 (mtp180) REVERT: n 123 ARG cc_start: 0.1686 (OUTLIER) cc_final: 0.0535 (tmt-80) REVERT: p 125 LYS cc_start: 0.2336 (OUTLIER) cc_final: 0.0748 (ptmt) REVERT: q 14 ARG cc_start: 0.3020 (OUTLIER) cc_final: 0.2008 (mmt-90) REVERT: q 29 GLN cc_start: 0.5598 (OUTLIER) cc_final: 0.4297 (mt0) REVERT: q 83 ARG cc_start: -0.0374 (OUTLIER) cc_final: -0.1003 (tmm-80) REVERT: r 100 GLN cc_start: 0.0757 (OUTLIER) cc_final: -0.0322 (pt0) REVERT: r 103 LYS cc_start: 0.2358 (OUTLIER) cc_final: -0.0376 (mtpt) REVERT: r 113 ARG cc_start: 0.3787 (tpp-160) cc_final: 0.3538 (ppt170) REVERT: s 55 SER cc_start: 0.6401 (OUTLIER) cc_final: 0.5768 (t) REVERT: s 85 ARG cc_start: 0.6272 (tmt170) cc_final: 0.4525 (tmm-80) REVERT: v 17 MET cc_start: 0.0911 (ptp) cc_final: 0.0099 (ptp) REVERT: v 28 PHE cc_start: 0.5238 (OUTLIER) cc_final: 0.5013 (m-80) REVERT: v 39 LYS cc_start: 0.0176 (OUTLIER) cc_final: -0.0706 (mtpt) REVERT: v 40 ARG cc_start: 0.4342 (mmt180) cc_final: 0.1759 (mmm-85) REVERT: v 83 VAL cc_start: 0.2626 (OUTLIER) cc_final: 0.1467 (p) REVERT: w 67 LEU cc_start: 0.4661 (mt) cc_final: 0.4250 (mp) REVERT: y 33 LYS cc_start: 0.0158 (OUTLIER) cc_final: -0.1049 (tttm) REVERT: y 75 HIS cc_start: -0.0392 (OUTLIER) cc_final: -0.3512 (m170) REVERT: y 82 GLN cc_start: -0.1543 (OUTLIER) cc_final: -0.2825 (tt0) REVERT: z 5 LYS cc_start: 0.3148 (mtmm) cc_final: 0.1793 (ttpt) REVERT: z 54 LYS cc_start: -0.1084 (OUTLIER) cc_final: -0.2587 (tttp) REVERT: z 67 ARG cc_start: 0.4083 (OUTLIER) cc_final: 0.3350 (ttm110) outliers start: 362 outliers final: 182 residues processed: 594 average time/residue: 1.4787 time to fit residues: 1512.9607 Evaluate side-chains 491 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 240 time to evaluate : 6.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 18 LYS Chi-restraints excluded: chain 5 residue 24 TYR Chi-restraints excluded: chain 5 residue 26 ILE Chi-restraints excluded: chain 5 residue 28 GLU Chi-restraints excluded: chain 5 residue 144 GLU Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain D residue 60 TRP Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 123 ARG Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 49 ARG Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 79 PHE Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 21 ARG Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 22 LYS Chi-restraints excluded: chain Q residue 48 ARG Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain R residue 92 TRP Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 95 ARG Chi-restraints excluded: chain S residue 99 ARG Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 25 VAL Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain X residue 60 ASP Chi-restraints excluded: chain X residue 78 TYR Chi-restraints excluded: chain Y residue 5 GLU Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain a residue 28 VAL Chi-restraints excluded: chain a residue 30 HIS Chi-restraints excluded: chain a residue 32 LEU Chi-restraints excluded: chain a residue 53 THR Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 19 HIS Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 20 PHE Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 46 HIS Chi-restraints excluded: chain c residue 49 TYR Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain e residue 4 ILE Chi-restraints excluded: chain e residue 28 ASN Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain g residue 16 PHE Chi-restraints excluded: chain g residue 23 TRP Chi-restraints excluded: chain g residue 188 ASP Chi-restraints excluded: chain h residue 77 ILE Chi-restraints excluded: chain h residue 144 LEU Chi-restraints excluded: chain h residue 166 GLU Chi-restraints excluded: chain h residue 172 ARG Chi-restraints excluded: chain h residue 184 TYR Chi-restraints excluded: chain i residue 53 VAL Chi-restraints excluded: chain i residue 200 ILE Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 29 ILE Chi-restraints excluded: chain k residue 49 TYR Chi-restraints excluded: chain k residue 50 PRO Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 69 GLU Chi-restraints excluded: chain k residue 75 GLU Chi-restraints excluded: chain k residue 82 ASP Chi-restraints excluded: chain k residue 88 MET Chi-restraints excluded: chain k residue 91 ARG Chi-restraints excluded: chain k residue 92 THR Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 4 ARG Chi-restraints excluded: chain l residue 21 GLU Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain l residue 25 LYS Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 58 GLU Chi-restraints excluded: chain l residue 62 PHE Chi-restraints excluded: chain l residue 85 TYR Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain l residue 120 LEU Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain l residue 140 ASP Chi-restraints excluded: chain l residue 143 ARG Chi-restraints excluded: chain m residue 72 VAL Chi-restraints excluded: chain n residue 39 PHE Chi-restraints excluded: chain n residue 45 ARG Chi-restraints excluded: chain n residue 46 MET Chi-restraints excluded: chain n residue 59 GLU Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 72 ILE Chi-restraints excluded: chain n residue 104 VAL Chi-restraints excluded: chain n residue 123 ARG Chi-restraints excluded: chain n residue 129 LYS Chi-restraints excluded: chain o residue 10 LEU Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain o residue 59 LYS Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain p residue 13 ARG Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 77 TYR Chi-restraints excluded: chain p residue 83 GLU Chi-restraints excluded: chain p residue 112 ASP Chi-restraints excluded: chain p residue 125 LYS Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain q residue 27 CYS Chi-restraints excluded: chain q residue 29 GLN Chi-restraints excluded: chain q residue 46 ASN Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 83 ARG Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain q residue 93 VAL Chi-restraints excluded: chain q residue 97 THR Chi-restraints excluded: chain r residue 17 ILE Chi-restraints excluded: chain r residue 33 ILE Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 100 GLN Chi-restraints excluded: chain r residue 103 LYS Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain r residue 110 LYS Chi-restraints excluded: chain s residue 6 MET Chi-restraints excluded: chain s residue 18 ASP Chi-restraints excluded: chain s residue 55 SER Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 17 ARG Chi-restraints excluded: chain t residue 27 VAL Chi-restraints excluded: chain t residue 31 LEU Chi-restraints excluded: chain t residue 42 HIS Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain t residue 49 ASP Chi-restraints excluded: chain t residue 51 HIS Chi-restraints excluded: chain t residue 65 LYS Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain t residue 89 ARG Chi-restraints excluded: chain v residue 28 PHE Chi-restraints excluded: chain v residue 29 VAL Chi-restraints excluded: chain v residue 34 TYR Chi-restraints excluded: chain v residue 39 LYS Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 68 SER Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain v residue 83 VAL Chi-restraints excluded: chain w residue 39 ILE Chi-restraints excluded: chain w residue 47 THR Chi-restraints excluded: chain w residue 68 LEU Chi-restraints excluded: chain x residue 52 HIS Chi-restraints excluded: chain y residue 14 SER Chi-restraints excluded: chain y residue 25 ARG Chi-restraints excluded: chain y residue 33 LYS Chi-restraints excluded: chain y residue 55 GLN Chi-restraints excluded: chain y residue 66 LEU Chi-restraints excluded: chain y residue 75 HIS Chi-restraints excluded: chain y residue 82 GLN Chi-restraints excluded: chain z residue 42 THR Chi-restraints excluded: chain z residue 54 LYS Chi-restraints excluded: chain z residue 55 ARG Chi-restraints excluded: chain z residue 63 GLU Chi-restraints excluded: chain z residue 67 ARG Chi-restraints excluded: chain z residue 69 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1089 random chunks: chunk 1015 optimal weight: 2.9990 chunk 118 optimal weight: 20.0000 chunk 600 optimal weight: 0.9980 chunk 769 optimal weight: 7.9990 chunk 596 optimal weight: 10.0000 chunk 886 optimal weight: 3.9990 chunk 588 optimal weight: 1.9990 chunk 1049 optimal weight: 30.0000 chunk 656 optimal weight: 1.9990 chunk 639 optimal weight: 0.9990 chunk 484 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN B 90 ASN ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 135 HIS L 35 HIS ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 GLN R 12 HIS R 86 GLN a 30 HIS ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 16 ASN ** p 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 6 GLN q 20 ASN ** q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 96 HIS ** t 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 26 ASN y 82 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1933 moved from start: 1.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.902 169797 Z= 0.276 Angle : 0.793 38.885 254261 Z= 0.412 Chirality : 0.042 1.968 32471 Planarity : 0.007 0.119 13456 Dihedral : 25.956 179.997 85496 Min Nonbonded Distance : 1.060 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.21 % Favored : 91.77 % Rotamer: Outliers : 4.00 % Allowed : 25.48 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.10), residues: 6015 helix: -1.79 (0.12), residues: 1723 sheet: -1.73 (0.17), residues: 899 loop : -2.86 (0.09), residues: 3393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 60 HIS 0.020 0.002 HIS a 30 PHE 0.033 0.001 PHE M 117 TYR 0.023 0.002 TYR X 78 ARG 0.010 0.001 ARG Z 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12030 Ramachandran restraints generated. 6015 Oldfield, 0 Emsley, 6015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12030 Ramachandran restraints generated. 6015 Oldfield, 0 Emsley, 6015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 257 time to evaluate : 6.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 28 GLU cc_start: 0.0468 (OUTLIER) cc_final: -0.1709 (mm-30) REVERT: 5 73 MET cc_start: 0.1313 (ptt) cc_final: 0.1067 (ptt) REVERT: 5 144 GLU cc_start: 0.0705 (OUTLIER) cc_final: -0.3021 (tp30) REVERT: 5 155 MET cc_start: 0.1184 (tpt) cc_final: 0.0698 (ttt) REVERT: B 7 LYS cc_start: -0.0152 (tptm) cc_final: -0.1903 (mmtt) REVERT: B 46 ASN cc_start: 0.1267 (OUTLIER) cc_final: -0.0813 (m-40) REVERT: B 171 TYR cc_start: -0.1291 (OUTLIER) cc_final: -0.2456 (m-80) REVERT: B 180 GLU cc_start: 0.4865 (tt0) cc_final: 0.4234 (tt0) REVERT: B 182 ARG cc_start: 0.5219 (OUTLIER) cc_final: 0.4359 (ttt180) REVERT: B 239 ASN cc_start: 0.4636 (OUTLIER) cc_final: 0.2592 (m110) REVERT: C 139 SER cc_start: 0.3530 (OUTLIER) cc_final: 0.3238 (m) REVERT: E 130 MET cc_start: 0.0248 (OUTLIER) cc_final: -0.1427 (mmm) REVERT: E 148 ARG cc_start: -0.0205 (OUTLIER) cc_final: -0.1131 (mtp-110) REVERT: G 1 MET cc_start: -0.1151 (tpt) cc_final: -0.1862 (tpt) REVERT: G 25 TYR cc_start: 0.0026 (OUTLIER) cc_final: -0.0261 (p90) REVERT: G 143 ILE cc_start: 0.0435 (OUTLIER) cc_final: -0.0262 (tt) REVERT: J 92 MET cc_start: -0.0168 (tpp) cc_final: -0.1015 (tpp) REVERT: J 118 MET cc_start: 0.2182 (mmt) cc_final: 0.1399 (mmt) REVERT: K 53 LYS cc_start: -0.1425 (OUTLIER) cc_final: -0.3072 (tmtt) REVERT: L 70 LYS cc_start: 0.6094 (mttm) cc_final: 0.5323 (mtmt) REVERT: L 109 LYS cc_start: 0.3431 (mtmt) cc_final: 0.0645 (mttt) REVERT: L 112 LEU cc_start: 0.0461 (OUTLIER) cc_final: 0.0223 (mp) REVERT: M 82 MET cc_start: 0.0615 (mtp) cc_final: 0.0038 (mtp) REVERT: M 110 GLU cc_start: 0.2086 (tm-30) cc_final: 0.0642 (pm20) REVERT: M 112 LEU cc_start: -0.2658 (OUTLIER) cc_final: -0.3222 (mt) REVERT: N 11 ASN cc_start: 0.1092 (OUTLIER) cc_final: 0.0789 (m-40) REVERT: N 20 MET cc_start: 0.2317 (ttp) cc_final: 0.0650 (mmp) REVERT: Q 22 LYS cc_start: 0.3913 (pttt) cc_final: 0.3318 (pttt) REVERT: R 70 GLU cc_start: -0.0287 (OUTLIER) cc_final: -0.0614 (tp30) REVERT: R 78 ARG cc_start: 0.1778 (OUTLIER) cc_final: -0.0429 (mtp-110) REVERT: R 92 TRP cc_start: 0.3093 (OUTLIER) cc_final: 0.1997 (m-10) REVERT: U 14 LEU cc_start: 0.5114 (OUTLIER) cc_final: 0.4727 (mm) REVERT: Z 47 MET cc_start: 0.1862 (tpp) cc_final: 0.0145 (ttt) REVERT: a 30 HIS cc_start: 0.1311 (OUTLIER) cc_final: -0.0495 (p-80) REVERT: b 19 HIS cc_start: 0.2464 (OUTLIER) cc_final: 0.2120 (t-90) REVERT: d 39 ARG cc_start: 0.3272 (mtt180) cc_final: 0.0535 (tmt-80) REVERT: e 47 LYS cc_start: 0.6147 (ttmt) cc_final: 0.5934 (mptt) REVERT: h 149 ILE cc_start: 0.0352 (OUTLIER) cc_final: -0.0369 (mt) REVERT: h 166 GLU cc_start: 0.5261 (OUTLIER) cc_final: 0.3333 (mm-30) REVERT: h 184 TYR cc_start: 0.4216 (OUTLIER) cc_final: 0.3637 (t80) REVERT: j 93 ARG cc_start: 0.2739 (OUTLIER) cc_final: 0.2069 (mtm-85) REVERT: l 85 TYR cc_start: 0.1701 (OUTLIER) cc_final: -0.1508 (m-10) REVERT: l 144 MET cc_start: -0.0793 (mmt) cc_final: -0.4185 (ptt) REVERT: l 151 PHE cc_start: 0.1323 (m-80) cc_final: 0.0610 (t80) REVERT: n 59 GLU cc_start: -0.0469 (OUTLIER) cc_final: -0.0939 (mm-30) REVERT: n 116 VAL cc_start: 0.0354 (OUTLIER) cc_final: -0.0856 (p) REVERT: n 123 ARG cc_start: 0.0251 (OUTLIER) cc_final: -0.0031 (ttt90) REVERT: o 59 LYS cc_start: 0.6076 (OUTLIER) cc_final: 0.5848 (mmmt) REVERT: o 60 ASP cc_start: 0.6113 (m-30) cc_final: 0.5475 (t70) REVERT: p 125 LYS cc_start: 0.0907 (OUTLIER) cc_final: 0.0583 (pttt) REVERT: q 9 ARG cc_start: 0.1303 (OUTLIER) cc_final: 0.0230 (ptm-80) REVERT: q 83 ARG cc_start: -0.1234 (OUTLIER) cc_final: -0.1622 (ptm160) REVERT: r 93 ARG cc_start: 0.3962 (mmp-170) cc_final: 0.0895 (mmm160) REVERT: r 113 ARG cc_start: 0.3871 (tpp-160) cc_final: 0.3511 (ppt170) REVERT: s 85 ARG cc_start: 0.5375 (tmt170) cc_final: 0.3748 (tmm-80) REVERT: s 98 LYS cc_start: 0.1538 (OUTLIER) cc_final: 0.1195 (mmtm) REVERT: t 53 ARG cc_start: 0.0482 (OUTLIER) cc_final: -0.4925 (ttp80) REVERT: v 40 ARG cc_start: 0.3835 (mmt180) cc_final: 0.1592 (tpp80) REVERT: x 20 GLU cc_start: 0.2092 (OUTLIER) cc_final: 0.1521 (pp20) REVERT: x 83 HIS cc_start: 0.1853 (p-80) cc_final: 0.0291 (p-80) REVERT: y 33 LYS cc_start: 0.1435 (OUTLIER) cc_final: 0.1182 (ptmm) REVERT: y 75 HIS cc_start: -0.0950 (OUTLIER) cc_final: -0.5139 (m170) REVERT: z 5 LYS cc_start: 0.2812 (mtmm) cc_final: 0.1734 (mttt) outliers start: 199 outliers final: 116 residues processed: 438 average time/residue: 1.4521 time to fit residues: 1105.9209 Evaluate side-chains 388 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 234 time to evaluate : 6.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 18 LYS Chi-restraints excluded: chain 5 residue 24 TYR Chi-restraints excluded: chain 5 residue 26 ILE Chi-restraints excluded: chain 5 residue 28 GLU Chi-restraints excluded: chain 5 residue 53 ASP Chi-restraints excluded: chain 5 residue 144 GLU Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain D residue 60 TRP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 25 TYR Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 123 ARG Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 135 HIS Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain K residue 49 ARG Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain P residue 88 ARG Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 92 TRP Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 45 HIS Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain X residue 78 TYR Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain a residue 30 HIS Chi-restraints excluded: chain a residue 32 LEU Chi-restraints excluded: chain a residue 53 THR Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 19 HIS Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain e residue 4 ILE Chi-restraints excluded: chain e residue 28 ASN Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain h residue 69 HIS Chi-restraints excluded: chain h residue 77 ILE Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 149 ILE Chi-restraints excluded: chain h residue 166 GLU Chi-restraints excluded: chain h residue 172 ARG Chi-restraints excluded: chain h residue 184 TYR Chi-restraints excluded: chain i residue 200 ILE Chi-restraints excluded: chain j residue 93 ARG Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 29 ILE Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 92 THR Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain l residue 85 TYR Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain n residue 39 PHE Chi-restraints excluded: chain n residue 46 MET Chi-restraints excluded: chain n residue 59 GLU Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 104 VAL Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 123 ARG Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain o residue 59 LYS Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain p residue 77 TYR Chi-restraints excluded: chain p residue 125 LYS Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 9 ARG Chi-restraints excluded: chain q residue 27 CYS Chi-restraints excluded: chain q residue 83 ARG Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain q residue 93 VAL Chi-restraints excluded: chain q residue 97 THR Chi-restraints excluded: chain r residue 17 ILE Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 110 LYS Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 98 LYS Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 29 VAL Chi-restraints excluded: chain t residue 31 LEU Chi-restraints excluded: chain t residue 38 HIS Chi-restraints excluded: chain t residue 42 HIS Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain t residue 49 ASP Chi-restraints excluded: chain t residue 53 ARG Chi-restraints excluded: chain t residue 65 LYS Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain t residue 89 ARG Chi-restraints excluded: chain v residue 29 VAL Chi-restraints excluded: chain v residue 34 TYR Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 39 ILE Chi-restraints excluded: chain w residue 47 THR Chi-restraints excluded: chain x residue 20 GLU Chi-restraints excluded: chain x residue 58 VAL Chi-restraints excluded: chain x residue 77 THR Chi-restraints excluded: chain y residue 14 SER Chi-restraints excluded: chain y residue 25 ARG Chi-restraints excluded: chain y residue 33 LYS Chi-restraints excluded: chain y residue 75 HIS Chi-restraints excluded: chain z residue 42 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1089 random chunks: chunk 649 optimal weight: 6.9990 chunk 419 optimal weight: 10.0000 chunk 626 optimal weight: 20.0000 chunk 316 optimal weight: 10.0000 chunk 206 optimal weight: 20.0000 chunk 203 optimal weight: 20.0000 chunk 667 optimal weight: 20.0000 chunk 715 optimal weight: 40.0000 chunk 518 optimal weight: 10.0000 chunk 97 optimal weight: 30.0000 chunk 825 optimal weight: 30.0000 overall best weight: 11.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 22 HIS 5 50 ASN 5 136 HIS ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN D 97 ASN D 163 ASN G 128 HIS ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 4 GLN ** d 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 28 ASN e 43 HIS ** f 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 37 GLN ** g 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 86 GLN m 16 ASN n 31 ASN ** p 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 109 ASN ** q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 29 GLN ** t 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2508 moved from start: 1.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.898 169797 Z= 0.593 Angle : 1.554 40.737 254261 Z= 0.755 Chirality : 0.071 1.974 32471 Planarity : 0.011 0.153 13456 Dihedral : 27.076 179.741 85496 Min Nonbonded Distance : 0.895 Molprobity Statistics. All-atom Clashscore : 37.98 Ramachandran Plot: Outliers : 0.62 % Allowed : 14.40 % Favored : 84.99 % Rotamer: Outliers : 6.10 % Allowed : 24.65 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 3.48 % Twisted General : 1.06 % 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: -4.11 (0.09), residues: 6015 helix: -2.32 (0.11), residues: 1636 sheet: -1.83 (0.18), residues: 806 loop : -3.32 (0.08), residues: 3573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.004 TRP D 60 HIS 0.066 0.005 HIS G 135 PHE 0.054 0.004 PHE L 66 TYR 0.076 0.005 TYR y 36 ARG 0.036 0.002 ARG p 127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12030 Ramachandran restraints generated. 6015 Oldfield, 0 Emsley, 6015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12030 Ramachandran restraints generated. 6015 Oldfield, 0 Emsley, 6015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 231 time to evaluate : 6.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 26 ILE cc_start: -0.2564 (OUTLIER) cc_final: -0.3543 (tt) REVERT: 5 28 GLU cc_start: 0.0686 (OUTLIER) cc_final: -0.1383 (mm-30) REVERT: 5 73 MET cc_start: 0.1240 (ptt) cc_final: 0.0871 (ptt) REVERT: 5 155 MET cc_start: 0.1010 (tpt) cc_final: 0.0315 (ttt) REVERT: B 7 LYS cc_start: 0.1311 (tptm) cc_final: -0.0722 (mptt) REVERT: B 46 ASN cc_start: 0.3322 (OUTLIER) cc_final: 0.1110 (t0) REVERT: B 171 TYR cc_start: -0.1428 (OUTLIER) cc_final: -0.3247 (m-80) REVERT: B 182 ARG cc_start: 0.6519 (OUTLIER) cc_final: 0.6265 (ttt180) REVERT: B 199 GLU cc_start: 0.3053 (OUTLIER) cc_final: 0.1794 (mp0) REVERT: B 239 ASN cc_start: 0.4751 (OUTLIER) cc_final: 0.3679 (t0) REVERT: D 79 ARG cc_start: 0.3237 (OUTLIER) cc_final: 0.2288 (ttt-90) REVERT: D 198 GLU cc_start: -0.1366 (OUTLIER) cc_final: -0.3179 (tp30) REVERT: E 130 MET cc_start: 0.0637 (OUTLIER) cc_final: -0.1448 (mmm) REVERT: G 1 MET cc_start: -0.0792 (tpt) cc_final: -0.2347 (tpp) REVERT: G 135 HIS cc_start: 0.1401 (OUTLIER) cc_final: 0.0302 (m90) REVERT: G 143 ILE cc_start: 0.1469 (OUTLIER) cc_final: 0.1011 (tt) REVERT: K 53 LYS cc_start: -0.0226 (OUTLIER) cc_final: -0.1939 (tppp) REVERT: L 47 ARG cc_start: 0.2454 (OUTLIER) cc_final: -0.0592 (pmt-80) REVERT: L 70 LYS cc_start: 0.6672 (mttm) cc_final: 0.5757 (mtmt) REVERT: M 82 MET cc_start: 0.0783 (mtp) cc_final: 0.0170 (mtp) REVERT: M 112 LEU cc_start: -0.2189 (OUTLIER) cc_final: -0.2795 (mt) REVERT: N 11 ASN cc_start: 0.2347 (OUTLIER) cc_final: 0.1728 (m-40) REVERT: Q 22 LYS cc_start: 0.3878 (OUTLIER) cc_final: 0.3173 (pttt) REVERT: R 40 MET cc_start: 0.1433 (ppp) cc_final: 0.1087 (pmm) REVERT: R 82 HIS cc_start: 0.4481 (OUTLIER) cc_final: 0.1472 (m-70) REVERT: R 92 TRP cc_start: 0.3776 (OUTLIER) cc_final: 0.2966 (m-10) REVERT: S 90 LYS cc_start: 0.0596 (OUTLIER) cc_final: -0.0125 (mtpt) REVERT: S 99 ARG cc_start: 0.3768 (OUTLIER) cc_final: 0.2192 (mtt180) REVERT: W 17 GLU cc_start: 0.2383 (OUTLIER) cc_final: 0.1390 (pt0) REVERT: W 83 GLU cc_start: 0.1646 (OUTLIER) cc_final: 0.1320 (pm20) REVERT: X 56 MET cc_start: 0.4326 (OUTLIER) cc_final: 0.4053 (mtt) REVERT: b 16 ARG cc_start: 0.2312 (OUTLIER) cc_final: 0.0039 (mpp80) REVERT: b 19 HIS cc_start: 0.3599 (OUTLIER) cc_final: 0.2651 (t-90) REVERT: c 49 TYR cc_start: -0.0153 (OUTLIER) cc_final: -0.1286 (t80) REVERT: d 39 ARG cc_start: 0.4078 (mtt180) cc_final: 0.0936 (tmt-80) REVERT: e 13 ARG cc_start: 0.3370 (OUTLIER) cc_final: 0.2912 (mpt-90) REVERT: e 19 LYS cc_start: 0.5582 (mtpt) cc_final: 0.4353 (pttp) REVERT: g 16 PHE cc_start: -0.1730 (OUTLIER) cc_final: -0.3625 (m-80) REVERT: g 23 TRP cc_start: 0.0225 (OUTLIER) cc_final: 0.0014 (p-90) REVERT: h 166 GLU cc_start: 0.5304 (OUTLIER) cc_final: 0.3464 (mm-30) REVERT: i 77 LYS cc_start: 0.0417 (OUTLIER) cc_final: -0.0350 (mmtt) REVERT: j 93 ARG cc_start: 0.2927 (OUTLIER) cc_final: 0.0182 (ttm-80) REVERT: j 96 MET cc_start: 0.0214 (tpp) cc_final: -0.0512 (mpp) REVERT: k 44 ARG cc_start: 0.2110 (OUTLIER) cc_final: 0.1625 (mmm160) REVERT: k 69 GLU cc_start: 0.0445 (OUTLIER) cc_final: -0.2501 (tp30) REVERT: k 75 GLU cc_start: -0.0669 (OUTLIER) cc_final: -0.3758 (tt0) REVERT: k 82 ASP cc_start: 0.0558 (OUTLIER) cc_final: -0.0179 (p0) REVERT: k 93 LYS cc_start: 0.1608 (pttt) cc_final: 0.1400 (pttt) REVERT: l 44 TYR cc_start: 0.2227 (OUTLIER) cc_final: 0.0814 (t80) REVERT: l 60 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.5779 (mm-30) REVERT: l 78 ARG cc_start: 0.5810 (ttt90) cc_final: 0.4857 (ttt-90) REVERT: l 86 GLN cc_start: 0.1598 (OUTLIER) cc_final: -0.0280 (pm20) REVERT: l 143 ARG cc_start: 0.1715 (OUTLIER) cc_final: 0.0211 (ttt90) REVERT: l 144 MET cc_start: 0.1328 (mmt) cc_final: -0.3486 (ptt) REVERT: n 39 PHE cc_start: 0.1890 (OUTLIER) cc_final: -0.2286 (p90) REVERT: n 59 GLU cc_start: 0.1712 (OUTLIER) cc_final: 0.0931 (mm-30) REVERT: n 116 VAL cc_start: 0.1852 (OUTLIER) cc_final: 0.0291 (p) REVERT: n 119 ARG cc_start: 0.6897 (ttp-170) cc_final: 0.4450 (mmm160) REVERT: n 123 ARG cc_start: 0.1949 (OUTLIER) cc_final: 0.0748 (tmt-80) REVERT: o 5 ARG cc_start: 0.2907 (OUTLIER) cc_final: 0.0560 (mtp85) REVERT: o 59 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6981 (tptp) REVERT: p 97 ILE cc_start: 0.5473 (tp) cc_final: 0.5073 (tp) REVERT: p 125 LYS cc_start: 0.1980 (OUTLIER) cc_final: 0.0707 (ptmt) REVERT: q 9 ARG cc_start: 0.1949 (OUTLIER) cc_final: 0.0779 (ptm-80) REVERT: q 14 ARG cc_start: 0.2928 (OUTLIER) cc_final: 0.2474 (tpp-160) REVERT: q 29 GLN cc_start: 0.6220 (OUTLIER) cc_final: 0.5462 (mt0) REVERT: q 82 ILE cc_start: -0.1442 (OUTLIER) cc_final: -0.2214 (tt) REVERT: q 83 ARG cc_start: 0.0200 (OUTLIER) cc_final: -0.0394 (ttt-90) REVERT: r 98 ARG cc_start: 0.5545 (OUTLIER) cc_final: 0.3633 (tpm170) REVERT: r 100 GLN cc_start: 0.1234 (OUTLIER) cc_final: 0.0526 (pt0) REVERT: r 113 ARG cc_start: 0.4231 (tpp-160) cc_final: 0.3648 (ppt170) REVERT: s 85 ARG cc_start: 0.6240 (tmt170) cc_final: 0.4487 (tmm-80) REVERT: s 89 MET cc_start: 0.2109 (ttp) cc_final: 0.1567 (ttp) REVERT: t 53 ARG cc_start: 0.0460 (OUTLIER) cc_final: -0.2540 (ttm170) REVERT: t 72 ARG cc_start: -0.0031 (OUTLIER) cc_final: -0.4843 (ttp-170) REVERT: v 40 ARG cc_start: 0.4246 (mmt180) cc_final: 0.0970 (mmm-85) REVERT: x 20 GLU cc_start: 0.2589 (OUTLIER) cc_final: 0.1962 (pp20) REVERT: y 33 LYS cc_start: 0.0598 (OUTLIER) cc_final: -0.0880 (ptmm) REVERT: y 75 HIS cc_start: -0.0062 (OUTLIER) cc_final: -0.3283 (m90) REVERT: z 5 LYS cc_start: 0.3102 (mtmm) cc_final: 0.1985 (ttpt) REVERT: z 54 LYS cc_start: -0.0553 (OUTLIER) cc_final: -0.1954 (ttmm) REVERT: z 67 ARG cc_start: 0.4203 (OUTLIER) cc_final: 0.3133 (ttm110) outliers start: 304 outliers final: 161 residues processed: 510 average time/residue: 1.4194 time to fit residues: 1233.6643 Evaluate side-chains 442 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 219 time to evaluate : 6.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 18 LYS Chi-restraints excluded: chain 5 residue 26 ILE Chi-restraints excluded: chain 5 residue 28 GLU Chi-restraints excluded: chain 5 residue 53 ASP Chi-restraints excluded: chain 5 residue 144 GLU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 60 TRP Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 123 ARG Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 135 HIS Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain K residue 49 ARG Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain L residue 66 PHE Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 31 PHE Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 22 LYS Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain R residue 92 TRP Chi-restraints excluded: chain S residue 90 LYS Chi-restraints excluded: chain S residue 99 ARG Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 45 HIS Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 83 GLU Chi-restraints excluded: chain X residue 4 VAL Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 56 MET Chi-restraints excluded: chain X residue 78 TYR Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain a residue 53 THR Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 16 ARG Chi-restraints excluded: chain b residue 19 HIS Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 46 HIS Chi-restraints excluded: chain c residue 49 TYR Chi-restraints excluded: chain d residue 26 ASN Chi-restraints excluded: chain e residue 13 ARG Chi-restraints excluded: chain e residue 26 HIS Chi-restraints excluded: chain e residue 28 ASN Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain g residue 16 PHE Chi-restraints excluded: chain g residue 23 TRP Chi-restraints excluded: chain h residue 77 ILE Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 166 GLU Chi-restraints excluded: chain h residue 172 ARG Chi-restraints excluded: chain h residue 184 TYR Chi-restraints excluded: chain i residue 53 VAL Chi-restraints excluded: chain i residue 77 LYS Chi-restraints excluded: chain i residue 200 ILE Chi-restraints excluded: chain j residue 93 ARG Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 8 PHE Chi-restraints excluded: chain k residue 29 ILE Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 44 ARG Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 69 GLU Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain k residue 75 GLU Chi-restraints excluded: chain k residue 82 ASP Chi-restraints excluded: chain k residue 88 MET Chi-restraints excluded: chain k residue 91 ARG Chi-restraints excluded: chain k residue 92 THR Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain l residue 25 LYS Chi-restraints excluded: chain l residue 44 TYR Chi-restraints excluded: chain l residue 49 THR Chi-restraints excluded: chain l residue 58 GLU Chi-restraints excluded: chain l residue 60 GLU Chi-restraints excluded: chain l residue 86 GLN Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 104 ILE Chi-restraints excluded: chain l residue 140 ASP Chi-restraints excluded: chain l residue 143 ARG Chi-restraints excluded: chain m residue 27 MET Chi-restraints excluded: chain n residue 39 PHE Chi-restraints excluded: chain n residue 43 THR Chi-restraints excluded: chain n residue 46 MET Chi-restraints excluded: chain n residue 59 GLU Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 123 ARG Chi-restraints excluded: chain n residue 129 LYS Chi-restraints excluded: chain o residue 5 ARG Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain o residue 59 LYS Chi-restraints excluded: chain o residue 91 ASP Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain p residue 13 ARG Chi-restraints excluded: chain p residue 77 TYR Chi-restraints excluded: chain p residue 83 GLU Chi-restraints excluded: chain p residue 116 ILE Chi-restraints excluded: chain p residue 125 LYS Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 9 ARG Chi-restraints excluded: chain q residue 14 ARG Chi-restraints excluded: chain q residue 27 CYS Chi-restraints excluded: chain q residue 29 GLN Chi-restraints excluded: chain q residue 46 ASN Chi-restraints excluded: chain q residue 82 ILE Chi-restraints excluded: chain q residue 83 ARG Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain q residue 93 VAL Chi-restraints excluded: chain q residue 97 THR Chi-restraints excluded: chain r residue 17 ILE Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 98 ARG Chi-restraints excluded: chain r residue 100 GLN Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain r residue 110 LYS Chi-restraints excluded: chain s residue 18 ASP Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 29 VAL Chi-restraints excluded: chain t residue 31 LEU Chi-restraints excluded: chain t residue 42 HIS Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain t residue 49 ASP Chi-restraints excluded: chain t residue 53 ARG Chi-restraints excluded: chain t residue 64 ARG Chi-restraints excluded: chain t residue 65 LYS Chi-restraints excluded: chain t residue 69 TYR Chi-restraints excluded: chain t residue 72 ARG Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain t residue 89 ARG Chi-restraints excluded: chain v residue 29 VAL Chi-restraints excluded: chain v residue 34 TYR Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 61 ILE Chi-restraints excluded: chain v residue 64 CYS Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 68 SER Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain v residue 83 VAL Chi-restraints excluded: chain w residue 39 ILE Chi-restraints excluded: chain w residue 47 THR Chi-restraints excluded: chain x residue 14 HIS Chi-restraints excluded: chain x residue 20 GLU Chi-restraints excluded: chain x residue 77 THR Chi-restraints excluded: chain y residue 14 SER Chi-restraints excluded: chain y residue 25 ARG Chi-restraints excluded: chain y residue 33 LYS Chi-restraints excluded: chain y residue 66 LEU Chi-restraints excluded: chain y residue 75 HIS Chi-restraints excluded: chain z residue 42 THR Chi-restraints excluded: chain z residue 54 LYS Chi-restraints excluded: chain z residue 63 GLU Chi-restraints excluded: chain z residue 67 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1089 random chunks: chunk 954 optimal weight: 9.9990 chunk 1005 optimal weight: 8.9990 chunk 917 optimal weight: 0.9980 chunk 978 optimal weight: 6.9990 chunk 588 optimal weight: 0.4980 chunk 426 optimal weight: 9.9990 chunk 768 optimal weight: 4.9990 chunk 300 optimal weight: 10.0000 chunk 883 optimal weight: 2.9990 chunk 925 optimal weight: 50.0000 chunk 974 optimal weight: 6.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 135 HIS L 104 GLN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN b 4 GLN f 37 GLN ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 16 ASN n 31 ASN ** n 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 38 GLN q 6 GLN ** q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 96 HIS s 35 ASN ** t 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2153 moved from start: 1.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.901 169797 Z= 0.305 Angle : 0.882 38.997 254261 Z= 0.452 Chirality : 0.046 1.988 32471 Planarity : 0.007 0.119 13456 Dihedral : 26.336 179.955 85496 Min Nonbonded Distance : 0.969 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.68 % Favored : 91.29 % Rotamer: Outliers : 3.91 % Allowed : 26.88 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.10), residues: 6015 helix: -1.77 (0.12), residues: 1678 sheet: -1.80 (0.17), residues: 901 loop : -2.95 (0.09), residues: 3436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 60 HIS 0.023 0.002 HIS G 135 PHE 0.044 0.002 PHE y 31 TYR 0.045 0.003 TYR Q 24 ARG 0.015 0.001 ARG p 127 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12030 Ramachandran restraints generated. 6015 Oldfield, 0 Emsley, 6015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12030 Ramachandran restraints generated. 6015 Oldfield, 0 Emsley, 6015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 245 time to evaluate : 6.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 28 GLU cc_start: 0.0744 (OUTLIER) cc_final: -0.1219 (mm-30) REVERT: 5 144 GLU cc_start: 0.0861 (OUTLIER) cc_final: -0.0130 (pp20) REVERT: 5 155 MET cc_start: 0.1611 (tpt) cc_final: 0.0897 (ttt) REVERT: B 7 LYS cc_start: 0.0790 (tptm) cc_final: -0.1428 (mmtt) REVERT: B 46 ASN cc_start: 0.1501 (OUTLIER) cc_final: -0.1460 (t0) REVERT: B 81 LEU cc_start: 0.1133 (mt) cc_final: -0.0008 (tp) REVERT: B 90 ASN cc_start: -0.0829 (OUTLIER) cc_final: -0.2587 (m-40) REVERT: B 171 TYR cc_start: -0.1059 (OUTLIER) cc_final: -0.1861 (m-80) REVERT: B 180 GLU cc_start: 0.4928 (tt0) cc_final: 0.4202 (tt0) REVERT: B 182 ARG cc_start: 0.5532 (OUTLIER) cc_final: 0.4476 (ttt180) REVERT: E 130 MET cc_start: 0.0561 (OUTLIER) cc_final: -0.1484 (mmm) REVERT: G 1 MET cc_start: -0.1014 (tpt) cc_final: -0.2748 (tpp) REVERT: G 101 ASP cc_start: 0.7208 (m-30) cc_final: 0.6713 (m-30) REVERT: J 92 MET cc_start: 0.0298 (tpp) cc_final: -0.0618 (tpp) REVERT: J 118 MET cc_start: 0.2273 (mmt) cc_final: 0.1149 (mmt) REVERT: K 1 MET cc_start: 0.5007 (ptm) cc_final: 0.4665 (ptt) REVERT: K 47 ILE cc_start: -0.1281 (OUTLIER) cc_final: -0.1806 (pt) REVERT: K 53 LYS cc_start: -0.0672 (OUTLIER) cc_final: -0.2111 (tmtt) REVERT: L 70 LYS cc_start: 0.6242 (mttm) cc_final: 0.5293 (mtmt) REVERT: M 13 HIS cc_start: 0.5862 (OUTLIER) cc_final: 0.5143 (m-70) REVERT: M 82 MET cc_start: 0.0705 (mtp) cc_final: 0.0141 (mtp) REVERT: Q 89 GLU cc_start: -0.0263 (OUTLIER) cc_final: -0.2105 (pm20) REVERT: R 92 TRP cc_start: 0.3501 (OUTLIER) cc_final: 0.2733 (m-10) REVERT: S 90 LYS cc_start: 0.0693 (OUTLIER) cc_final: -0.0265 (mtpt) REVERT: S 99 ARG cc_start: 0.3427 (OUTLIER) cc_final: 0.2332 (mtm-85) REVERT: U 14 LEU cc_start: 0.5240 (OUTLIER) cc_final: 0.4988 (mm) REVERT: W 17 GLU cc_start: 0.2249 (OUTLIER) cc_final: 0.1267 (pt0) REVERT: W 83 GLU cc_start: 0.1445 (OUTLIER) cc_final: 0.0927 (pm20) REVERT: X 47 VAL cc_start: 0.0167 (OUTLIER) cc_final: -0.0034 (p) REVERT: b 19 HIS cc_start: 0.3134 (OUTLIER) cc_final: 0.2726 (t-90) REVERT: d 22 MET cc_start: -0.4686 (ttp) cc_final: -0.6161 (ttp) REVERT: d 39 ARG cc_start: 0.3255 (mtt180) cc_final: 0.0738 (tmt-80) REVERT: e 19 LYS cc_start: 0.4959 (mtpt) cc_final: 0.3993 (pttp) REVERT: e 26 HIS cc_start: 0.4363 (OUTLIER) cc_final: 0.3608 (m-70) REVERT: g 16 PHE cc_start: -0.2072 (OUTLIER) cc_final: -0.3909 (m-80) REVERT: h 149 ILE cc_start: 0.0642 (OUTLIER) cc_final: 0.0170 (mt) REVERT: h 166 GLU cc_start: 0.4941 (OUTLIER) cc_final: 0.3089 (mm-30) REVERT: h 184 TYR cc_start: 0.4482 (OUTLIER) cc_final: 0.3792 (t80) REVERT: i 77 LYS cc_start: 0.0589 (OUTLIER) cc_final: 0.0381 (mptt) REVERT: j 93 ARG cc_start: 0.3019 (OUTLIER) cc_final: 0.0633 (ttm-80) REVERT: k 75 GLU cc_start: -0.1323 (OUTLIER) cc_final: -0.4127 (tt0) REVERT: k 82 ASP cc_start: -0.0961 (OUTLIER) cc_final: -0.1406 (p0) REVERT: l 13 LEU cc_start: 0.3184 (OUTLIER) cc_final: 0.2817 (mp) REVERT: l 143 ARG cc_start: 0.2266 (OUTLIER) cc_final: 0.1873 (mtp85) REVERT: l 144 MET cc_start: -0.1408 (mmt) cc_final: -0.3072 (ptt) REVERT: n 39 PHE cc_start: 0.0954 (OUTLIER) cc_final: -0.2954 (p90) REVERT: n 59 GLU cc_start: 0.0391 (OUTLIER) cc_final: 0.0151 (mm-30) REVERT: n 116 VAL cc_start: 0.1349 (OUTLIER) cc_final: -0.0038 (p) REVERT: n 123 ARG cc_start: 0.1218 (OUTLIER) cc_final: 0.0889 (ttt90) REVERT: o 59 LYS cc_start: 0.6387 (OUTLIER) cc_final: 0.5912 (mtmt) REVERT: o 60 ASP cc_start: 0.6306 (m-30) cc_final: 0.5254 (t70) REVERT: p 125 LYS cc_start: 0.1419 (OUTLIER) cc_final: 0.0777 (pttt) REVERT: q 9 ARG cc_start: 0.1889 (OUTLIER) cc_final: 0.1625 (ptm160) REVERT: r 93 ARG cc_start: 0.3338 (mmp-170) cc_final: 0.1690 (tpp-160) REVERT: r 113 ARG cc_start: 0.3922 (tpp-160) cc_final: 0.3541 (ppt170) REVERT: t 4 SER cc_start: 0.3391 (OUTLIER) cc_final: 0.1880 (p) REVERT: t 53 ARG cc_start: 0.0158 (OUTLIER) cc_final: -0.2975 (ttp-170) REVERT: v 40 ARG cc_start: 0.3815 (mmt180) cc_final: 0.2155 (mmm-85) REVERT: w 67 LEU cc_start: 0.3724 (mm) cc_final: 0.3394 (mt) REVERT: x 20 GLU cc_start: 0.2818 (OUTLIER) cc_final: 0.2362 (pp20) REVERT: x 44 MET cc_start: 0.0670 (mtt) cc_final: -0.2653 (ttm) REVERT: y 75 HIS cc_start: -0.0978 (OUTLIER) cc_final: -0.4741 (m170) REVERT: z 5 LYS cc_start: 0.2472 (mtmm) cc_final: 0.1610 (ttpt) REVERT: z 67 ARG cc_start: 0.4125 (OUTLIER) cc_final: 0.3560 (ttm110) REVERT: z 70 LEU cc_start: 0.0240 (OUTLIER) cc_final: -0.0556 (mp) outliers start: 195 outliers final: 115 residues processed: 423 average time/residue: 1.3895 time to fit residues: 1013.7596 Evaluate side-chains 390 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 232 time to evaluate : 6.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 18 LYS Chi-restraints excluded: chain 5 residue 28 GLU Chi-restraints excluded: chain 5 residue 53 ASP Chi-restraints excluded: chain 5 residue 144 GLU Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 58 HIS Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 221 ARG Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 60 TRP Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 123 ARG Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 135 HIS Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 49 ARG Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain P residue 88 ARG Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 92 TRP Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 90 LYS Chi-restraints excluded: chain S residue 95 ARG Chi-restraints excluded: chain S residue 99 ARG Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 45 HIS Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 83 GLU Chi-restraints excluded: chain X residue 47 VAL Chi-restraints excluded: chain X residue 60 ASP Chi-restraints excluded: chain X residue 78 TYR Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain a residue 53 THR Chi-restraints excluded: chain b residue 19 HIS Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain d residue 26 ASN Chi-restraints excluded: chain e residue 26 HIS Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain g residue 16 PHE Chi-restraints excluded: chain h residue 77 ILE Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 149 ILE Chi-restraints excluded: chain h residue 166 GLU Chi-restraints excluded: chain h residue 172 ARG Chi-restraints excluded: chain h residue 184 TYR Chi-restraints excluded: chain i residue 77 LYS Chi-restraints excluded: chain i residue 200 ILE Chi-restraints excluded: chain j residue 93 ARG Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 8 PHE Chi-restraints excluded: chain k residue 29 ILE Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 75 GLU Chi-restraints excluded: chain k residue 82 ASP Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain l residue 13 LEU Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain l residue 25 LYS Chi-restraints excluded: chain l residue 44 TYR Chi-restraints excluded: chain l residue 58 GLU Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 143 ARG Chi-restraints excluded: chain m residue 27 MET Chi-restraints excluded: chain n residue 39 PHE Chi-restraints excluded: chain n residue 46 MET Chi-restraints excluded: chain n residue 59 GLU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 123 ARG Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain o residue 59 LYS Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain p residue 13 ARG Chi-restraints excluded: chain p residue 77 TYR Chi-restraints excluded: chain p residue 125 LYS Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 9 ARG Chi-restraints excluded: chain q residue 27 CYS Chi-restraints excluded: chain q residue 29 GLN Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain q residue 93 VAL Chi-restraints excluded: chain r residue 17 ILE Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain r residue 110 LYS Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 31 LEU Chi-restraints excluded: chain t residue 38 HIS Chi-restraints excluded: chain t residue 42 HIS Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain t residue 49 ASP Chi-restraints excluded: chain t residue 53 ARG Chi-restraints excluded: chain t residue 65 LYS Chi-restraints excluded: chain t residue 69 TYR Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain t residue 89 ARG Chi-restraints excluded: chain v residue 29 VAL Chi-restraints excluded: chain v residue 34 TYR Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 83 VAL Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 39 ILE Chi-restraints excluded: chain w residue 47 THR Chi-restraints excluded: chain x residue 20 GLU Chi-restraints excluded: chain x residue 77 THR Chi-restraints excluded: chain y residue 14 SER Chi-restraints excluded: chain y residue 25 ARG Chi-restraints excluded: chain y residue 55 GLN Chi-restraints excluded: chain y residue 66 LEU Chi-restraints excluded: chain y residue 75 HIS Chi-restraints excluded: chain z residue 42 THR Chi-restraints excluded: chain z residue 67 ARG Chi-restraints excluded: chain z residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1089 random chunks: chunk 642 optimal weight: 2.9990 chunk 1034 optimal weight: 5.9990 chunk 631 optimal weight: 0.7980 chunk 490 optimal weight: 0.9990 chunk 719 optimal weight: 6.9990 chunk 1084 optimal weight: 10.0000 chunk 998 optimal weight: 3.9990 chunk 863 optimal weight: 4.9990 chunk 89 optimal weight: 30.0000 chunk 667 optimal weight: 4.9990 chunk 529 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 ASN B 46 ASN ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 89 ASN ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 86 GLN ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 31 ASN ** n 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 91 HIS t 37 ASN ** t 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2157 moved from start: 1.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.902 169797 Z= 0.295 Angle : 0.841 39.623 254261 Z= 0.431 Chirality : 0.043 1.982 32471 Planarity : 0.007 0.121 13456 Dihedral : 26.155 179.992 85496 Min Nonbonded Distance : 0.954 Molprobity Statistics. All-atom Clashscore : 20.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.51 % Favored : 89.48 % Rotamer: Outliers : 3.37 % Allowed : 27.56 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.10), residues: 6015 helix: -1.43 (0.12), residues: 1681 sheet: -1.70 (0.17), residues: 898 loop : -2.83 (0.09), residues: 3436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 248 HIS 0.023 0.002 HIS G 135 PHE 0.034 0.002 PHE y 31 TYR 0.031 0.002 TYR X 78 ARG 0.038 0.001 ARG X 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12030 Ramachandran restraints generated. 6015 Oldfield, 0 Emsley, 6015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12030 Ramachandran restraints generated. 6015 Oldfield, 0 Emsley, 6015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 237 time to evaluate : 6.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 28 GLU cc_start: 0.1098 (OUTLIER) cc_final: -0.0927 (mm-30) REVERT: 5 73 MET cc_start: 0.1578 (ptt) cc_final: 0.1082 (ptt) REVERT: 5 144 GLU cc_start: 0.0982 (OUTLIER) cc_final: -0.0109 (pp20) REVERT: 5 155 MET cc_start: 0.1974 (tpt) cc_final: 0.1239 (ttt) REVERT: B 7 LYS cc_start: 0.0634 (tptm) cc_final: -0.1551 (mmtt) REVERT: B 81 LEU cc_start: 0.0916 (mt) cc_final: 0.0170 (tp) REVERT: B 171 TYR cc_start: -0.1152 (OUTLIER) cc_final: -0.2066 (m-80) REVERT: B 182 ARG cc_start: 0.5575 (OUTLIER) cc_final: 0.4797 (ttt180) REVERT: B 239 ASN cc_start: 0.4529 (OUTLIER) cc_final: 0.2568 (t0) REVERT: D 60 TRP cc_start: 0.1430 (OUTLIER) cc_final: -0.3620 (t60) REVERT: E 130 MET cc_start: 0.0590 (OUTLIER) cc_final: -0.1501 (mmm) REVERT: G 1 MET cc_start: -0.1472 (tpt) cc_final: -0.3038 (tpp) REVERT: J 92 MET cc_start: -0.0212 (tpp) cc_final: -0.3200 (mmp) REVERT: J 118 MET cc_start: 0.2438 (mmt) cc_final: 0.1308 (mmt) REVERT: K 1 MET cc_start: 0.5379 (ptm) cc_final: 0.5013 (ptt) REVERT: K 47 ILE cc_start: -0.1547 (OUTLIER) cc_final: -0.2244 (pt) REVERT: K 53 LYS cc_start: -0.0708 (OUTLIER) cc_final: -0.2225 (tmtt) REVERT: K 78 ARG cc_start: 0.5401 (mtm-85) cc_final: 0.4976 (mtm110) REVERT: L 70 LYS cc_start: 0.6180 (mttm) cc_final: 0.5344 (mtmt) REVERT: M 6 ARG cc_start: 0.3526 (ttt-90) cc_final: 0.1661 (tpm170) REVERT: M 82 MET cc_start: 0.0462 (mtp) cc_final: -0.0133 (mtp) REVERT: N 1 MET cc_start: 0.1798 (ttt) cc_final: 0.1329 (tmm) REVERT: N 20 MET cc_start: 0.2701 (ttp) cc_final: 0.0854 (mmp) REVERT: N 110 MET cc_start: 0.0684 (OUTLIER) cc_final: 0.0367 (tpp) REVERT: Q 20 GLN cc_start: 0.3309 (tp-100) cc_final: 0.2762 (pp30) REVERT: Q 24 TYR cc_start: 0.0686 (m-80) cc_final: 0.0243 (m-80) REVERT: Q 89 GLU cc_start: -0.0038 (OUTLIER) cc_final: -0.2124 (pm20) REVERT: S 90 LYS cc_start: 0.0869 (OUTLIER) cc_final: 0.0108 (mtpt) REVERT: S 95 ARG cc_start: 0.3062 (OUTLIER) cc_final: 0.2376 (ttm170) REVERT: S 99 ARG cc_start: 0.3414 (OUTLIER) cc_final: 0.2189 (mtm-85) REVERT: U 14 LEU cc_start: 0.5132 (OUTLIER) cc_final: 0.4856 (mm) REVERT: W 17 GLU cc_start: 0.2250 (OUTLIER) cc_final: 0.1259 (pt0) REVERT: W 69 PHE cc_start: 0.2051 (OUTLIER) cc_final: 0.1340 (p90) REVERT: W 83 GLU cc_start: 0.1322 (OUTLIER) cc_final: 0.0910 (pm20) REVERT: a 30 HIS cc_start: 0.1094 (OUTLIER) cc_final: -0.1881 (p90) REVERT: b 19 HIS cc_start: 0.3308 (OUTLIER) cc_final: 0.3078 (t-90) REVERT: d 39 ARG cc_start: 0.3071 (mtt180) cc_final: 0.0606 (tpt90) REVERT: e 19 LYS cc_start: 0.5229 (mtpt) cc_final: 0.3969 (pttp) REVERT: e 26 HIS cc_start: 0.3888 (OUTLIER) cc_final: 0.3273 (m-70) REVERT: e 47 LYS cc_start: 0.6212 (ttmt) cc_final: 0.5972 (mptt) REVERT: g 16 PHE cc_start: -0.1914 (OUTLIER) cc_final: -0.3812 (m-80) REVERT: h 149 ILE cc_start: 0.0945 (OUTLIER) cc_final: 0.0406 (mt) REVERT: h 166 GLU cc_start: 0.5317 (OUTLIER) cc_final: 0.3101 (mm-30) REVERT: h 184 TYR cc_start: 0.4274 (OUTLIER) cc_final: 0.3722 (t80) REVERT: i 206 LYS cc_start: 0.5379 (mttt) cc_final: 0.4048 (tttt) REVERT: j 93 ARG cc_start: 0.2465 (OUTLIER) cc_final: 0.1369 (mtm-85) REVERT: k 8 PHE cc_start: -0.0414 (OUTLIER) cc_final: -0.2408 (p90) REVERT: k 82 ASP cc_start: -0.0738 (OUTLIER) cc_final: -0.1148 (p0) REVERT: l 86 GLN cc_start: 0.1407 (OUTLIER) cc_final: -0.0307 (mt0) REVERT: l 143 ARG cc_start: 0.2373 (OUTLIER) cc_final: 0.2049 (ttm110) REVERT: l 144 MET cc_start: -0.1100 (mmt) cc_final: -0.2625 (ptt) REVERT: n 39 PHE cc_start: 0.0777 (OUTLIER) cc_final: -0.0123 (m-10) REVERT: n 116 VAL cc_start: 0.1211 (OUTLIER) cc_final: -0.0315 (p) REVERT: n 123 ARG cc_start: 0.1242 (OUTLIER) cc_final: -0.0108 (mmt-90) REVERT: o 59 LYS cc_start: 0.6357 (OUTLIER) cc_final: 0.6148 (mmmm) REVERT: p 125 LYS cc_start: 0.1128 (OUTLIER) cc_final: 0.0471 (pttt) REVERT: q 9 ARG cc_start: 0.2188 (OUTLIER) cc_final: 0.0788 (ptm-80) REVERT: r 93 ARG cc_start: 0.3415 (mmp-170) cc_final: 0.0700 (mmm160) REVERT: r 113 ARG cc_start: 0.3990 (tpp-160) cc_final: 0.3354 (ppt170) REVERT: s 85 ARG cc_start: 0.5878 (tmt170) cc_final: 0.4281 (tmm-80) REVERT: t 4 SER cc_start: 0.3704 (OUTLIER) cc_final: 0.2636 (p) REVERT: t 53 ARG cc_start: 0.0232 (OUTLIER) cc_final: -0.2633 (ttp-170) REVERT: v 40 ARG cc_start: 0.4041 (mmt180) cc_final: 0.1616 (mmm-85) REVERT: x 20 GLU cc_start: 0.2349 (OUTLIER) cc_final: 0.1776 (pp20) REVERT: x 44 MET cc_start: 0.0276 (mtt) cc_final: -0.2694 (ttm) REVERT: y 55 GLN cc_start: 0.1114 (OUTLIER) cc_final: 0.0701 (mt0) REVERT: y 75 HIS cc_start: -0.1269 (OUTLIER) cc_final: -0.4824 (m170) REVERT: z 5 LYS cc_start: 0.2557 (mtmm) cc_final: 0.1750 (ttpt) REVERT: z 67 ARG cc_start: 0.4047 (OUTLIER) cc_final: 0.3404 (ttm110) REVERT: z 70 LEU cc_start: 0.0415 (OUTLIER) cc_final: -0.0319 (mp) outliers start: 168 outliers final: 108 residues processed: 387 average time/residue: 1.3971 time to fit residues: 928.6159 Evaluate side-chains 376 residues out of total 4981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 225 time to evaluate : 6.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 18 LYS Chi-restraints excluded: chain 5 residue 28 GLU Chi-restraints excluded: chain 5 residue 53 ASP Chi-restraints excluded: chain 5 residue 144 GLU Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 58 HIS Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 60 TRP Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 123 ARG Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain I residue 135 MET Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 49 ARG Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 22 LYS Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 90 LYS Chi-restraints excluded: chain S residue 95 ARG Chi-restraints excluded: chain S residue 99 ARG Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 45 HIS Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 69 PHE Chi-restraints excluded: chain W residue 83 GLU Chi-restraints excluded: chain X residue 60 ASP Chi-restraints excluded: chain X residue 78 TYR Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain a residue 30 HIS Chi-restraints excluded: chain a residue 53 THR Chi-restraints excluded: chain b residue 19 HIS Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain d residue 26 ASN Chi-restraints excluded: chain e residue 26 HIS Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain g residue 16 PHE Chi-restraints excluded: chain h residue 77 ILE Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 149 ILE Chi-restraints excluded: chain h residue 166 GLU Chi-restraints excluded: chain h residue 172 ARG Chi-restraints excluded: chain h residue 184 TYR Chi-restraints excluded: chain i residue 200 ILE Chi-restraints excluded: chain j residue 93 ARG Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 8 PHE Chi-restraints excluded: chain k residue 29 ILE Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 82 ASP Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain l residue 25 LYS Chi-restraints excluded: chain l residue 44 TYR Chi-restraints excluded: chain l residue 86 GLN Chi-restraints excluded: chain l residue 140 ASP Chi-restraints excluded: chain l residue 143 ARG Chi-restraints excluded: chain n residue 39 PHE Chi-restraints excluded: chain n residue 46 MET Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 123 ARG Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain o residue 59 LYS Chi-restraints excluded: chain o residue 102 LEU Chi-restraints excluded: chain p residue 13 ARG Chi-restraints excluded: chain p residue 77 TYR Chi-restraints excluded: chain p residue 125 LYS Chi-restraints excluded: chain q residue 9 ARG Chi-restraints excluded: chain q residue 27 CYS Chi-restraints excluded: chain q residue 29 GLN Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain q residue 93 VAL Chi-restraints excluded: chain r residue 17 ILE Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain r residue 110 LYS Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 31 LEU Chi-restraints excluded: chain t residue 38 HIS Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain t residue 49 ASP Chi-restraints excluded: chain t residue 53 ARG Chi-restraints excluded: chain t residue 65 LYS Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain t residue 89 ARG Chi-restraints excluded: chain u residue 20 VAL Chi-restraints excluded: chain v residue 29 VAL Chi-restraints excluded: chain v residue 34 TYR Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 83 VAL Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 39 ILE Chi-restraints excluded: chain w residue 47 THR Chi-restraints excluded: chain x residue 14 HIS Chi-restraints excluded: chain x residue 20 GLU Chi-restraints excluded: chain x residue 77 THR Chi-restraints excluded: chain y residue 14 SER Chi-restraints excluded: chain y residue 25 ARG Chi-restraints excluded: chain y residue 55 GLN Chi-restraints excluded: chain y residue 66 LEU Chi-restraints excluded: chain y residue 75 HIS Chi-restraints excluded: chain z residue 42 THR Chi-restraints excluded: chain z residue 67 ARG Chi-restraints excluded: chain z residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1089 random chunks: chunk 686 optimal weight: 30.0000 chunk 920 optimal weight: 9.9990 chunk 264 optimal weight: 40.0000 chunk 796 optimal weight: 0.1980 chunk 127 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 865 optimal weight: 5.9990 chunk 362 optimal weight: 6.9990 chunk 888 optimal weight: 4.9990 chunk 109 optimal weight: 40.0000 chunk 159 optimal weight: 20.0000 overall best weight: 5.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 135 HIS ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 86 GLN ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5325 r_free = 0.5325 target = 0.319635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.5313 r_free = 0.5313 target = 0.318283 restraints weight = 397756.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.5312 r_free = 0.5312 target = 0.318339 restraints weight = 426370.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.5310 r_free = 0.5310 target = 0.318191 restraints weight = 248618.472| |-----------------------------------------------------------------------------| r_work (final): 0.5311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5311 r_free = 0.5311 target_work(ls_wunit_k1) = 0.318 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5311 r_free = 0.5311 target_work(ls_wunit_k1) = 0.318 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.5311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2175 moved from start: 1.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.902 169797 Z= 0.338 Angle : 0.883 59.199 254261 Z= 0.458 Chirality : 0.044 1.989 32471 Planarity : 0.007 0.121 13456 Dihedral : 26.156 179.993 85496 Min Nonbonded Distance : 0.951 Molprobity Statistics. All-atom Clashscore : 21.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.49 % Favored : 89.49 % Rotamer: Outliers : 3.53 % Allowed : 27.38 % Favored : 69.08 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.10), residues: 6015 helix: -1.40 (0.12), residues: 1681 sheet: -1.70 (0.17), residues: 898 loop : -2.82 (0.09), residues: 3436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 248 HIS 0.012 0.002 HIS t 38 PHE 0.039 0.002 PHE c 20 TYR 0.031 0.002 TYR B 161 ARG 0.051 0.001 ARG S 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21662.56 seconds wall clock time: 389 minutes 57.84 seconds (23397.84 seconds total)